Gene	Tg/KO	Strain	Behavioural phenotypes					Plasticity phenotypes		Comments	Refs
			wm	cxt	cue	ext	obj	LTP	LTD
NMDA receptor-related signalling
NR2B	Tg	B6/CBF1	↑	↑	↑	↑	↑	↑	—	NA	9
Cdk5	C-KO	NA	↑	↑	—	↑	ND	↑	ND	Only reverse water maze enhanced	38
p25	C-Tg	C57Bl/6J	↑	↑	—	ND	ND	↑	ND	Only transient expression enhances memory	41
KIF17	Tg	BDF	↑	ND	ND	ND	ND	ND	ND	Working memory is also enhanced	29
Cavβ3	KO	B6/129	ND	↑	—	ND	↑	↑	—	NA	26
Calcium homeostasis-related signalling
RyR3	KO	C57Bl/6J	↑	ND	ND	ND	ND	↑	↓	But also see 50	189
Ncx2	KO	B6/129	↑	↑	—	ND	↑	↑	↓	NA	53
Kinase and phosphatase
Calcineurin	C-I	C57Bl/6J	↑	ND	↑	↓	↑	↑	—	But also see 75	72, 73
PP1	C-I	C57Bl/6J	↑	ND	ND	ND	↑	↑	↓	NA	64, 190
AC1	Tg	C57Bl/6	ND	—	—	↓	↑	↑	ND	NA	80
Ap oa1	Tg	C57Bl/6J	ND	↑	ND	ND	↑	↑	ND	NA	82
CaMKIV	Tg	C57Bl/6N	ND	↑	ND	ND	ND	↑	ND	Also see 93	94
RNA and protein synthesis
eIF2α	Tg	C57Bl/6J	↑	↑	↑	ND	ND	↑	ND	NA	104
GCN2	KO	129SvEv	↑	↓	—	ND	ND	↑	—	Learning and LTP are impaired with strong training	103
ATF4, C/EBP	C-I	C57Bl/6	↑	ND	ND	ND	ND	↑	↓	Learning is enhanced after only weak training	99
Proto-oncogenes
H-ras	Tg	B6/129	↑	↑	ND	ND	ND	↑	ND	NA	135
Cbl-b	KO	C57Bl/6	↑	ND	ND	ND	ND	—	ND	Only remote memory is enhanced	140
Structural genes
tPA	Tg	NA	↑	ND	ND	ND	ND	↑	—	NA	117
HB-GAM	Tg	FVB/NHsd	↑	—	↓	ND	ND	↑, —	ND	Gene controls inhibition and this complicates the LTP studies	131, 132
TLCN	KO	C57 × CBA	—	—	ND	ND	ND	↑	ND	Learning and memory for non-aversive tasks are enhanced	126
GAP43	Tg	C57Bl/6	↑	ND	ND	ND	ND	↑	ND	But also see 192	191
GABA-related signalling
GABAAα5	KO	B6/129	↑	ND	ND	ND	ND	—	ND	NA	163
GRPR	KO	C57Bl/6J	—	↑	↑	ND	ND	↑	ND	LTP in amygdala is enhanced	193
Glial signalling
S100b	KO	C57Bl/6J	↑	↑	ND	ND	ND	↑	ND	NA	148
DAAO	KO	NA	↑	ND	ND	ND	ND	↑	ND	NA	151
Miscellaneous
ORL1	KO	B6/129	↑	↑	—	ND	ND	↑	ND	Enhanced fear memory only 7 days after training	21, 42
5-HT3R	Tg	B6SJL/F2	ND	↑	—	—	ND	ND	ND	NA	154
MAOA	KO	C3H/HeJ	ND	↑	↑	ND	ND	ND	ND	NA	155
HDC	KO	C57Bl/6 (129Sv)	↑	↑	↑	ND	↓	↑	—	Water maze phenotype was found in 129Sv background	157, 158
HCN1	KO	B6/129	↑	—	—	ND	ND	↑	ND	LTP at perforant path is enhanced. Also see 195	194
DEF45	KO	B6/129	↑	ND	ND	ND	↑	ND	ND	Better recognition memory, only up to 3 hours after training	196, 197
Kvβ1.1	KO	C57Bl/6	↑	ND	ND	ND	ND	↑	ND	18 month-olds mice were used. Also 198	164
EC-SOD	Tg	C57Bl/6 × C3H	↑	↓	—	ND	ND	↑	ND	20 month-olds mice were used. Also see 200	199

Details of above table: GABA, γ-aminobutyric acid; C-I, conditional inhibition; C-KO, conditional knockout; C-Tg, conditional transgenic; cue, cued fear conditioning; cxt, context fear conditioning; ext, fear extinction; KO, knockout; LTD, long-term depression; LTP, long-term potentiation; NA, not applicable; ND, not determined; NMDA, N-methyl-D-aspartate; obj, object recognition task; Tg, transgenic; wm, water maze; —, no change.

TLCN (telencephalin / ICAM-5) knockout in mice improves hippocampus LTP (x). TLCN is a negative regulator of dendritic spine maturation in hippocampal neurons. TLCN knockout promotes more mature spines (x).

STIM1 overexpression - LTD impaired, lower anxiety-like behavior, improvements in contextual learning. perturbation of metabotropic glutamate receptor signaling.

neuritin overexpression - reduced degradation of the DNA repair factor poly ADP-ribose polymerase 1 (PARP1) in the hippocampus, indicating decreased hippocampal apoptosis rate, and a greater number of surviving hippocampal neurons during the first week after transient global ischemia and also showing improved recovery of spatial learning. This is mainly an ischemia study but lower hippocampus apoptosis sounds useful. In injury/recovery shows signs of upregulation of NF-200, synaptophysin, GAP-43 which are "regeneration markers" in mice.

Immediate early genes and enhancement

Some "immediate early genes" seem to have an enhancement effect in mice (x)?

• Zif268 (Egr-1) - an IEG transcription factor - this zinc finger transcription factor has lots of roles in memory recall, learning. (x)
• Narp - an IEG effector - transgenic overexpression or virus-driven increase enhances excitatory drive onto parvalbumin interneurons, rescues ocular dominance plasticity, and improves cognitive flexibility.
• Arc - an IEG effector - sustained Arc expression promotes LTP consolidation, and Arc-mediated priming of mGluR-dependent LTD is required for synaptic depression. Elevation of Arc (via transgenic or virus strategies) enhances synaptic plasticity and memory consolidation. (Arc is a weird one and I'm not sure if we have any evidence of Arc in the human brain yet.)

Intelligence

from "Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence" n=78308 table 1 (note that these only explain at most one IQ point or something):

rsID	Annotation	Locus	Ref	Alt	Ref frequency (UK Biobank)	z	P value	Direction	n	nGWS
rs2490272	FOXO3 intronic	6q21	T	C	0.63	7.44	9.96 x 10^-14	++++−+++	78307	28
rs9320913	Intergenic	6q16.1	A	C	0.48	6.61	3.79 x 10^-11	++++−+++	78307	13
rs10236197	PDE1C intronic	7p14.3	T	C	0.63	6.46	1.03 x 10^-10	+++++−++	78286	35
rs2251499	Intergenic	13q33.2	T	C	0.26	6.31	2.74 x 10^-10	++++++++	78307	22
rs36093924	CYP2D7 ncRNA_intr	22q13.2	T	C	0.46	−6.31	2.87 x 10^-10	?−−?????	54119	100
rs7646501	Intergenic	3p24.2	A	G	0.74	6.02	1.79 x 10^-9	?++−++++	65866	5
rs4728302	EXOC4 intronic	7q33	T	C	0.60	−5.97	2.42 x 10^-9	−−−+−−+−	78307	45
rs10191758	ARHGAP15 intronic	2q22.3	A	G	0.61	−5.93	3.06 x 10^-9	?−−?????	54119	17
rs12744310	Intergenic	1p34.2	T	C	0.22	−5.88	4.20 x 10^-9	?−−−−−−−	65866	28
rs66495454	NEGR1 upstream	1p31.1	G	GTCCT	0.62	−5.75	9.08 x 10^-9	?−−?????	54119	1
rs113315451	CSE1L intronic	20q13.13	A	ATTAT	0.43	5.71	1.15 x 10^-8	?++?????	54119	1
rs12928404	ATXN2L intronic	16p11.2	T	C	0.59	5.71	1.15 x 10^-8	++++++++	78307	19
rs41352752	MEF2C intronic	5q14.3	T	C	0.97	−5.68	1.35 x 10^-8	?−−?????	54119	1
rs13010010	LINC01104 ncRNA_intr	2q11.2	T	C	0.38	5.65	1.56 x 10^-8	++++++++	78308	11
rs16954078	SKAP1 intronic	17q21.32	A	T	0.21	−5.55	2.84 x 10^-8	?−−−−+−−	65866	7
rs11138902	APBA1 intronic	9q21.11	A	G	0.54	5.49	4.12 x 10^-8	+++++−++	78307	1
rs6746731	ZNF638 intronic	2p13.2	T	G	0.43	−5.46	4.88 x 10^-8	−−−−−+−−	78307	1
rs6779302	Intergenic	3p24.3	T	G	0.37	−5.45	4.99 x 10^-8	?−−?????	54119	1

• CON2 copy number variations seem to increase IQ as the number of CON2 copies go up, see Olduvai protein domain and DUF1220

• copy number variants of DUF1220 (ref) for cognitive ability and brain size (but also a schizophrenia and autism risk factor)

• 1q21.1-1q21.2 DUF1220 copy number variations correlated with brain size etc and is very human-specific. The DUF1220 domain is also called (or has been reamed to) Olduvai domain.

from "A genome-wide association study for extremely high intelligence" (2018):

• chromosome 10 high IQ via ADAM12 mutants rs4962322, rs4962520, and rs10794073 explaining up to 1% of high IQ but it may have no impact on IQ in the normal range. ADAM12 can "shed" HB-EGF, an EGFR ligand. HB-EGF/EGFR signaling supports hippocampal plasticity and learning. ADAM12 cleaves IGF-binding proteins (IGFBP-3/-5), increasing free IGF available to activate IGF1 receptors. IGF1 signaling is strongly implicated in synaptic plasticity, LTP and memory across animal and human studies. Reports exist of ADAM12 expression in oligodendrocyte lineage cells and during demyelination.
• X chromosome gene SH2D1A is associated with high IQ.

• plexins gene family showed a significant association with high IQ. Plexins are transmembrane proteins which act as receptors to semaphorins. The plexin-semaphorin pathway has been linked to axon guidance, neural connectivity, axon regeneration in the central nervous system, mental disability, bone disorders, cancer, and inflammatory diseases. Consider regulation of semaphorin receptor activity. Consider different expression in brain-expressed genes and their regulatory reasons, instead of whole body.

• TODO: incorporate results from "GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence" like ZNF638 rs1804020, TMEM89 rs9834639, SLC26A6 rs13324142, BSN rs34762726, CCDC36 rs13068038, C3orf62 rs13077498, MST1 rs3197999, RNF123 rs34823813, TSNARE1 rs79460462

from "A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence" (2019):

• 0.71 IQ point explanation power: NEGR1 intron rs34305371 (chr1:72.73Mb). NEGR1 is a neuronal cell-adhesion molecule in the IgLON family and NEGR2 promotes neurite outgrowth, connectivity, and synaptogenesis in models (FGFR2-linked signaling, ADAM10-regulated shedding).
• 0.5 IQ point explanation power: IP6K1 intronic rs7618501 (chr3:49.77Mb). IP6K1 makes inositol pyrophosphates (like 5-IP7) that influence synaptic vesicle release and neuronal signaling. IP6K1 affects presynaptic function and neuronal migration in models.
• 0.5 IQ point explanation power: intergenic allele (nearest SUMO2P2 pseudogene) rs11793831 (chr9:23.36Mb). might be related to SUMO/ubiquitin pathways.
• 0.4 IQ point explanation power: ATXN2L intronic allele rs8049439-C (chr16:28.84Mb). ATXN2L (ataxin-2-like) is a stress-granule and RNA-metabolism protein related to ATXN2. ATXN2/ATXN2L influence RNA handling and neuronal stress responses. General theme here is post-transcriptional/RNA-granule control in neurons.
• 0.4 IQ point explanation power: STAU1 intergenic allele rs2426132 (chr20:47.72Mb). STAU1 encodes an RNA-binding protein that mediates dendritic mRNA transport and local translation, important for long-term synaptic plasticity.

• oligodendrocyte differentiation is involved in intelligence differences via structure and maintenance of white matter in the brain.

• from "Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function" such as mutations in GATAD2B (NuRD complex transcriptional repressor; neurodevelopmental regulator), SLC39A1 (zinc transporter related to ion homeostasis), and AUTS2 (broad brain neurodevelopment regulator and transcriptional control during brain development); ATXN1/ATXN1L/ATXN2L/ATXN7L2 (ataxin-like genes possibly related to RNA processing/chromatin in neurons); DCDC2 (doublecortin-domain protein) associated with neuronal migration and associated with normal variation in reading and spelling; reaction time and brain region volumes have been correlated with MAPT, WNT3, CRHR1, KANSL1, and NSF; etc. TTBK1 (neuron-specific tau kinase, regulates tau phosphorylation, related to axonal/synaptic maintenance pathways), CWF19L1 (related to spliceosome and neuronal survival), RBFOX1 (regulator of alternative splicing in neurons; neuronal RNA splicing factor, interacts with ATXN2), RAI1 (transcriptional regulator), NMNAT2 (axon survival/Wallerian degeneration), FOXO3 (longevity transcription factor).

• CHRFAM7A: Human restricted CHRFAM7A gene increases brain efficiency (2024) -- "CHRFAM7A direct allele carriers demonstrated an upward shift in cognitive performance including cognitive processing speed, learning and memory, reaching statistical significance in visual immediate recall (FDR corrected p = 0.018). The shift in cognitive performance was associated with smaller whole brain volume (uncorrected p = 0.046) and lower connectivity by resting state functional MRI in the visual network (FDR corrected p = 0.027) ... direct allele carriers harbor a more efficient brain consistent with the cellular biology of actin cytoskeleton and synaptic gain of function."; CHRFAM7A is also mentioned in "lineage-specific copy number variations article".

• Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes -- "[...] a duplication at 2q12.3 associated with higher cognitive performance. [...] We identified a novel association between a duplication at 2q12.3 and positive effects on cognitive ability [...] EDAR, SH3RF3, SEPT10, SOWAHC [..] The 865 kb duplication .. equivalent to 6.5 points of intelligence quotient (IQ). Given that the median age of our dataset is 60.7 years, it is possible that this duplication may be associated with a neuroprotective effect. We suspect that many more CNVs associated with higher cognitive ability will be identified in the future as sample sizes increase." maybe overexpression of SH3RF3 or additional gene dose of SH3RF3 via copy number variation may increase learning or intelligence by several different mechanisms: more LTP cycles per day by faster return to baseline after plasticity; increased encoding capacity via increased dendritic spine density; reduction in learning-related apoptosis. Negative regulation of Rac1/JNK scaffolding.

• Identification of a unique, de novo MYCBP2 variant in an individual with highly superior autobiographical memory -- "Using whole exome sequencing of the HSAM individual and their unaffected parents, we identified a unique de novo missense variant in MYCBP2, which encodes an E3 ubiquitin-protein ligase. To explore the potential behavioral consequences of this variant, we introduced the homologous variant into C. elegans, which resulted in reduced forgetting and increased membrane-bound glutamate receptor in relevant neuronal cells." See the deubiquitin theory.

• RIMS1 allele causing blindness but also significantly increased verbal intelligence. Note that the RIMS1/RIM1 result is now questioned and may be instead related to PROM1: "a later re-analysis of the same ophthalmic pedigree concluded the retinal disease was explained by PROM1, casting doubt on the original assignment of the ocular phenotype to RIMS1". It is not clear to me whether the improved cognitive phenotype is linked to RIMS1, PROM1, both, or neither.

• The human cognition-enhancing CORD7 mutation increases active zone number and synaptic release -- here is a drosophila electrophysiology study of the RIMS1/RIM1 mutation.

• Enhanced learning and memory in patients with CRB1 retinopathy -- reminds me of the RIMS1/RIM1 retinopathy verbal intelligence (VIQ) boost. CRB1 retinopathy seems to be different.

Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development -- "Brain size and cognitive skills are the most dramatically changed traits in humans during evolution and yet the genetic mechanisms underlying these human-specific changes remain elusive. Here, we successfully generated 11 transgenic rhesus monkeys (8 first-generation and 3 second-generation) carrying human copies of MCPH1, an important gene for brain development and brain evolution. Brain-image and tissue-section analyses indicated an altered pattern of neural-cell differentiation, resulting in a delayed neuronal maturation and neural-fiber myelination of the transgenic monkeys, similar to the known evolutionary change of developmental delay (neoteny) in humans. Further brain-transcriptome and tissue-section analyses of major developmental stages showed a marked human-like expression delay of neuron differentiation and synaptic-signaling genes, providing a molecular explanation for the observed brain-developmental delay of the transgenic monkeys. More importantly, the transgenic monkeys exhibited better short-term memory and shorter reaction time compared with the wild-type controls in the delayed-matching-to-sample task. The presented data represent the first attempt to experimentally interrogate the genetic basis of human brain origin using a transgenic monkey model and it values the use of non-human primates in understanding unique human traits."

BEC1/KCNH3 knockout enhances cognitive function -- "The K+ channel, one of the determinants for neuronal excitability, is genetically heterogeneous, and various K+ channel genes are expressed in the CNS. The therapeutic potential of K+ channel blockers for cognitive enhancement has been discussed, but the contribution each K+ channel gene makes to cognitive function remains obscure. BEC1 (KCNH3) is a member of the K+ channel superfamily that shows forebrain-preferential distribution. Here, we show the critical involvement of BEC1 in cognitive function. BEC1 knock-out mice performed behavioral tasks related to working memory, reference memory, and attention better than their wild-type littermates. Enhanced performance was also observed in heterozygous mutants. The knock-out mice had neither the seizures nor the motor dysfunction that are often observed in K+ channel-deficient mice. In contrast to when it is disrupted, overexpression of BEC1 in the forebrain caused the impaired performance of those tasks. It was also found that altering BEC1 expression could change hippocampal neuronal excitability and synaptic plasticity. The results indicate that BEC1 may represent the first K+ channel that contributes preferentially and bidirectionally to cognitive function." Also there is a selective inhibitor of KCNH3 called ASP2905 (N-(4-fluorophenyl)-N'-phenyl-N"-(pyrimidin-2-ylmethyl)-1,3,5-triazine-2,4,6-triamine).

SP0535: A human-specific de novo gene promotes cortical expansion and folding -- "Here, a human-specific de novo gene, SP0535, is identified that is preferentially expressed in the ventricular zone of the human fetal brain and plays an important role in cortical development and function. In human embryonic stem cell-derived cortical organoids, knockout of SP0535 compromises their growth and neurogenesis. In SP0535 transgenic (TG) mice, expression of SP0535 induces fetal cortex expansion and sulci and gyri-like structure formation. The progenitors and neurons in the SP0535 TG mouse cortex tend to proliferate and differentiate in ways that are unique to humans. SP0535 TG adult mice also exhibit improved cognitive ability and working memory. Mechanistically, SP0535 interacts with the membrane protein Na+/K+ ATPase subunit alpha-1 (ATP1A1) and releases Src from the ATP1A1-Src complex, allowing increased level of Src phosphorylation that promotes cell proliferation. Thus, SP0535 is the first proven human-specific de novo gene that promotes cortical expansion and folding, and can function through incorporating into an existing conserved molecular network."

NOTCH2NL overexpression: Human-specific notch2nl genes expand cortical neurogenesis through delta/notch regulation; NOTCH2NLB overexpression leads to clonal expansion of human cortical progenitors. -- "The cerebral cortex underwent rapid expansion and increased complexity during recent hominid evolution. Gene duplications constitute a major evolutionary force, but their impact on human brain development remains unclear. Using tailored RNA sequencing (RNA-seq), we profiled the spatial and temporal expression of hominid-specific duplicated (HS) genes in the human fetal cortex and identified a repertoire of 35 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among them NOTCH2NL, human-specific paralogs of the NOTCH2 receptor, stood out for their ability to promote cortical progenitor maintenance. NOTCH2NL promote the clonal expansion of human cortical progenitors, ultimately leading to higher neuronal output. At the molecular level, NOTCH2NL function by activating the Notch pathway through inhibition of cis Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes active during human corticogenesis and reveals how human-specific NOTCH paralogs may have contributed to the expansion of the human cortex."

white non-hispanics with a heterozygous genotype at rs3848874 in the glutamate ionotropic receptor AMPA type subunit 3 (GRIA3) gene show higher verbal IQ (VIQ) scores (ref)

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• IGF-2 (insulin-like growth factor 2), but only for memory consolidation

"The role of non-coding RNA in memory formation has been reported in a number of publications [46, 47]. RNA-mediated “memory transfer” was recently demonstrated in the marine mollusk Aplysia [48]. Total RNA was extracted from neurons of Aplysia subjected to sensitization training by tail electroshock and injected into neurons of naive mollusks. Snails injected with the RNA of the trained snails showed higher levels of siphon withdrawal reflex as compared to the control group. These data confirm the epigenetic hypothesis of memory formation and can be used in future studies on the possibility of memory stimulation."

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• TODO: "Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence" (2018) (biorxiv)
  • CADM2 rs74599180-C, rs74599180-C, rs74599180-G -- CADM2 mutations are associated with information processing speed, number of sexual partners, age at first sexual intercourse; rs17518584 associated with DSST performance (p = 0.013), and also with language/semantic categorization, executive function, overall cognition, also with Stroop word color; see also ref for more CADM2 variants. There are more than 20 CADM2 mutations that have been associated with intelligence.
    • CADM2 encodes a neural cell-adhesion molecule involved in neuron cell-cell adhesion, glutamate signaling, GABA transport.
  • TTLL7 rs41293013-C, TMOD2 rs17610835-G, GLDN rs112714914-G, KMT2D rs55776396-C, SREK1IP1 rs80170948-G, TRAIP rs2271960-C, TRAIP rs2271961-C, TRAIP rs7648987-G, ATXN2L rs8049439-C (already mentioned elsewhere on this page), ATXN2L rs72793812-G, ATXN2L rs62036622-G, ATXN2L rs4451951-C, ATXN2L rs8062405-G, SH2B1 rs8055982-C, SH2B1 rs11864107-C, SH2B1 rs8061590-C, SH2B1 rs7198606-G, SH2B1 rs9972768-C, ATP2A1 rs8061590-G, SLC39A1 rs3791187-C, ... it's a long list.
  • FOXO3 rs2802290-G, rs2802292-G, rs2490272-C, rs2764265-C, more...
  • FGF8 rs749694-G, rs10883688-C, rs7077446-G, rs10786648-C
  • TET2 rs55838312, rs2647257, rs12645144, rs2454206, rs11726786, rs13109676, rs13123752, rs7670522, rs2726519, rs2726518, rs2133086, rs7678440, rs2726459, rs7683416, rs2726458, rs2647246, rs2647248, rs10010325, rs1391438, rs11735256, rs6839705, rs1015521, rs6533182, rs2726492, rs2647256, rs992493, more..
  • RBFOX1 16,144 SNPs associated with intelligence; DCC has 5,431, etc...
  • kinesin motor protein KIF16B is associated with intelligence, as are scaffolds RIMS2 and SHANK3. these are good engineering targets to consider.
• TODO: "Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals" (2018)

• TODO: "Identification of novel loci associated with infant cognitive ability"

• rs768023 (related to FOXO3, LACE1) is strongly correlated with cognitive ability or intelligence

• intelligence gwas results in gwas catalog (there's a few thousand associations)

• consider rs11793831-T, rs2013208-T, rs6906737-A, rs7646366-A, rs62037363-T, rs28888764-A, rs6931604-T, rs2426132-C, rs6019535-A, rs6019537-A, rs2624839-T, rs1343775-A, rs4587178-T, rs6931604-T, rs34811474-A, rs942353-T

• memory - APOC1, APOC1P1, PVRL2, APOE, TOMM40, GLI3, LOC102723536, LOC105371152, PHBP14, RN7SL776P, CECR1, CECR3, etc.

• delayed expression of GPR89B possibly extends expansion of neural progenitor cells. Consider an inducible approach for neuron progenitor expansion like Nestin-tTA/TetO-NICD or Cre-on Rosa26-NICD with Dox control, turn it on during early neurogenesis and then dox off to allow for neuronal differentiation. Conditional notch1 (NICD) activation in radial cells. Ligand-based alternative: injection via short ventricular infusion of DLL4-Fc/Jag1-Fc (via temporary osmotic pump) to enlarge the progenitor pool, then stop infusion to allow for differentiation.

• 1q21.1-1q21.2 DUF1220 copy number variations correlated with brain size etc and is very human-specific

• "HYDIN2... This part of 1q21.1 is involved in the development of the brain. It is assumed to be a dosage-sensitive gene. When this gene is not available in the 1q21.1 area it leads to microcephaly. HYDIN2 is a recent duplication (found only in humans) of the HYDIN gene found on 16q22.2." See 1q21.1 microduplication causing disparity between non-verbal performance and verbal performance ref.

• neuronal apoptosis inhibitory protein (NAIP or BIRC1) on 5q13 (try increasing the strength of the inhibitory effect?). There is at least one copy of this gene in the human genome. It may have a dose-specific effect.

• "Several other genes implicated in lineage-specific copy number variations in humans include: a neurotransmitter transporter for γ-aminobutyric acid (GABA) (SLC6A13), a leucine zipper-containing gene highly expressed in brain (KIAAA0738), α7 cholinergic receptor/Fam7 fusion gene (CHRFAM7A), a p21-activated kinase (PAK2), a Rho GTPase-activating protein (SRGAP2), a Rho guanine nucleotide exchange factor (ARHGEF5) that is a member of the rhodopsin-like G protein-coupled receptor family, and Rho-dependent protein kinase (ROCK1)."

• SRGAP2, SRGAP2B and SRGAP2C: "Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation". "SRGAP2, a gene recently implicated in neocortical development, has undergone two human-specific duplications. Here we find that both duplications (SRGAP2B and SRGAP2C) are partial and encode a truncated F-BAR domain. SRGAP2C is expressed in the developing and adult human brain and dimerizes with ancestral SRGAP2 to inhibit its function. In the mouse neocortex, SRGAP2 promotes spine maturation and limits spine density. Expression of SRGAP2C phenocopies SRGAP2 deficiency. It underlies sustained radial migration and leads to the emergence of human-specific features, including neoteny during spine maturation and increased density of longer spines." transgenic monkeys with human SRGAP2C: "We generated transgenic cynomolgus macaques (Macaca fascicularis) carrying the human-specific SRGAP2C gene. Longitudinal MRI imaging revealed delayed brain development with region-specific volume changes, accompanied by altered myelination levels in the temporal and occipital regions. On a cellular level, the transgenic monkeys exhibited increased deep-layer neurons during fetal neurogenesis and delayed synaptic maturation in adolescence. Moreover, transcriptome analysis detected neotenic expression in molecular pathways related to neuron ensheathment, synaptic connections, extracellular matrix and energy metabolism. Cognitively, the transgenic monkeys demonstrated improved motor planning and execution skills." Also, expression of the human-specific gene duplication SRGAP2C leads to a specific increase in feedforward and feedback cortico-cortical connectivity: "Moreover, humanized SRGAP2C mice display improved cortical sensory coding, and an enhanced ability to learn a cortex-dependent sensory discrimination."

• "Another gene showing an HLS copy number increase, USP10, encodes a ubiquitin-specific protease, an enzymatic class implicated in learning and memory and in synaptic growth (DiAntonio et al. 2001). Overexpression of the USP10 homologue in Drosophila leads to uncontrolled synaptic overgrowth and elaboration of the synaptic branching pattern (DiAntonio et al. 2001), raising the possibility that the human-specific copy number increase for USP10 could be relevant to expanded synaptic growth in humans."

more on deubiquitinalization and learning:

• The deubiquitination theory of enhanced cognitive ability
• The deubiquitinase USP6 affects memory and synaptic plasticity through modulating NMDA receptor stability
• USP8 deubiquitinates SHANK3 to control synapse density and SHANK3 activity-dependent protein levels

• Reducing K63 polyubiquitination levels in the aged hippocampus improves memory, see also "Decreases in K63 polyubiquitination in the hippocampus". However a different result is observed in amygdala for K63 polyubiquitination reduction. Also: CRISPR-dCas9 mediated upregulation of linear polyubiquitination in the hippocampus improves memory in young adult, but not aged, rats (ref).

• TODO: consider the following. Synapse-targeted DUB fusions (e.g., PSD-95 targeting nanobody or GluA1 targeting nanobody fused to USP46 catalytic domain) under drug-inducible recruitment to acutely dial deubiquitination during/after training. possibly an optogenetic activation method could be used here. AMPAR/PSD ubiquitination ramps right after training activity; transient deubiquitination should stabilize synapses and speed consolidation. Target activation of this to occur about 5 minutes after training or exposure. However, if the rate-limiting step sits in the first few minutes between trials, boosting deubiquitination during the first half of each ITI should let you shorten optimal spacing, like in the middle of each 10 minute gap between exposures.

• NR2B overexpression (enhanced maze solving in mice, "Doogie mice" 1999) (NR2B subunit of the NMDA receptor) (notably, memory performance of "Doogie" mice was retained in advanced age, see: Maintenance of superior learning and memory function in NR2B transgenic mice during ageing (2007); or this ref about NMDA receptor 2b (NR2B) overexpression)

• NR2A overexpression (Hobbie-J mice) ref
• see also GRIN2B overexpression and various mutations of GRIN2B mentioned elsewhere on this page such as episodic memory SNPs (GRIN2B rs2192977 and GRIN2B rs12829455).

"Chemical upregulation of the NR2B subunit with magnesium L-threonate and/or D-cycloserine also resulted in memory enhancement in animals and humans" (from "Enhancement of declarative memory (2018))

• Wang, D., Jacobs, S. A., and Tsien, J. Z. (2014) Targeting the NMDA receptor subunit NR2B for treating or preventing age-related memory decline, Expert Opin. Ther. Targets, 18, 1121-1130
• Kalisch, R., Holt, B., Petrovic, P., De Martino, B., Kloppel, S., Buchel, C., and Dolan, R. J. (2009) The NMDA agonist D-cycloserine facilitates fear memory consolidation in humans, Cereb. Cortex, 19, 187-196

"Most genetic manipulations that potentiate NMDA-related molecular mechanisms were found to enhance memory performance. Thus, transgenic mice overexpressing KIF17 (protein that transports NR2B along the microtubules) exhibited enhanced learning and memory in the Morris water maze task [9]."

• Wong, R. W.-C., Setou, M., Teng, J., Takei, Y., and Hirokawa, N. (2002) Overexpression of motor protein KIF17 enhances spatial and working memory in transgenic mice, Proc. Natl. Acad. Sci. USA, 99, 14500-14505 -- "The kinesin superfamily proteins (KIFs) play essential roles in receptor transportation along the microtubules. KIF17 transports the N-methyl-d-aspartate receptor NR2B subunit in vitro, but its role in vivo is unknown. To clarify this role, we generated transgenic mice overexpressing KIF17 tagged with GFP. The KIF17 transgenic mice exhibited enhanced learning and memory in a series of behavioral tasks, up-regulated NR2B expression with the potential involvement of a transcriptional factor, the cAMP-dependent response element-binding protein, and increased phosphorylation of the cAMP-dependent response element-binding protein. Our results suggest that the motor protein KIF17 contributes to neuronal events required for learning and memory by trafficking fundamental N-methyl-d-aspartate-type glutamate receptors."

"α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors functionally coupled with NMDA receptors are other popular targets in the studies on memory strengthening. Chemical activation of AMPA receptors by ampakines (benzamides, benzothiadiazines, biaryl propylsulfonamides, 3-trifluoromethylpyrazoles) have been found to facilitate memory (for detailed review, see [10]). AMPA receptors are regulated by the protein kinase Mζ (PKMζ), a product of the PKCζ gene in the brain, that has been shown to affect the long-term memory storage in invertebrates and vertebrates (see review [11]). For example, overexpression of PKMζ in the rat neocortex enhanced long-term memory, whereas the dominant negative PKMζ with amino acid substitution in the active site disrupted memory [12]. In monkeys, higher levels of PKMζ were associated with more accurate recognition memory [13]. "

"Another popular target in the memory improvement studies is cAMP response element-binding protein (CREB), a transcription factor that regulates expression of immediate early genes, such as c-Fos and zif268. In general, any manipulation that that leads to the upregulation of CREB expression results in memory enhancement. To give a few examples, local overexpression of CREB in the basolateral amygdala enhanced memory in the classic fear conditioning [14] and social defeat [15] tests. Overexpression of calcium/calmodulin-dependent protein kinase IV (CAMKIV) that directly regulates CREB in the forebrain of mice improved memory in the social recognition and Morris water maze tests [16, 17]. CCAAT/enhancerbinding protein (C/EBP), a product of the early C/EBP gene, is involved in the activation of late response genes in synaptic plasticity. Upregulation of C/EBP expression enhances memory performance. Thus, suppression of the negative C/EBP regulator, ATF4, improved performance of the experimental animals in the Morris water maze test [18]."

"Among many attempts to find chemical agents potentiating CREB-mediated pathways, the most productive approach to memory enhancement in AD patients involved modulation of phosphodiesterase (PDE) that negatively regulates the cAMP/CREB pathway by hydrolyzing cAMP. Hence, PDE inhibitors should enhance memory. Indeed, some PDE inhibitors, namely Rolipram and Sildenafil, have shown positive result in AD mouse models. Cilostazol a selective inhibitor of PDE3, partially prevents cognitive decline and memory loss in AD patients [19]. For more detailed information on the inhibitors on CREB-dependent pathways, see the review [20]."

"... ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion." (ref)

Memory in aged mice is rescued by enhanced expression of the GluN2B subunit of the NMDA receptor

"adult Nr3a KO mice were reported to have increased pain sensation and enhanced abilities in learning and memory tasks (Mohamad et al., 2013)." -- "Using wild-type (WT) and GluN3A knockout (KO) mice, we show here that deletion of GluN3A affected multiple behavioural functions in adult animals. GluN3A KO mice showed impaired locomotor activity on a variety of motor function tests, and increased sensitivity to acute and sub-acute inflammatory pain. GluN3A KO mice also showed enhanced recognition and spatial learning and memory functions. Hippocampal slices from juvenile and adult GluN3A KO mice showed greater long-term potentiation (LTP) compared with WT slices. GluN3A deletion resulted in increased expression of Ca2+/calmodulin-dependent kinase II (CaMKII) in the forebrain, and the phosphorylated CaMKII level upon LTP induction was significantly higher in the GluN3A KO hippocampus compared with WT controls. CaMKII inhibition abrogated the enhanced LTP in GluN3A KO slices."

"The enhancement of learning and memory in GluN3A KO mice is similar to that seen in the 'smart mice' overexpressing GluN2B (NR2B; Tang et al. 1999). GluN2B, however, has been identified as a pro-death NMDAR subunit (Liu et al. 2007), whereas deletion or downregulation of GluN3A in the adult brain does not increase the risk of excitotoxicity or ischaemic injury (Nakanishi et al. 2009). In this respect, GluN3A appears to be a more realistic target for learning and memory modulation than GluN2B. To this end, the role of GluN3A in adult behaviour should be confirmed with conditional GluN3A manipulation studies."

Long-term α1A-adrenergic receptor stimulation improves synaptic plasticity, cognitive function, mood, and longevity (in mice) (2011) -- "α1-adrenergic receptors (α1ARs) activation was recently shown to increase neurogenesis... Here, we studied the effects of long-term α1AAR stimulation using transgenic mice engineered to express a constitutively active mutant (CAM) form of the α1AAR. CAM-α1AAR mice showed enhancements in several behavioral models of learning and memory. In contrast, mice that have the α1AAR gene knocked out displayed poor cognitive function. Hippocampal brain slices from CAM-α1AAR mice demonstrated increased basal synaptic transmission, paired-pulse facilitation, and long-term potentiation compared with wild-type (WT) mice. WT mice treated with the α1AAR-selective agonist cirazoline also showed enhanced cognitive functions. In addition, CAM-α1AAR mice exhibited antidepressant and less anxious phenotypes in several behavioral tests compared with WT mice. Furthermore, the lifespan of CAM-α1AAR mice was 10% longer than that of WT mice. Our results suggest that long-term α1AAR stimulation improves synaptic plasticity, cognitive function, mood, and longevity."

TrkB (RTK): Postnatal neuronal TrkB overexpression activated PLCγ1 signaling and improved multiple learning tasks despite reduced CA1 LTP. See: Transgenic mice overexpressing the full-length neurotrophin receptor trkB exhibit increased activation of the trkB-PLCgamma pathway, reduced anxiety, and facilitated learning (2004).

mineralocorticoid receptor overexpression in mouse forebrain using CaMKIIα promoter. See: Forebrain mineralocorticoid receptor overexpression enhances memory, reduces anxiety and attenuates neuronal loss in cerebral ischaemia (2007).

TrkC (NT-3 receptor) (Ntrk3) overexpression in mice

possible evidence for mouse transgenic overexpression of GAP-43 (the axonal protein kinase C substrate)? See Enhanced learning after mouse genetic overexpression of a brain growth protein GAP-43 (2000). "... dramatically enhanced learning and long-term potentiation in transgenic mice. If the overexpressed GAP-43 was mutated by a Ser-to-Ala substitution to preclude its phosphorylation by protein kinase C, then no learning enhancement was found. These findings provide evidence that a growth-related gene regulates learning and memory and suggest an unheralded target, the GAP-43 phosphorylation site, for enhancing cognitive ability."

AAV overexpression of IGF-2 in hippocampus of aged mice preserved/boosted CA1 spine density and improved hippocampal memory (ref); pharmacological/peptide IGF-2 also acts as a memory enhancer. Some evidene for adult neurogenesis neuron survival and maturation with IGF1. Maybe activate neuronal expression of IGF2 or IGF1 at different times during development or aging via custom genetic circuits?

CRTC1 (CREB co-activator): overexpressing constitutively active CRTC1 in dorsal hippocampus enhanced long-term memory and was accompanied by enlargement of dendritic spines (ref, 2014)

auditory fear memory enhancement and memory consolidation by increasing the function or overexpression of BAF53b (2017), a postmitotic neuron-specific subunit of the BAF nucleosome-remodeling complex.

overexpression of valosin-containing protein (VCP)/p97 (AAA+ ATPase) to increase (hippocampal?) dendritic spine density and formation (spinogenesis), modulating contextual fear memory and social interaction. Also shows contextual memory and social behavior restored by leucine supplementation. "... These findings indicate that leucine supplementation likely enhances mitochondrial activity and protein trafficking/transportation and increases the expression of cytoskeleton molecules to support dendritic spine formation in Nf1+/– mice."

negative results in mice:

• CREB is not indicated; overexpression of CREB in mice does not seem to enhance memory formation: ref, ref.
• possibly conflicting evidence for BDNF overexpression? possibly need more timing-controlled BDNF overexpression, like during development or aging? possibly BDNF overexpression in mice improves motor coordination.

growth hormone overexpression in hippocampus in mice seems to improve memory in certain assays?

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in transgenic mice, stabilized beta-catenin causes markedly enlarged brains with increased cortical surface area and even sulci/gyri–like folds.

beta-catenin expression: Regulation of cerebral cortical size by control of cell cycle exit in neural precursors -- "Transgenic mice expressing a stabilized beta-catenin in neural precursors develop enlarged brains with increased cerebral cortical surface area and folds resembling sulci and gyri of higher mammals. [...] Compared with wild-type precursors, a greater proportion of transgenic precursors reenter the cell cycle after mitosis. These results show that beta-catenin can function in the decision of precursors to proliferate or differentiate during mammalian neuronal development and suggest that beta-catenin can regulate cerebral cortical size by controlling the generation of neural precursor cells."

ARHGAP11B and human cortex size, see "Human-specific ARHGAP11B increases size and folding of primate neocortex in the fetal marmoset) and "Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion -- "Evolutionary expansion of the human neocortex reflects increased amplification of basal progenitors in the subventricular zone, producing more neurons during fetal corticogenesis. In this work, we analyze the transcriptomes of distinct progenitor subpopulations isolated by a cell polarity-based approach from developing mouse and human neocortex. We identify 56 genes preferentially expressed in human apical and basal radial glia that lack mouse orthologs. Among these, ARHGAP11B has the highest degree of radial glia-specific expression. ARHGAP11B arose from partial duplication of ARHGAP11A (which encodes a Rho guanosine triphosphatase-activating protein) on the human lineage after separation from the chimpanzee lineage. Expression of ARHGAP11B in embryonic mouse neocortex promotes basal progenitor generation and self-renewal and can increase cortical plate area and induce gyrification. Hence, ARHGAP11B may have contributed to evolutionary expansion of human neocortex."

pharmacological inhibition of mitochondria permeability transition pore (mPTP) opening via cyclosporine A mimics basal progenitor expansion by ARHGAP11B; bacteria-derived mitochondrial toxin bongkrekic acid (BKA) inhibits adenine nucleotide translocase (ANT) function which also mimics basal progenitor expansion by ARHGAP11B. See Human-specific ARHGAP11B acts in mitochondria to expand neocortical progenitors by glutaminolysis for more information about what makes human ARHGAP11B cause mammalian brains to grow so much larger.

((there's also an ARHGAP15 intronic SNP rs10191758 (A-to-G) at 2q22.3 associated with a small variation in IQ. is that related?))

cyclin-dependent kinase inhibitor (CKI) member p27kip1 when knocked out from mouse neural progenitor cells causes a higher basal level of neural progenitor cell proliferation, and also has high NPC proliferation after adult ischemia incidents. p27kip1 constrains proliferation of neural progenitor cells. See also:

• Nakayama K, Ishida N, Shirane M, et al. Mice lacking p27(Kip1) display increased body size, multiple organ hyperplasia, retinal dysplasia, and pituitary tumors. Cell. 1996;85:707–720. doi: 10.1016/s0092-8674(00)81237-4.
• Kiyokawa H, Kineman RD, Manova-Todorova KO, et al. Enhanced growth of mice lacking the cyclin-dependent kinase inhibitor function of p27(Kip1). Cell. 1996;85:721–732. doi: 10.1016/s0092-8674(00)81238-6.

PTEN regulates neuronal arborization and social interaction in mice -- deletion of PTEN in "limited differentiated neuronal populations in the cerebral cortex and hippocampus of mice. Resulting mutant mice showed abnormal social interaction and exaggerated responses to sensory stimuli. We observed macrocephaly and neuronal hypertrophy, including hypertrophic and ectopic dendrites and axonal tracts with increased synapses. This abnormal morphology was associated with activation of the Akt/mTor/S6k pathway and inactivation of Gsk3beta."

possibly some studies doing AAV-Cre-mediated PETN loss in adult cortex causing cortical thickening and neuronal hypertrophy in the targeted area?

Cdk4/CyclinD1 overexpression in neural stem cells shortens G1, delays neurogenesis, and promotes the generation and expansion of basal progenitors (2009) -- "During mouse embryonic development, neural progenitors lengthen the G1 phase of the cell cycle and this has been suggested to be a cause, rather than a consequence, of neurogenesis. To investigate whether G1 lengthening alone may cause the switch of cortical progenitors from proliferation to neurogenesis, we manipulated the expression of cdk/cyclin complexes and found that cdk4/cyclinD1 overexpression prevents G1 lengthening without affecting cell growth, cleavage plane, or cell cycle synchrony with interkinetic nuclear migration. Specifically, overexpression of cdk4/cyclinD1 inhibited neurogenesis while increasing the generation and expansion of basal (intermediate) progenitors, resulting in a thicker subventricular zone and larger surface area of the postnatal cortex originating from cdk4/cyclinD1-transfected progenitors. Conversely, lengthening of G1 by cdk4/cyclinD1-RNAi displayed the opposite effects. Thus, G1 lengthening is necessary and sufficient to switch neural progenitors to neurogenesis, and overexpression of cdk4/cyclinD1 can be used to increase progenitor expansion and, perhaps, cortical surface area."

Expansion of the neocortex and protection from neurodegeneration by in vivo transient reprogramming -- ".. Transient Yamanaka factor (YF) expression during development expands neocortex; YF-treated mice show enhanced cognitive skills; Intermittent YF expression is tolerated by adult principal hippocampal neurons. [..] Embryonic induction of YFs perturbed cell identity of both progenitors and neurons, but transient and low-level expression is tolerated by these cells. Under these conditions, YF induction led to progenitor expansion, an increased number of upper cortical neurons and glia, and enhanced motor and social behavior in adult mice. Additionally, controlled YF induction is tolerated by principal neurons in the adult dorsal hippocampus." There are many other ways to genetically cause cortex expansion and proliferation besides Yamanaka factors. See morphogenesis for more advanced synthetic biology techniques.

Sonic hedgehog (Shh) signaling enhancement (ligand) increases HOPX-positive outer radial glial cells and also increases cerebral cortical folding in gyrencephalic ferret cortex (ref), see also ref

PSD-95 overexpression - intracerebroventricular injection for postsynaptic density scaffolding protein 95 (PSD-95) overexpression, previously developed an epigenetic editing strategy where a zinc finger DNA-binding domain targeting the Dlg4/PSD95 gene promoter was fused to the transactivation domain VP64 and driven under a CMV promoter. AAV-PhP.B-mediated delivery of this artificial transcription factor (ATF) CMV-PSD95-6ZF-VP64 improved cognition in [an intentionally impaired] mouse model."

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BDNF overexpression increases dendrite complexity in hippocampal dentate gyrus (2002) -- "Utilizing transgenic mice where BDNF overexpression was controlled by the β-actin promoter, we evaluated the effects of long-term overexpression of BDNF on the dendritic structure of granule cells in the hippocampal dentate gyrus. BDNF transgenic mice provided the opportunity to investigate the effects of modestly increased BDNF levels on dendrite structure in the complex in vivo environment. While the elevated BDNF levels were insufficient to change levels of TrkB receptor isoforms or downstream TrkB signaling, they did increase dendrite complexity of dentate granule cells. These cells showed an increased number of first order dendrites, of total dendritic length and of total number of branch points. These results suggest that dendrite structure of granule cells is tightly regulated and is sensitive to modest increases in levels of BDNF. [..] previous in vitro observations that BDNF influences synaptic plasticity by increasing complexity of dendritic arbors."

Neuroligin-1 overexpression in newborn dentate granule cells in vivo -- "To examine the role of neuroligins as synapse-inducing molecules in vivo, we infected dividing neural precursors in adult mice with a retroviral construct that increased neuroligin-1 levels during granule cell differentiation. By 21 days post-mitosis, exogenous neuroligin-1 was expressed at the tips of dendritic spines and increased the number of dendritic spines. Neuroligin-1-overexpressing cells showed a selective increase in functional excitatory synapses and connection multiplicity by single afferent fibers, as well as an increase in the synaptic AMPA/NMDA receptor ratio. In contrast to its synapse-inducing ability in vitro, neuroligin-1 overexpression did not induce precocious synapse formation in adult-born neurons. However, the dendrites of neuroligin-1-overexpressing cells did have more thin protrusions during an early period of dendritic outgrowth, suggesting enhanced filopodium formation or stabilization. Our results indicate that neuroligin-1 expression selectively increases the degree, but not the onset, of excitatory synapse formation in adult-born neurons."

Enhancement by knockout of memory suppressor genes

Some knockouts confer a cognitive benefit. See "memory suppressor genes".

NSG2 knockout: Knockout of AMPA receptor binding protein Neuron-specific gene 2 (NSG2) enhances associative learning and cognitive flexibility. "To date, most gene deletions shown to enhance cognitive ability generally affect a limited number of pathways such as NMDA receptor- and translation-dependent plasticity, or GABA receptor- and potassium channel-mediated inhibition. While endolysosomal trafficking of AMPA receptors is a critical mediator of synaptic plasticity, mutations in genes that affect AMPAR trafficking either have no effect or are deleterious for synaptic plasticity, learning and memory. NSG2 is one of the three-member family of Neuron-specific genes (NSG1-3), which have been shown to regulate endolysosomal trafficking of a number of proteins critical for neuronal function, including AMPAR subunits (GluA1-2) ... NSG2 KO animals demonstrated enhanced recall in the Morris water maze, accelerated reversal learning in a touch-screen task, and accelerated acquisition and enhanced recall on a trace fear conditioning task. Together, these data point to a specific involvement of NSG2 on multiple types of associative learning, and expand the repertoire of pathways that can be targeted for cognitive enhancement." NSG2 regulates endolysosomal trafficking of AMPAR subunits (GluA1/2); its loss probably shifts AMPAR handling to favor stronger associative encoding and easier updating. It probably tweaks the balance of LTP/LTD and/or receptor recycling/endocytosis. The paper emphasizes this is unexpected given prior AMPAR-traffic mutants often hurt plasticity. If you don't want to knockout NSG2, then consider point mutations to blunt NSG2-GluA1/2 interaction, or disrupt dileucine/tyrosine-based motifs to bias NSG2 away from AMPAR trafficking.

Other knockout targets:

• PDE4D (with or without PDE4A) is a suppressor of memory consolidation. ("PDE4 as a target for cognitive enhancement"); PDE4B Y358C mice as a hypomorphic cognition-enhancing model. With PDE4D or PDE8B knockouts, there is increased CREB activation, improved performance in radial arm maze, Morris water maze, contextual fear conditioning, etc.; or make hypomorphic PDE4B (Pde4bY358C) to inhibit PDE4B.
• PAIP2A inhibits translation during memory consolidation. Consider conditional knockout or heterozygote.
• FKBP12 inhibits mTOR-Raptor complex and has protein synthesis dependent effects on consolidation. Systemic loss will effect many tissues, so this must only be a conditional knockout in forebrain.
• GABRA5 (GABAA receptor subunit α5) is a suppressor of acquisition.
• GAT1 (Slc6a1) reduces GABA reuptake; heterozygotes for GAT1 show better performance across tasks.
• Caspase-2 stabilizes AMPAR endocytosis and promotes forgetting.
• PIWIL1/2 provides small RNA silencing which impedes LTM. Make the change via dual knockdown in adult hippocampus only.
• KCNH3 (Kv12.2) potassium channel loss-of-function: previously discussed on this page.
• NCX2 knockout

There are a few other options but they have higher pleiotropy or system-wide effects (doesn't mean they are unusable just requires more thoughtfulness):

• eIF2α-kinases (PKR, GCN2; PERK only if tightly restricted): reduced eIF2α phosphorylation, lowered L-LTP threshold, enhanced hippocampal memory. (x)
• ATF4 / ICER (CREB repressors) are suppressors of memory consolidation
• inhibit Rac1 after learning rather than as a germline knockout
• STEP (PTPN5)
• HDAC2
• Cdk5

Other mutations (which reduce functionality in a favorable way) to consider instead of knockout:

• eIF2α S51A heterozygote: "Mice with phosphorylation-deficient eIF2α display enhanced spatial memory, fear memory, taste memory, and elevated late-phase LTP (L-LTP) (Costa-Mattioli et al., 2007). Phosphorylation of eIF2α suppresses memory formation via two distinct mechanisms. First, eIF2-dependent production of memory-supporting proteins is decreased (Boye and Grallert, 2020). Second, the translation of the CREB inhibitor ATF4 is increased (Lu et al., 2004; Vattem and Wek, 2004). The memory suppressor genes PKR, GCN2, and PERK all code for kinases that phosphorylate eIF2α at the S51 residue, thereby suppressing eIF2α-dependent consolidation and synaptic plasticity (Costa-Mattioli et al., 2005; Sharma et al., 2018; Zhu et al., 2011)." (ref)
• PDE4D catalytic hypomorph: partial loss of PDE4D activity raises cAMP/PKA/CREB signaling during consolidation. PDE4 inhibitors and KOs consistently enhance LTM. Hypomorphic or regulatory-domain mutations mimic pharmacologic effects without systemic toxicity.
• FKBP12-mTOR interface mutant: weakening FKBP12 binding to mTOR removes a brake on translation-dependent memory consolidation. Ensure calcineurin binding remains intact.
• enhanced sensory temporal acuity and temporal coding in auditory midbrain via Kv3.1 mutant

Injection and infusion

fetal microinjection of FGF2 into embryonic ventricles (mouse E11.5) induces cortical gyrification (Cortical gyrification induced by fibroblast growth factor 2 in the mouse brain) -- "Gyrification allows an expanded cortex with greater functionality to fit into a smaller cranium. However, the mechanisms of gyrus formation have been elusive. We show that ventricular injection of FGF2 protein at embryonic day 11.5—before neurogenesis and before the formation of intrahemispheric axonal connections—altered the overall size and shape of the cortex and induced the formation of prominent, bilateral gyri and sulci in the rostrolateral neocortex. We show increased tangential growth of the rostral ventricular zone (VZ) but decreased Wnt3a and Lef1 expression in the cortical hem and adjacent hippocampal promordium and consequent impaired growth of the caudal cortical primordium, including the hippocampus. At the same time, we observed ectopic Er81 expression, increased proliferation of Tbr2-expressing (Tbr2+) intermediate neuronal progenitors (INPs), and elevated Tbr1+ neurogenesis in the regions that undergo gyrification, indicating region-specific actions of FGF2 on the VZ and subventricular zone (SVZ). However, the relative number of basal radial glia—recently proposed to be important in gyrification—appeared to be unchanged. These findings are consistent with the hypothesis that increased radial unit production together with rapid SVZ growth and heightened localized neurogenesis can cause cortical gyrification in lissencephalic species. These data also suggest that the position of cortical gyri can be molecularly specified in mice. In contrast, a different ligand, FGF8b, elicited surface area expansion throughout the cortical primordium but no gyrification. Our findings demonstrate that individual members of the diverse Fgf gene family differentially regulate global as well as regional cortical growth rates while maintaining cortical layer structure."

Estradiol mediates fluctuation in hippocampal synapse density during the estrous cycle in the adult rat -- "We have found that the density of synapses in the stratum radiatum of the hippocampal CA1 region in the adult female rat is sensitive to estradiol manipulation and fluctuates naturally as the levels of ovarian steroids vary during the 5 day estrous cycle. In both cases, low levels of estradiol are correlated with lower synapse density, while high estradiol levels are correlated with a higher density of synapses. These synaptic changes occur very rapidly in that within approximately 24 hr between the proestrus and estrus stages of the estrous cycle, we observe a 32% decrease in the density of hippocampal synapses. Synapse density then appears to cycle back to proestrus values over a period of several days. To our knowledge, this is the first demonstration of such short-term steroid-mediated synaptic plasticity occurring naturally in the adult mammalian brain." and another study suggests that endogenous hippocampus estradiol not peripheral estradiol is responsible for female rat "novel object recognition" skill, however they only tested this via inhibition of the production of hippocampal estradiol via microinjection of letrozole (an aromatase inhibitor) into the hippocampi of rats.

intracortical infusion or injection for the purposes of proliferation & neurogenesis:

• EGF (ICV infusion) — robust SVZ proliferation; expands migratory cells along RMS; note reports of hyperplastic SVZ “polyp” lesions with prolonged dosing in rats. Journal of Neuroscience, PLOS, Liebert Publishing
• TGF-α (EGF-family; ICV) — SVZ hyperproliferation and parenchymal recruitment (documented alongside EGF; caution for dysplasia). gupea.ub.gu.se
• HB-EGF (ICV infusion) — increases BrdU+ cells in SVZ and dentate gyrus. MDPI
• Betacellulin (BTC) (EGF-family ligand; ICV) — increases V-SVZ proliferation in adult rodents. Cell
• BDNF (ICV infusion) — drives new neurons beyond OB/RMS into striatal, septal, thalamic, hypothalamic parenchyma. Journal of Neuroscience
• NGF (chronic ICV) — increases DG proliferation & new neuron survival; cognitive benefits reported. PubMed, ScienceDirect
• IGF1 (ICV) — restores/boosts hippocampal neurogenesis in aged rats. PubMed
• IGF2 (intrahippocampal protein injection) — enhances memory with evidence for synaptic and neurogenic support. PMC
• VEGF (ICV) — neurogenic and angiogenic effects in adult rodent brain (hippocampus). ResearchGate
• EPO (erythropoietin) (ICV) — increases hippocampal neurogenesis, improves outcomes post-injury. ScienceDirect

intracortical injection or infusion for the purposes of dendritic branching, dendritic spine density, and synaptogenesis:

• Reelin (acute protein supplementation/injection to hippocampus or cortex) — causes increased dendritic spine density, increased CA1 LTP, cognitive enhancement; rescues synaptic plasticity in deficit models. PubMed, PMC -- reelin injection boosts NMDAR function and promotes AMPAR insertion via ApoER2/VLDLR signaling.
• BDNF (ICV) — causes increased neurogenesis and widely reported increased dendritic complexity/spines; related to activity-dependent synaptogenesis. Journal of Neuroscience
• VGF-derived peptide TLQP-62 (intrahippocampal) — causes increased dendritic branching & synaptic potentiation via BDNF/TrkB-dependent mechanism; enhances memory. Journal of Neuroscience, MDPI
• Neuregulin-1 (NRG1) (ICV) — rescues dendritic spine density and ameliorates synaptic deficits via ErbB signaling. Cell
• CXCL12/SDF-1 (ICV) — promotes dendritic spine formation and cognitive recovery after neuroinflammation. PubMed
• Growth hormone (GH) (ICV) — causes increased spine density & dendritic length in hippocampus; improved memory. bioRxiv
• Hevin/SPARCL1 (astrocyte-secreted matricellular protein) — potent excitatory synaptogenic organizer in visual/cortical circuits in vivo. PMC

synaptic plasticity:

• injection of chondroitinase ABC for the purposes of digesting or loosening the perineuronal net, or otherwise allowing ECM flexibility, to re-enable some level of juvenile synaptic plasticity. ChABC cleaves the glycosaminoglycan (GAG) chains of CSPGs in the PNN, reducing their inhibitory effect. This loosens or dismantles the PNN structure, allowing more synaptic remodeling and axonal sprouting. The removal of CSPG inhibition reduces signaling through PTPσ and NgR1, decreasing RhoA activity and cytoskeletal stabilization, and promotes increased TrkB signaling and BDNF sensitivity. Pharmacological or genetic reduction of CSPG synthesis (e.g., targeting aggrecan or link proteins) can also achieve a similar effect as chondroitinase ABC treatment. Otx2 is a transcription factor that stabilizes PNNs around parvalbumin neurons and a reduction of Otx2 might be able to destablize PNN.
• co-administration of hyaluronidase (cleaving the hyaluronan backbone that scaffolds PNNs) with chondroitinase ABC for a one-time treatment
• plasticity enhancement via cortical injection or infusion: one could administer intracortical microinfusions of ChABC (in aCSF) via stereotactically placed cannulae targeting visual or prefrontal cortex to digest CSPGs and reopen critical-period plasticity windows; combine this with AAV-mediated C6ST-1 overexpression injected intraparenchymally into the same regions to shift sulfation ratios toward the juvenile 6S-enriched state that fails to stabilize PNNs; deliver Otx2-blocking peptides or siRNA-loaded nanoparticles via intracortical infusion to prevent Otx2's glycan-mediated accumulation in PV+ interneurons and thus delay PNN maturation; co-infuse recombinant BDNF or inject AAV-BDNF to activate TrkB signaling within the now-permissive ECM; supplement with intracortical Reelin protein injection (purified or via AAV-Reelin) to potentiate ApoER2-Dab1 cascades enhancing NMDAR/AMPAR function and spine plasticity; for sexually dimorphic or estrogen-responsive circuits, perform local estradiol microinjections or deliver aromatase-expressing AAV to boost local estrogen synthesis; administer recombinant kalirin-7 protein or AAV-kalirin-7 to cortical targets to drive Rac1-dependent actin remodeling and spine enlargement; and finally, to modulate glycosyltransferase activity, inject AAVs encoding dominant-negative ST8SIA2/4 to reduce polysialylation maturation signals or hyaluronidase co-infusions to shorten HA chains—all delivered via convection-enhanced delivery or slow osmotic minipump infusion over days to weeks, creating a synergistic multi-target approach that simultaneously dissolves the mature restrictive ECM while driving robust neurotrophic and cytoskeletal remodeling programs to restore juvenile-like cortical synaptic plasticity. ... or instead of AAV, consider a one-time treatment, or RNA-informed therapies, or infusion of a cell therapy (such as a neuronal cell therapy or a microbial cell therapy), or intracortical electroporation of cDNA.

• Infusion of a one-time protein or monoclonal antibody treatment can reopen plasticity temporarily but it will rebuild. It is not clear to me how long the window would remain open after a single treatment of a protein therapy. ECM will regenerate. PNN will re-lock eventually (but when?). Using a gene therapy might be able to produce more lasting results, of course, if you target glycan production or something... Or intracortical infusion with a replenishable renewable supply via exterior access, such as osmotic minipumps with subcutaneous syringe injection reservoire for refills.

• intrahippocampal injection of insulin, IGF2, IGF1, etc; insulin increases NMDAR surface delivery/phosphorylation and modulates AMPAR trafficking.

• intrahippocampal injection of BDNF increases GluA1/GluA2 levels/trafficking and GluA1 phosphorylation; BDNF-driven plasticity is NMDAR/TrkB-linked.
• intrahippocampal injection of glucose
• direct hippocampal lactate infusion enhanced spatial memory and increased plasticity markers (e.g., Arc/Arg3.1); a large body of work shows astrocyte-to-neuron lactate transport is required for LTP and long-term memory. (ref)
• hippocampal pyruvate infusions
• temporary NgR1 antagonism to increase synaptic plasticity (transgenic NgR1 downregulation or knockout seems to reduce short-term object recognition). Various studies have used NgR1(310)ecto-Fc infused intracerebroventricularly. Or administration of NEP1-40 (NgR1 antagonist peptide) and fasudil (ROCK inhibitor).
• maybe: intraparenchymal injection of foxp2 protein to increase language acquisition rate in children (or normalize foxp2 expression level sex differences in adolescent language acquisition)?
• TODO: what about direct injection of amphetamine, nictoine, L-DOPA, glutamate, or other neurotransmitters? what would be the best targeted locations for this?

More intelligence related TODOs

consider the possibility of:

• possibly some brain size gains from reducing developmental apoptosis (like via Apaf1, caspase pathway mutants, or other apoptosis escape) of surplus neural precursors escaping programmed cell death?
• yamanaka factor direct injection into cortical areas? in utero? in adult?
• various cell cycle control factors either genomically encoded and expressed, or via intracortical injection
• injection of kalirin-7 (a regulator of spine plasticity)
• consider maybe: Chondroitinase ABC (protein enzyme; intracortical infusion) — digests CSPGs/PNNs, reopens adult visual-cortex plasticity, enabling new synaptic connections and circuit re-wiring.
• consider maybe: Otx2 homeoprotein (protein delivered to visual cortex) — modulates PV-cell/PNN state to reopen or shift critical-period plasticity, facilitating structural/synaptic remodeling. PMC
• consider maybe: intrahippocampal injection of APP-alpha - improved motor learning and memory in mice.
• hippocampus or amygdala injection of Tat-GluA2_3Y peptide (block AMPAR endocytosis and keep AMPARs at synapses)
• intracortical delivery of exosomes or extracellular vesicles? intracerebral intraparenchymal mitochondria injection?
• oxygen-loaded microbubbles and ultrasound targeting (sonoperfusion), perfluorocarbon oxygen carriers emulsions to increase cerebral oxygenation and mitochondrial function, etc
• Intracerebral injection of extracellular vesicles from mesenchymal stem cells
• faster action potentials. faster recovery. more dendrites per neuron. more receptors per synapse (davidad says estimates are 150 to 300 receptors per human synapse), less ubiquitin, more DUB, more basal radial glia cells.

faster action potentials:

• Kv3 channel mechanisms: Kv3.1/3.2 enable ultra-fast action potential repolarization; transfection/overexpression of Kv3.1 makes normally slow neurons capable of high-rate firing.
• BK channel β4 (KCNMB4) loss narrows action potentials and alters excitability in dentate granule cells

need to double check and confirm these mouse results:

• overexpression of neuronal caveolin-1 (SynCav1) to increase dendritic arborization and synaptic preservation in aging mice?
• Cdk4 + Cyclin-D1: increasing expression of these cell-cycle genes in adult dentate gyrus expands neural stem/progenitor pools, increases adult neurogenesis, and improves memory.
• TLX (Nr2e1, orphan nuclear receptor): TLX expression expands adult hippocampal stem/progenitor cells (increased AHN) and has been linked to enhanced learning/memory in mice.

IF1 overexpression enhances long-term memory (maybe in a dose proportional manner?). See other IF1 content on this page about IF1 overexpression and longevity.

possible engineering targets:

• deubiquitinization efficiency?
• neurotransmitter receptors, binding efficiency, regulation, lifecycle stuff (production, membrane localization, (thermo)stability, destruction)
• agonists, antagonists
• copy number variations of deubiquitinization
• spinogenesis, synaptogenesis, synapse pruning, axon growth, dendritic growth, neurites, mitochondria modifications
• NLGN3 R451 - mice showed increased social defecits, but also enahnced spatial learning and memory.
• Dicer1 knockout in forebain?

other TODO to consider:

• upregulate endogenous TFAM
• PGC-1α stabilization mutant: A "degron-null" PGC-1α engineered by mutating key phosphodegron residues, converting the inhibitory S570 to a non-phosphorylatable alanine, and optionally trimming unstable regions plus adding an inducible degron, to prolong its active, mitochondrial biogenesis-driving state.
• Hyperactive MFN1: engineered Mfn1 variant that weakens GTPase-helix-bundle autoinhibitory contacts while preserving HR2 coiled-coil integrity, aiming to shift the conformational equilibrium toward the fusion-competent state and enhance mitochondrial network elongation.
• Cleavage-biased OPA1: An OPA1 mutant with selectively blunted OMA1-sensitive cleavage (rather than completely cleavage-dead) via local loop and charge edits around the S1 site, to favor long-form OPA1, stabilize cristae structure, and improve respiratory efficiency.

possibly it would be better to focus on the engineering of entire systems of growth and pruning rather than just growth, unless existing pruning mechanisms can accommodate irrelevant-needs-to-be-pruned overgrowth. It is not clear if there is a specific balance or synaptic plasticity rate, or synaptogenesis rate to pruning rate etc, that needs to be hit in order to have significantly improved cognitive ability or learning.

how to better increase the information density of neurons or synapses?

• TODO: process "Parrot genomes and the evolution of heightened longevity and cognition" (2018) "The parent paralogs of several other parrot-specific duplicated genes (CEP83, SLC9A5, RSPH3, and LRRC37A; Table 1) are involved in critical aspects of neuronal cell structure and integrity, including regulation of actin cytoskeleton, microtubule sliding, filopodial extension, and the structure of cilia and dendritic spines, disruptions of which can lead to cognitive impairment. LRRC37A, in particular, is a member of a large gene family with involvement in the immune system and in nervous system development, and which is greatly expanded in primates. In humans, LRRC37 is broadly expressed, with enrichment in the cerebellum and thymus. Our evidence of a duplication in parrots points to a convergent expansion of this gene family in both primates and parrots, suggesting a possible link with the increased cognitive capacities of these two unrelated taxa."
• Evolution of cortical neurons supporting human cognition has a nice overview of what makes human cortical pyramidal neurons different, in particular very extensive dendritic trees and neurite growth. The highest most protracted overproduction of human synapses (up to third decade of life) was described for associative layer IIIC pyramidal neurons in the human dorsolateral prefrontal cortex. Also indicated is action potential speed of information transfer and overall cortical neuron metabolic efficiency.
• Large and fast human pyramidal neurons associate with intelligence
• Human neocortical expansion involves glutamatergic neuron diversification
• Comparative transcriptomics reveals human-specific cortical features
• Molecular mechanisms of the specialization of human synapses in the neocortex

• Human voltage-gated Na+ and K+ channel properties underlie sustained fast action potential signaling

• TODO: genetics of theory of mind - "our data indicate that individuals with the DAT 9R/9R gene variant may have a decreased ability to accurately interpret and understand the mental and emotional states of others", lots of other mutations mentioned in the article.

  • mutations causing a lack of theory of mind or a loss of theory of mind:
    • DRD4 - 7-repeat allele: Dopamine-D4 receptor; the 7R allele lowers receptor density, and female 7R carriers show significantly worse affective ToM than non-carriers.
    • DRD4 - long (≥6-repeat) alleles: Dopamine-D4 receptor; long repeats reduce receptor availability, so children with ≥1 long allele score lower on representational ToM than short-allele homozygotes.
    • DAT1 9/9 genotype: Dopamine transporter; the 9-repeat variant increases striatal DAT protein, lowers synaptic dopamine, and 9/9 adults make more errors on the Reading-the-Mind-in-the-Eyes test than 10-allele carriers.
    • COMT rs2020917-C/C or T/T homozygotes: Catechol-O-methyl-transferase; these genotypes yield sub-optimal prefrontal dopamine and adults perform worse on cognitive-ToM tasks than C/T heterozygotes.
    • COMT rs737865-T/T: Catechol-O-methyl-transferase; T/T individuals have reduced cortical dopamine and display lower cognitive mind-reading scores than C/C carriers.
    • MAO-A low-activity alleles (2, 3 or 5 repeats): Monoamine-oxidase A; low-activity alleles leave serotonin/dopamine elevated but adults show poorer ToM performance than high-activity (3.5 or 4-repeat) carriers.
    • EFHC2 rs7055196-G: EF-hand calcium-binding protein; the G-allele lowers gene expression in social-cognition circuits and adult males carrying G score lower on advanced ToM tasks than A-allele carriers.
    • GTF2IRD1, GTF2I, GTF2IRD2 deletions (1.5 Mb or 1.8 Mb): Transcription factors at 7q11.23; hemizygous deletion removes these genes, producing visuo-spatial and social-cognition deficits-healthy deletion carriers perform worse on ToM tasks than non-deleted controls.
  • better theory of mind:
    • DRD4 - 7-repeat (7R) allele: Dopamine‑D4 receptor; the 7R allele reduces dopamine‑receptor binding, and carriers (especially females) show significantly lower affective‑ToM scores.
    • DRD4 - short (< 6-repeat) alleles: Dopamine-D4 receptor; fewer repeats give higher receptor density/better dopamine signal and children with two short alleles score better on representational ToM tasks than long-allele carriers.
    • OXTR rs1042778-GG: Oxytocin receptor; the G-allele raises receptor expression and preschool G/G homozygotes outperform A/A peers on affective mind-reading tests.
    • OXTR rs53576-A: Same receptor; the A-variant heightens oxytocin sensitivity and adolescent A-carriers correctly identify more emotional eye-region faces than G/G individuals.
    • COMT rs2020917-CT heterozygotes: Catechol-O-methyl-transferase that degrades dopamine; the C/T genotype yields optimal prefrontal dopamine and adult C/T carriers achieve higher cognitive-ToM scores than either homozygote group.
    • COMT rs737865-CC: A synonymous COMT SNP in linkage disequilibrium with functional variants; C/C adults show elevated cortical dopamine and superior cognitive mind-reading relative to T/T subjects.
    • MAO-A high-activity alleles (3.5 or 4 repeats): Monoamine-oxidase A metabolises serotonin/dopamine; adults with high-activity alleles display better ToM performance than low-activity (2-, 3-, 5-repeat) carriers.
    • EFHC2 rs7055196-A: EF-hand calcium-binding protein; the A-allele enhances gene expression in social-cognition circuits and adult males carrying A score higher on advanced ToM tasks than G-allele peers.

modulated alcohol cravings - rs1799971

rs4680 "worrier/warrior" cognitive effects

dopamine D3 receptor knockout improves cognitive performance. Dopamine D3 receptor (D3R) antagonism and genetic knockout seem to produce pro-cognitive effects, suggesting that D3R normally acts as an inhibitory modulatory "brake" on learning and memory processes. D3R-knockout mice exhibit enhanced performance in hippocampus-dependent tasks such as passive-avoidance learning, object-recognition memory, and certain forms of associative learning, accompanied by increased activation of intracellular plasticity pathways (e.g., ERK1/2 and CREB phosphorylation) that facilitate memory consolidation. Pharmacological studies parallel these findings: selective D3R antagonists improve attention, working memory, recognition memory, and cognitive flexibility, while D3R agonists or overactivation impair these domains, partly via suppression of hippocampal gamma oscillations and dampening of synaptic plasticity. Dopamine D3 receptors inhibit hippocampal gamma oscillations by disturbing CA3 pyramidal cell firing synchrony.

5-HT1B receptor knockout mice show enhanced spatial memory performance. Also some increased social aggression. This knockout may have a deleterious effect on performance on a long delay working memory task.

Adenosine A2A receptor knockout mice show enhancement of working memory and inactivation of AA2AR in striatal neurons enhances reversal learning.

CCR5-delta32 mutation may improve memory consolidation and synaptic plasticity. FDA-approved CCR5 antagonists (maraviroc, vicriviroc, cenicriviroc, leronlimab) may also be sufficient for this and do not require germline genetic engineering. It is unclear if baseline mice or baseline human experience cognitive improvements from genetic CCR5-delta32 mutation or even pharmacological antagonism. This was previously discussed in public with regards to the Jiankui He lab and the three germline modified human embryos with speculation that the chosen target was also chosen for its potential cognitive benefits.

Overexpressing Tet1S (short isoform, lacking large N-terminal regulatory regions) supports memory formation, while full-length Tet1 overexpression restricts memory formation. Global Tet1 knockout enhanced hippocampal-dependent memory but this is possibly because it included the knockout of full-length Tet1. However, the catalytic domain alone disrupts DNA demethylation programs and therefore impairs synaptic plasticity. Earlier Tet1 memory studies did not distinguish between different Tet1 isoforms? The short isoform of Tet1 called Tet1S lacks most of the repressive N-terminal domain, it's associated with activity-dependent demethylation, and promotes rapid transcriptional induction of plasticity genes. More broadly, Tet1 regulates memory by controlling the epigenetic permissiveness of activity-dependent plasticity genes through DNA demethylation and therefore changes gene expression patterns required for synaptic plasticity. Depending on which Tet1 isoform or domain is manipulated, Tet1 can either enhance or impair memory because the full-length form is partly repressive, while the short isoform is pro-plasticity.

Amphetamine-related enhancement

The following ideas are based on the concept of tracing the mechanism of action of amphetamine with regards to amphetamine-linked cognitive benefits.

idea: increase expression of D1 receptor in layer II/III + V mPFC pyramidal neurons.

idea: increase α2A receptor mediated inhibition of cAMP in pyramidal neurons.

Nicotine-related enhancement

The following ideas are based on the concept of tracing the mechanism of action of nicotine with regards to nicotine-linked cognitive benefits.

idea: Knock-in a mutant α4 subunit (Chrna4) with increased agonist sensitivity, expressed specifically in layer V/II-III mPFC pyramidal neurons. α4β2 is the main high-affinity nAChR in PFC; low nicotine doses preferentially act here and enhance attention/working memory. Stronger/longer α4β2 activation would lead to more depolarization + more M-current suppression and therefore higher persistent firing during tasks. Also, point mutations in nAChR subunits are well-characterized.

idea: overexpression of α4 and β2 subunits in pyramidal neurons of mPFC and hippocampus to increase receptor density, therefore producing larger nicotinic currents for endogenous ACh, resulting in stronger gain modulation of excitatory cells. Cognitive enhancement from nicotine is strongest in circuits rich in α4β2; more receptors should amplify endogenous cholinergic tone.

idea: α7 (Chrna7) overexpression in hippocampal CA1 pyramidal neurons. α7 is heavily implicated in LTP and episodic/recognition memory; α7 agonists can mimic aspects of nicotine’s memory enhancement.

idea: knock-in an α7 variant with increased Ca2+ permeability or slower desensitization, restricted to CA1/CA3 pyramidal neurons. Avoid excitotoxicity somehow.

idea: overexpress α5 (Chrna5) in α4β2-containing receptors on layer V mPFC pyramidal neurons.

idea: overexpress α4/β2 selectively in basal forebrain cholinergic neurons.

idea: α4β2 overexpression targeted to presynaptic glutamatergic terminals in hippocampus. Presynaptic restriction can be tricky compared to these other ideas.

idea: overexpress both α4β2 nAChRs and dopamine D1 receptors in PFC pyramidal neurons.

Astrocyte-specific changes (speculative)

Here are some astrocyte-specific modifications that might be beneficial:

• optimize glutamate uptake dynamics. Targets for this in astrocytes would include EAAT2/GLT-1 (Slc1a2) and EAAT1/GLAST (Slc1a3). GLT-1 overexpression in astrocytes. Increase glutamate transporter expression. Or modestly treat kinetic properties of the glutamate transporter.
• enhance potassium buffering. Overexpression of Kir4.1 (KCNJ10) in astrocytes. Increase membrane expression. Modify gating kinetic. Enhance trafficking.
• astrocyte-specific MCT1 overexpression (as mentioned elsewhere on this page). Lactate export can be targeted by targeting MCT1 (SLC16A1) for lactate uptake and MCT4 (SLC16A3) for lactate export from glycolytic tissues (fast-twitch muscles, astrocytes). MCT4 is upregulated by hypoxia (HIF-1a). Shift LDH-A to favor lactate. GLUT1 for glucose uptake at astrocyte endfeet. Mild tweaks of trafficking signals to bias them into perisynaptic processes. (Astrocyte-derived lactate is linked to memory formation; more efficient lactate supply could support energetically expensive phases of LTP.)
• Basigin (BSG / CD147) and EMB (GP70) are chaperone proteins required for proper functioning of MCT1, MCT3, and MCT4.
• improve mitochondria or PGC-1α associated mitochondrial biogenesis in astrocytes
• increase astrocyte neurotrophic factor support by placing cDNA for BDNF, GDNF, thrombospondins (TSP1/2), hevin (SPARCL1) under an astrocyte-specific promoter. Some mutational work could be done to alter receptor specificity or increase protein stability in extracellular space. There are also astrocyte-expressed synapse maturation factors (Hevin (SPARCL1), SPARC, glypican-4, glypican-6) that could be overexpressed, or otherwise modified for altered binding properties to synaptic partners (e.g., neurexin/neuroligin bridging by hevin).
• improve handling of oxidative stress in astrocytes to protect synapses from ROS, via overexpression or more of several antioxidant enzymes (SOD2 (mitochondrial superoxide dismutase), catalase, mitochondrial catalase, glutathione-related enzymes (GCLC, GCLM, GPx, etc.)).
• enhance regulation of extracellular adenosine via overexpression of CD39 (ENTPD1), CD73 (NT5E), or ENT1/2 (equilibrative nucleoside transporters). Increase their catalytic efficiency or surface localization. These changes alter the time course of adenosine buildup and clearance.

• enhance targeting of aquaporin-4 (AQP4) to the astrocytic endfeet (perivascular localization), such as via α-syntrophin interaction stabilization. The goal is to prevent depolarization of the aquaporin-4 channels and make clearance more efficient per hour of sleep. It is not clear to me whether a benefit would exist regardless of the outcome of the general theory of sleep related glymphatic clearance system.

• TODO: maybe target SLC16A7 (MCT2) - a high efficiency lactose transporter found in neurons and liver.

• TODO: explore gain of function enhancement of lactate dehydrogenase (maybe there's a 2x efficiency gain available here?)

Inspired by oxygen supplementation therapy

Normobaric oxygen supplementation in humans improves scores on psychometric testing. Inspired by this (and the high altitude modifications elsewhere on this page), here are several changes to consider.

• Mitochondria-targeted catalase (MCAT) overexpression: make a better human catalase targeted to the mitochondria inside neurons. Improved catalase also has a pro-longevity effect (see elsewhere on this page). probably something to do with redox signaling. It might interfere with adaptive metabolism due to less ROS. Some ROS signaling triggers kinases in neurons? etc. Higher catalase is associated with lower self-reports of depression symptoms. MCAT overexpression also correlated with longevity, downregulates oxidative damage. study: mitochondria-targeted catalase overexpression does not prevent cellular senescence or SASP accumulation (in cells or aged mouse adipose), suggesting mitochondrial ROS aren't always causal in natural aging senescence.
• neuroglobin overexpression has a neuroprotective effect against intermittent hypoxia (in mice).
• idea: Astrocyte-specific MCT1 overexpression (e.g., GFAP- or Aldh1l1-driven) to increase lactate efflux capacity. Astrocytes store glycogen and export L-lactate via MCT1 (SLC16A1). Neurons import lactate mainly via MCT2, oxidize it to pyruvate, and feed the TCA cycle. Late-phase LTP is ATP-hungry. Lactate can also trigger plasticity pathways. However, too much astrocyte generated lactate without matched neuronal uptake (via MCT2, PDH) might cause acid damage.
• idea: Neuron-specific MCT2 overexpression. MCT2 (SLC16A7) is the high-affinity neuronal lactate transporter; its expression tracks synaptic density and plasticity. Increases lactate capture from astrocyte supplied lactate. This should help with LTP consolidation. Consider redox state with respect to swings in pyruvate/lactate ratio.
• idea: add myoglobin to neurons.
• idea: add cytoglobin to astrocytes.
• idea: Neuron-biased SOD1 up-tuning under an activity/ROS-responsive promoter (e.g., ARE or c-fos/NRF2 hybrid), so antioxidant capacity scales with demand. But you also don't want to over-dampen ROS signaling. Mis-timed SOD1 could shift redox to H2O2 burden unless downstream peroxidases/catalase can keep up, so maybe use the MCAT overexpression too.
• idea: add G6PD overexpression to neurons. G6PD is the rate-limiting enzyme of the pentose phosphate pathway, generating NADPH for glutathione/peroxiredoxin systems and supporting biosynthesis during plasticity. Extra NADPH headroom supports rapid glutathione recycling during learning, limiting ROS-induced synaptic instability. Supports de novo synthesis (lipids, nucleotides) relevant to spine remodeling and local protein synthesis. Glycolsis might be impacted by this?
• idea: brain-endothelial-restricted PHD2 hypomorph to slightly raise HIF activity locally, thereby promoting angiogenesis and better-perfused capillary networks.

Tweaked synaptic plasticity

Tweak or partially destabilize postsynaptic protein complexes to allow for more synaptic plasticity or synaptic remodeling of receptors etc. For example: "FRMPD2 (FERM and PDZ domain containing 2) encodes a scaffold protein that participates in cell-cell junction and polarization, localized at photoreceptor synapses and the postsynaptic membrane in hippocampal neurons in mice. A partial duplication of the ancestral FRMPD2 created the 5’-truncated FRMPD2B paralog ~2.3 mya. FRMPD2B encodes 320 aa of the C-terminus, versus 1,284 aa for the ancestral, maintaining two of three PDZ domains involved in protein binding but lacking the KIND and FERM domains. Ancestral FRMPD2 expresses in the human prenatal cortex during upper layer formation, while FRMPD2B is evident postnatally. The paralogs also show divergent evolutionary signatures, with FRMPD2 strongly conserved and FRMPD2B exhibiting possible positive selection. Combined, we propose a model in which truncated human-specific FRMPD2B counteracts the function of full-length FRMPD2 leading to altered synaptic features in humans, possibly through interactions of its PDZ2 domain with GluN2A of NMDA receptors at the postsynaptic terminal. Its postnatal expression would avoid the detrimental effects of inhibiting FRMPD2 during early fetal development (i.e., microcephaly). We note that recurrent deletions and duplications in chromosome 10q11.21q11.23 impact both paralogs in children with intellectual disability, autism, and epilepsy. FRMPD2B could plausibly contribute to the upregulation of glutamate signaling and increased synaptic plasticity observed in human brains compared with other primates that is fundamental to learning and memory."

speculation: Based on that proposed FRMPD2B model above, FRMPD2B increases synaptic plasticity in the postnatal brain by acting as a dominant-negative regulator of the ancestral FRMPD2 scaffold protein at glutamatergic synapses. The truncated FRMPD2B retains two PDZ domains, including PDZ2 which can bind to GluN2A subunits of NMDA receptors, but lacks the N-terminal KIND and FERM domains that enable full-length FRMPD2 to properly organize and stabilize postsynaptic protein complexes. When FRMPD2B competes with full-length FRMPD2 for binding sites at the postsynaptic density, it likely disrupts the normal scaffolding function that would otherwise constrain synaptic architecture and receptor organization. This competitive inhibition could destabilize rigid postsynaptic assemblies, allowing for more dynamic NMDA receptor trafficking, enhanced receptor mobility, and reduced constraints on synaptic remodeling. This frees the NMDA receptors to diffuse laterally, possibly reduces anchoring to F-actin, and favors a switch from GluN2B- to GluN2A-dominant NMDA currents that lowers the threshold for calcium-dependent CaMKII/CREB signaling and AMPA receptor phosphorylation, thereby potentiating long-term synaptic potentiation and in aggregate increases the heightened postnatal plasticity characteristic of the human brain. The resulting increase in glutamate receptor availability and synaptic structural flexibility would facilitate activity-dependent strengthening and weakening of synapses. By expressing only postnatally, FRMPD2B avoids interfering with FRMPD2's essential roles in early cortical development while specifically modulating synaptic plasticity during the critical period of postnatal synapse refinement and circuit maturation when human cognitive abilities develop.

Other approaches to tweak postsynaptic protein complex stability include increasing ABHD17 or decreasing zDHHC2 to nudge PSD-95 palmitoylation which controls its clustering and AMPAR anchoring; modestly increasing depalmitoylation (e.g., ABHD17A/B/C) shrinks PSD-95 nanoclusters and increases remodeling, yet leaves the scaffold intact.

Or, alternatively, AMPAR anchoring hinges on stargazin/TARP C-tail binding to PSD-95 PDZs. Mild disruption (short PDZ-ligand peptide or phospho-mimic C-tail) increases AMPAR lateral diffusion and turnover.

Disruption of stargazin-PSD-95 increases AMPAR diffusion and that PDZ-ligand phosphorylation modulates this coupling.

Alternatively, brief chondroitinase ABC (or related strategies) reopens critical-period-like plasticity in adult cortex, such as to loosen the extracellular perineuronal net or extracellular matrix.

increase synaptic plasticity: overexpression of chondroitin 6-O-sulfotransferase (C6ST-1) to elevate the plasticity-favoring 6S/4S chondroitin sulfate ratio while suppressing 4-sulfated CS-A accumulation.

Prolonged NMDA receptor phosphorylation

idea: intentionally prolong NMDA receptor phosphorylation or otherwise have control over increasing NMDA receptor phosphorylation. This should should: (i) increase channel activity and Ca2+ influx, (ii) keep more NMDARs at synapses by suppressing endocytosis, and (iii) bias plasticity thresholds toward potentiation. However, you also don't want to chronically suppress LTD.

STEP inhibition to sustain GluN2B phosphorylation: The goal is to maintain tyrosine phosphorylation of GluN2B at Y1472 to increase synaptic NMDAR stability and Ca2+ signaling. The neuron-specific phosphatase STEP (PTPN5) dephosphorylates GluN2B-Y1472, promoting receptor endocytosis. Inhibiting STEP prolongs phosphorylation, keeping NMDARs at the surface. Use TC-2153, a selective STEP inhibitor shown to restore learning and synaptic function. You can possibly target excitatory neurons using CaMKIIα-CreERT2.

PKA activation during learning windows: Boost PKA-dependent phosphorylation of NMDAR NR1 subunits (e.g., S897), enhancing receptor trafficking and Ca2+ currents only during training or learning periods. Gs-coupled signaling activates adenylyl cyclase, then cAMP, then PKA, which phosphorylates NR1, increasing NMDAR surface delivery and open probability. One chemogenetic approach is to express Gs-DREADDs (designer Gs-coupled receptors) under a CaMKIIα promoter; administer ligand (CNO or equivalent) just before behavioral training. Pair learning with natural β-adrenergic or dopaminergic bursts: brief noradrenaline or dopamine surges known to facilitate LTP induction.

Local activation of Src/Fyn kinases at the PSD: Increase tyrosine phosphorylation of GluN2B (Y1472) and GluN2A to potentiate NMDAR currents and facilitate synaptic plasticity. Src-family kinases (Fyn, Src) phosphorylate NMDARs and PSD-95, strengthening receptor function. Overactivation is harmful. One option is optogenetic recruitment of Fyn to synapses. Another option is chemically inducible dimerization to transiently localize Fyn to PSDs. Increasing Reelin or EphB signaling will also recruit Src/Fyn to synapses and increase NMDA phosphorylation. Elsewhere on this page we discuss the possibility of direct injection of Reelin into the cortex for enhanced learning.

Pair behavioral training with brief LC (locus coeruleus) or VTA optogenetic activation, or timed low-dose β-AR (β-adrenergic receptor, a G-protein-coupled membrane receptor that binds norepinephrine/epinephrine and activates cAMP signaling to mediate arousal, memory, and synaptic plasticity) or D1 receptor (D1R) agonists (such as SKF-38393, SKF-82958, A-77636, and apomorphine (partial)). Restrict stimulation to minutes during learning tasks to mimic physiological reinforcement signals. See this review on benzazepine D1 agonists.

Gain of function proposals for specific neuron proteins

NR2B / GRIN2B (GluN2B; NMDAR subunit): Raise synaptic abundance/surface residency (e.g., boost forward transport or recycling), modestly bias open probability/deactivation toward longer currents, or preserve PDZ-anchoring to keep NR2B at spines.

KIF17 (kinesin-2 motor for NR2B cargo): Increase motor-cargo interaction or expression to elevate NR2B delivery; consider domain designs that favor spine-targeted drop-off. Maybe a dimerization design to transport more NR2B cargo to synapses? Amplify its ability to traffic NMDA receptor subunits, particularly NR2B/GRIN2B, to dendritic spines and synapses, thereby enhancing synaptic plasticity and cognitive performance. One strong concept is to increase KIF17-cargo coupling by engineering or stabilizing its interaction with NR2B-containing vesicles through optimized tail or adaptor domains, ensuring more efficient receptor delivery to the postsynaptic membrane. Another is to boost motor processivity or run length by modifying its motor domain or coiled-coil regions, allowing KIF17 to transport cargo more persistently along microtubules. Enhanced spine-targeting motifs could improve the precision of cargo delivery to active synapses. Various kinesin motors have been improved in the literature too: ref, processivity run length, dimerization, increase processivity by shortening long neck linkers, etc. Exploit subunit composition (head identity) because KIF3B is the more processive head. Increase landing rate. KIF16B is another target to optimize for receptor trafficking, implicated in intelligence GWAS.

SNX27 (endosomal recycling adaptor with PDZ domain): discussed below.

Kv3.1 / KCNC1 (fast-spiking interneuron K+ channel): Boost PV-cell channel density or slightly speed gating; keep cell-type specificity to avoid dampening pyramidal excitability. Consider excitability/inhibitory balance issues.

Reelin: A compact multivalent R3-R6 "mini-Reelin", optionally fused to the C-terminal region (CTR), could maximize ApoER2/VLDLR clustering and downstream Dab1 signaling with greater efficiency than the full protein. Engineering cleavage-resistant or pre-cleaved variants would extend the half-life or diffusion of active fragments, maintaining higher local signaling levels. Oligomerization modules at the N-terminus could ensure receptor clustering even at low concentrations, while ECM-anchoring or mild heparan-binding tags would confine activity to perisynaptic zones that mediate plasticity. Additional refinements: ApoER2-biased mutations, optimized RGD presentation for integrin co-activation. ref

USP46: focus on stabilizing its active conformation and targeting its deubiquitinase activity to synaptic substrates that support learning and memory. Constructing a pre-assembled USP46–UAF1–WDR20 complex (for example, through single-chain or fusion designs) could lock the enzyme in its fully active, allosterically enhanced state, bypassing the need for cofactor availability. Adding synaptic localization motifs, such as short targeting sequences or receptor-binding peptides, would increase local enzyme concentration at postsynaptic AMPA receptor nanodomains or inhibitory synapses. Engineering substrate-selector fusions could bias USP46 toward specific receptor subunits, enhancing recycling rather than degradation, and loop-stabilized or allosterically active variants could further raise catalytic efficiency.

SNX27

Overexpression of SNX27 / Rab11-axis to raise recycling flux back to the membrane. -- "Sorting nexin 27 (SNX27) is an endosomal adaptor protein associated with a variety of nervous system diseases, and it is mainly responsible for the trafficking of postsynaptic membrane receptors. Here, we first generated a neuron-specific human-SNX27 transgenic mouse model (hSNX27 Tg) that exhibited enhanced excitatory synaptic transmission and long-term potentiation (LTP). In addition, we found that the hSNX27 Tg mice displayed enhanced learning and memory, lower-level anxiety-like behavior, and increased social interaction. SNX27 overexpression promotes synaptic function and cognition through modulating glutamate receptors."

SNX27 boosts LTP mostly by recycling PDZ-motif cargos (e.g., GluA1) from endosomes back to the surface, in cooperation with retromer (VPS26/29/35) and activity-coupled K-Ras/CaM signaling. To achieve SNX27 gain of function, generally one should target: increase cargo affinity/avidity (PDZ), increase retromer coupling (between β3–β4 hairpin and VPS26), increase endosomal residency/targeting (PX), increase activity gating (RA/CaM/K-Ras), increase lifetime/concentration (stability/oligomerization).

1) Dimerization of SNX27. Multivalency is a classic way to boost capture/recycling for trafficking adaptors without altering their specificity. Simply increasing the number of PDZ pockets that sample the same endosomal surface usually increases effective on-rate and lowers apparent off-rate. This change should cause boost to PDZ-cargo capture (AMPARs, neuroligins) and hand-off to retromer.

2) Strengthen the natural PDZ-retromer allostery (β3-β4 hairpin and VPS26 interface tuning). Target here is better cargo affinity and faster sorting into retromer tubules.

3) Make the PDZ pocket electrostatically "sticky" at the rim via small charge tweaks around a peptide-binding groove to favor typical PDZ-motif flanks.

Several other protein changes are possible for SNX27 of course.

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Note that for overexpression of either receptors in neurons or modulated expression, either upregulated or downregulated, in any neuron can have different performance and behavioral outcomes depending on the region or type of neuron in which this different gene expression program is executed. It may be interesting to look at transcription factors and synthetic transcription factors or other promoters that are cell type specific or cell fate specific in order to get a specific effect in a specific type of neuron or in specific circuits. Likewise, modulated expression in every cell throughout the body is likely non-ideal.

Other speculative intelligence enhancements via transgenic/germline

Reasoning: Increase projections between left RLPFC and IPC

White matter tract cross-sectional width betwen left rostrolateral prefrontal cortex (left RLPFC) and IPC (inferior parietal cortex) predicts reasoning ability or intelligence. Increase the number of projections or axons to increase intelligence.

RLPFC neurodevelopment background context

Axon pathfinding for long-range cortico-cortical afferent fibers proceeds through the intermediate zone/subplate which is a transient waiting compartment that hosts early synaptogenesis and guides corticocortical afferents. The subplate serves as a fetal/adolescent waiting comparment for these fibers.

Apical radial glia (aRG) in the ventricular zone and basal/outer radial glia (bRG/oRG) in the expanded outer SVZ generate excitatory pyramids. The oRG pool is massively expanded in primates/humans, especially in frontal cortex, and is a key source of upper-layer (II/III) SATB2+ intratelencephalic (IT) projection neurons that furnish association fibers. Intratelencephalic (IT) projection neurons are an SATB2+ excitatory pyramidal cell whose axon remains within the telencephalon to link ipsi- or contralateral cortical areas.

Developmental genetics specify projection identity: SATB2 promotes callosal/IT fate and represses CTIP2/FEZF2 (subcerebral) programs; perturbing this axis flips cortico-cortical neurons to subcortical targets in mice. Rostrolateral PFC (including BA10/RLPFC) progenitors sit under rostralizing morphogen gradients (e.g., FGF8/17; high PAX6), whereas IPL progenitors sit under relatively caudalizing gradients (e.g., EMX2/NR2F1/COUP-TFI). Early areal fate biases in these pools seed later differences in long-range connectivity. More late-born SATB2+ L2/3 IT neurons gives rise to more cortico-cortical axons available to form long association bundles like SLF II/III.

FGF8/17 (anterior organizer) and PAX6/EMX2/NR2F1 gradients set rostral–caudal cortical identity.

VZ areal enhancers mapped by the cortical regionalization TF network (CRTFN) can bias expression to rostral vs caudal progenitor pools; recent work even dissects Nr2f1 (COUP-TFI) enhancer modules with distinct regional functions. Pairing these with excitatory-lineage drivers lets you confine manipulations to RLPFC or IPL pools that ultimately seed SLF II/III partners.

oRG cells are self-renewing asymmetric progenitors such that a single oRG cell can produce multiple downstream cells over its lifetime before terminal differentiation. This only expands the late-born excitatory neuron pool, a subset of which will become SLF II/III neurons depending on areal fate.

Approaches

Here are several different ideas for how one might increase the density of intratelencephalic projections between left rostrolateral prefrontal cortex and inferior parietal cortex:

• expand the basal/outer radial glia progenitor pool to produce more late-born upper-layer (II/III; L2/L3) SATB2+ intratelencephalic (IT) projection neurons.
• bias the arealization of the expanded oRG progenitor pool towards SLF II/III fate.
• lengthen neurogenesis or add extra oRG/IP divisions by manipulating cell-cycle regulators (e.g., Cdk4/cyclin D1, p27^kip1^, Tbr2/Eomes timing), Notch and FGF signaling, which maintain oRG self-renewal, or transcriptional temporal identity programs (e.g., Hmga2, Zbtb20). Studies have extended neurogenesis artificially (like Pilaz et al., Neuron 2009; Nonaka-Kinoshita et al., Cell Reports 2013 (prolonged neurogenesis by Hmga2 modulation)) by altering these pathways, leading to extra upper-layer neuron production. p27Kip1 downregulation has a similar effect as the cyclin D1 and cyclin E2 overexpression for G1 duration shortening. FGF2/FGF8/FGF17 gradients maintain self-renewal in rostral progenitors. Notch and Wnt sustain oRG cycling; BMP antagonism favors neurogenic vs. gliogenic outcomes. SHH contributes to SVZ proliferation in outer zones.

Regulation of cerebral cortex size and folding by expansion of basal progenitors

Forced G1-phase reduction alters mode of division, neuron number, and laminar phenotype in the cerebral cortex -- forced a ~25 % shortening of TG1 (G1 duration) by overexpressing Cyclin D1 + Cyclin E1 in embryonic cortical progenitors, and observed enhanced progenitor self-renewal at the expense of differentiation, resulting in increased basal progenitor pools and later "supernumerary supragranular neuron production".

Bilateral anterior capsulotomy and IQ enhancement

Background

In certain cases of treatment resistant obsessive compulsive disorder, a surgical procedure is able to increase IQ by about 5 to 10 IQ points through a bilateral anterior capsulotomy procedure.

Bilateral (both hemispheres) anterior capsulotomy is a lesioning procedure of the anterior limb of the internal capsule (ALIC)) The internal capsule is a dense sheet of white matter carrying projection fibers between the cerebral cortex and subcortical nuclei (especially the thalamus, basal ganglia, and brainstem). The anterior limb lies between the head of the caudate nucleus (medially) and the lentiform nucleus (laterally).

Within this region run fronto-thalamic and fronto-striatal fibers, key components of the cortico-striato-thalamo-cortical (CSTC) loops implicated in mood, anxiety, and obsessive-compulsive circuits.

Overactivity of OFC-MD-striatum circuits is reduced. Also lesions the fibers between the anterior cingulate and thalamus, which dampens the pathological overdrive of emotional-motivational signaling. Rigid overcontrol and maladaptive habit reinforcement is reduced by lesioning the projections through ALIC to the head of the caudate, putamen, and nucleus accumbens for the prefrontal-striatal fibers. Fibers from thalamic nuclei (esp. MD and anterior nucleus) ascend through the same region to prefrontal areas. Lesioning the capsule affects both descending (corticofugal) and ascending (thalamocortical) communication, dampening bidirectional overactivation.

These are corticofugal neurons that are destined during development for the internal capsule, instead of SLF or callosal. The progenitors are radial glia of the rostral dorsal pallium under FGF8, SP8, FEZF2 influence. The guidance profile includes DCC, Neuropilin-1, Robo1. These are not intratelencephalic neurons (like for SLF II/III). They share the same early corridor (IZ/IC) but diverge because their transcriptional programs encode opposite guidance receptor repertoires.

While corticofugal axons descend, thalamocortical axons grow upward through the internal capsule from diencephalic progenitors (Gbx2+, Lhx2+, Otx2+ lineages). Corticofugal axons provide scaffolds and guidance cues (e.g. L1CAM, NCAM, Netrin) for thalamic axons. Thalamic axons express complementary receptors (DCC, TAG-1, Robo1/2) and pause until the cortical plate matures.

When the ascending MD -> PFC thalamocortical fibers are interrupted in a capsulotomy: The mediodorsal thalamus loses direct excitatory access to OFC/ACC/PFC. That means fewer thalamic relay signals reinforcing emotional salience or intrusive self-referential loops. Functionally, it decreases the "gain" of the recurrent cortico-thalamo-cortical amplifier.

The fibers lesioned in bilateral anterior capsulotomy come from a deep, early corticofugal lineage whose axons (and their thalamic reciprocals) occupy the anterior limb of the internal capsule. They are developmentally and molecularly distinct from the later-born associative (SLF, callosal) tracts that share the intermediate zone transiently but express opposite transcriptional and guidance signatures. By cutting both descending and ascending members of this fronto-thalamo-striatal system, the surgery functionally disinhibits cognitive networks and reduces affective interference, sometimes manifesting as improved cognitive clarity or apparent increases in measured IQ.

Approach

Here's a developmental-genetic strategy to reduce fronto-thalamo-striatal connectivity either by programming fewer corticofugal projection neurons during embryogenesis or by installing an optogenetic "soft lesion" capability for postnatal functional silencing. During corticogenesis, transcriptional regulators (FEZF2, CTIP2, TBR1) specify the subcerebral projection neuron identity in deep-layer progenitors; modulating their dosage, timing, or downstream effectors (e.g., DCC, Robo1, Neuropilin-1 expression levels) could systematically reduce the number of ALIC-destined neurons born from rostral dorsal pallium radial glia, thereby genetically "pre-lesioning" the pathway.

Alternatively, these same projection neurons could be tagged during development with a cell-type-specific promoter driving expression of inhibitory opsins (eNpHR, GtACR) or chemogenetic receptors (hM4Di), enabling selective, reversible silencing of the corticofugal limb (and indirectly weakening the thalamocortical return loop) on demand, recapitulating the functional disinhibition and cognitive enhancement observed after surgical capsulotomy without permanent tissue damage.

Both approaches (genomic reduction of pathway neuron number or optogenetic functional suppression) would exploit the developmental lineage specificity and guidance-receptor signatures that distinguish internal-capsule projection neurons from associative cortical circuits, offering a molecularly precise, genetically encoded equivalent of the therapeutic lesion.

General cognitive improvement

Core theory: Intelligent, abstract reasoning emerges from a hierarchically-nested cortical oscillatory architecture in which brief, symbol-carrying γ-bursts (30–100 Hz) are phase-locked to the trough of any available slow rhythm, such as θ (4–8 Hz) during active maintenance, δ (1–4 Hz) during rest or deep reasoning, or even α (8–13 Hz) during anticipatory coding. Meanwhile, β-oscillations (13–30 Hz) broadcast from prefrontal–basal-ganglia–thalamic loops to hold or update the current task set. Superior capacity therefore requires (i) sharp, PV-interneuron-governed γ packets that can nest inside whichever slow carrier is dominant, (ii) resilient slow clocks (septal/hippocampal θ, thalamic δ, or occipital α) that preserve phase consistency, (iii) switch-ready β desynchronization, and (iv) myelin-optimized long-range tracts that keep multi-area phase-lags constant across the slow-fast pairings in play. Any intervention that tightens this flexible slow→γ nesting (δ/θ/α–γ) while preserving rapid re-nesting yields measurable gains in working-memory span, reasoning speed, and abstract depth.

Superior cognitive capacity depends on four biological ingredients: sharply timed gamma packets sculpted by parvalbumin-positive interneurons that fit snugly inside the dominant slow wave; steady phase relationships in the slow clocks themselves across time; beta rhythm desynchronization when the task set needs to change; and heavily myelinated long-range fibers maintaining fixed phase lags among distant areas so that slow-fast coupling remains coherent.

Various proposals for general cognitive improvement:

• enhancement of Kv3.1/3.2 potassium in fast-spiking PV+ interneurons channels plus low-dose brain-wide cholinergic agonism (e.g., chronic low-dose donepezil or galantamine). Kv3 up-regulation speeds repolarization in all fast-spiking neurons, so every local cortical column sharpens its γ bursts and tightens spike timing, while diffuse cholinergic tone globally elevates γ propensity and θ–γ PAC. Some issues here with phase alignment vs amplitude, homeostatic pushback, and cholinergic bluntness of the agonism.
• or, instead: PV-targeted Kv3 up-tuning (Cre-dependent), SST phase-tuning (HCN/M-current), a mild, activity-dependent myelination bias, and receptor-specific pro-γ tweaks (e.g., α7 nAChR up-bias) instead of global AChE inhibition; together these could lift γ and improve θ–γ–β nesting.
• various optogenetic interventions to improve external closed-loop control of cortical oscillatory architecture
• cognitive pacemaker (see separate section)

See https://diyhpl.us/~bryan/irc/chatgpt/2025-10-05-working-memory.txt from https://gnusha.org/logs/2025-10-05.log for more information.

Significantly increase working memory capacity

With non-trivial cell engineering and protein engineering, it may be possible to get biological working memory capacity of 7 +- 2 items to increase towards 20 or 30 items.

Working memory capacity can be theoretically expanded by interventions that (1) tighten cross-frequency coupling precision, (2) stabilize inter-areal phase timing, (3) speed β gating dynamics, and (4) enlarge representational dimensionality.

See https://diyhpl.us/~bryan/irc/chatgpt/2025-10-05-working-memory.txt from https://gnusha.org/logs/2025-10-05.log for more information.

Increase compatibility with a cognitive pacemaker

What is a cognitive pacemaker? A cognitive pacemaker is a closed-loop, phase-locked neuromodulation system designed to stabilize and optimize the brain’s intrinsic oscillatory dynamics across distributed cortical–subcortical networks. It functions like an electronic phase-locked loop (PLL) that continuously measures the phase and amplitude of endogenous slow rhythms. These endogenous slow rhythms include δ (1–4 Hz) during rest, θ (4–8 Hz) for working memory and sequencing, α (8–13 Hz) for anticipatory coding, and β (13–30 Hz) for task-set maintenance. The cognitive pacemaker then delivers precisely timed stimulation bursts that reinforce coherent γ-band (30–100 Hz) “packets” generated by parvalbumin-positive interneuron networks. By maintaining phase alignment between slow “carrier” rhythms and fast γ events across prefrontal, hippocampal, thalamic, and basal-ganglia circuits, the pacemaker can enhance communication-through-coherence and improve cognitive throughput, memory encoding, and attentional stability. Technologically, it integrates high-resolution EEG/MEG or iEEG sensing, low-latency digital phase detection and prediction, and isolated current drivers (for tACS, tTIS, TMS, tFUS, DBS, or optogenetic stimulation) that inject micro-stimulation at specific phase angles of the ongoing rhythm while avoiding artifact and charge buildup. Its PLL-style controller tracks and predicts oscillatory phase in real time, adjusts for conduction delays, and modulates stimulation frequency, amplitude, or phase offset according to brain state. Because neural oscillations underlie not only cognition but also pathological synchrony, the same architecture could suppress epileptiform bursts, normalize β hyper-synchrony in Parkinson's or depression, promote δ–σ coordination in sleep, or transiently boost θ–γ coupling for reasoning and learning. In essence, a cognitive pacemaker is a general-purpose, adaptive timing interface between biophysics and computation and it's an engineered feedback system that restores or enhances the brain's hierarchical rhythm structure without overwriting its natural dynamics.

It is possible to build a cognitive pacemaker using closed-loop stimulation with EEG and/or intracortical EEG and a stimulation strategy. However, the benefits of a cognitive pacemaker could be extended through germline intervention such as by encoding optogenetics into the genome.

It is not clear which aspects of oscillatory waves in the human brain are byproducts versus which aspects are causative. Depolarization of neurons at a certain timestep might be able to faster prepare neurons for incoming spikes at a rate faster than the rate at which natural cellular pacemakers in the brain are able to orchestrate the ensembles. That's just one example where a cognitive pacemaker might be able to help. Another example use case for a "cognitive pacemaker" is for shortening, aborting, predicting, modulating or eliminating epileptic seizures. A cognitive pacemaker might come in handy if other tweaks are made to the brain that might have a chance of causing seizures or epilepsy. This kind of device might also be able to assist with more restful sleep, lucid dreaming, perception, semantic encoding, reward training, etc.

Here are several modifications that might be able to improve the performance or integration of a cognitive pacemaker:

• various optogenetics

Sleep

See also sleep.

short sleepers? 4-5 hours of sleep/night, plus resistance to sleep deprivation -- see http://gnusha.org/logs/2016-11-25.log

Warning: the identified genetics of short sleep humans may not be accurate: https://forum.effectivealtruism.org/posts/nSwaDrHunt3ohh9Et/cause-area-short-sleeper-genes?commentId=GCQf5qjG4LyEdEJov

• "The transcriptional repressor DEC2 regulates sleep length in mammals" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884988/ (hDEC2-P385R)

• DEC2 BHLHE41 Y362H (a second DEC2 mutation) is also associated with short sleep and resistance to sleep deprivation, see "A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans" https://go.aastweb.org/Resources/journalclub/journalcluboctober2014.pdf

• BHLHE41 - rs121912617

A familial natural short sleep mutation in dec2 extends healthspan and lifespan in Drosophila (2025) -- "We used a Drosophila model to study the effects of the DEC2 dec2P384R mutation on animal health. Expression of a human Dec2 dec2P384R mutation in sleep-controlling neurons reduces sleep, and, remarkably, the short sleeping flies live significantly longer with improved health. The improved physiological effects were enabled, in part, by enhanced mitochondrial fitness and upregulation of multiple stress response pathways. Additionally, we demonstrate that dec2P384R boosts mitochondrial respiratory capacity in both flies and mammalian cells, suggesting a conserved mechanism by which this mutation promotes healthy aging. ... Expression of the human dec2P384R mutation in Drosophila sleep-regulating dorsal fan-shaped body (dFB) neurons was sufficient to reduce the total sleep per day. Remarkably, despite reduced sleep, these flies exhibited significantly extended lifespans, enhanced stress resistance, improved memory, and improved late-age mobility. ... Using AlphaFold3,54 we generated predicted structures of WT DEC2 and DEC2P384R proteins and compared their overall structures..."

GRM1 (R889W or S458A), variations in a glutamate receptor contribute to a short sleeper phenotype. "Two independent mutations found in GRM1 cause familial natural short sleep. Both mGluR1 mutations have less activity than wild-type receptors in vitro. Both mutant mouse models have shorter sleep duration than control mice. Brain slices from mutant mice showed increased excitatory synaptic transmission. In vitro, both of the mutations exhibited loss of function in receptor-mediated signaling." Human carriers of Grm1b-R889W or Grm1-S458A sleep 100 minutes less than controls.

NPSR1 - Mutant neuropeptide S receptor reduces sleep duration with preserved memory consolidation pop article Humans with Npsr1-Y206H show reductions in sleep time of 180 minutes.

ADRB1 - Mutation in Beta1-Adrenergic Receptor Affects Sleep/Wake Behaviors pop article; the ADRB1 short sleep mutation seems to still be in play even if DEC2 is out? Humans with Adrb1-A187V show reductions in sleep time of 132 minutes.

hSIK3 - A mutation in salt-induced kinase 3 (hSIK3-N783Y) is identified in a human subject exhibiting the natural short sleep duration trait. (Short sleep shows up when SIK3 activity is suppressed, either by a loss-of-function variant (hSIK3-N783Y) or by keeping PKA sites (T469/S551) phosphorylated so 14-3-3 can inhibit SIK3 (as happens with calcineurin loss and its impact on the phosphatase-kinase pathway for sleep regulation). Dephosphorylation of those sites increases sleep.) This individual self-reported needing only 3 hours, but recordings indicated she slept for 6 hours/night.

WW domain containing oxidoreductase (WWOX) gene (rs16948804 and rs4887991) although this result is underpowered in human GWAS and it's not the best short sleep phenotype candidate.

NR3A knockout produces a short sleep phenotype in mice.

intracerebroventricular (ICV) infusion of orexin-A increases wakefulness in narcoleptic mice. There are various orexin receptor agonists such as takeda's oveporextin, suntinorexton, firazorexton, alixorexton, etc. "What about automatic orexin peptide administration in sync with your personal circadian rhythm (think of insulin pumps)?"

Isaak Freeman proposes several ideas:

• Semi-permanent (months?) silencing the mRNA transcripts, e.g. with siRNA, short hairpin RNA, etc
• Flagging DEC2 or other inhibitor proteins for faster intracellular degradation
• Destabilizing the protein, snipping in variants, etc.
• "There's a lot of room to explore here: We're already given at least 6 mutations whose effects to potentially emulate; we could target inhibitors and/or the wakefulness mechanisms themselves; we could try lots of different paths (molecules, antibodies, editing, RNA, simulation, ...)."

Luke Piette: "If we could reduce the inhibitory effects of DEC2, reduce the level of inhibitive capabilities of beta-1 adrenergic receptors (involved in ADRB1), or increase the sensitivity of NPSR1 G protein encoded receptors to NPS, we could reduce sleep time without harming cognitive processes or long term health."

Helena Rosengarten proposes:

• gene editing of DEC2 in adult neurons, possibly through intranasal therapy via the olfactory bulb
• antisense oligonucleotides to target DEC2 mRNA
• targeted protein degradation of DEC2, such as by using autophagy-targeting chimeras (AUTOTACs), or other methods of targeting protein degradation (lysosomal degradation tagging, autophagy receptor interaction, add autophagy tags, KFERQ-like motifs recognized by chaperones, ...)
• small molecule inhibition of DEC2

https://guzey.com/theses-on-sleep/

Resisting sleep deprivation by breaking the link between sleep and circadian rhythms

"TNFα G308A polymorphism is associated with resilience to sleep deprivation-induced psychomotor vigilance performance impairment in healthy young adults" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467999/

Inactivation of the DREAM complex mimics the molecular benefits of sleep

Mitochondrial origins of the pressure to sleep (not a human study)

here is what gpt-o3 says about sleep pressure invulnerability: "Candidate mechanisms, supported by transgenic or knockout studies, include: (1) overexpression of adenosine kinase (ADK), which accelerates adenosine clearance and blunts its accumulation; (2) loss-of-function or dominant-negative mutations in adenosine A1 or A2A receptors, rendering sleep-promoting regions insensitive to adenosine's somnogenic signal; (3) hyperactive ENT1 transporters, which remove adenosine too efficiently from synapses; (4) mutations in mitochondrial respiratory proteins that reduce electron leak, thereby weakening the redox trigger for pressure buildup; and (5) loss of prostaglandin D2 synthesis (e.g., in PTGDS), blocking the immune-to-sleep cascade that normally amplifies pressure. Each of these could be tested via CRISPR in mice by introducing: a promoter duplication for ADK (upregulate or otherwise promote expression); a single-point mutation in Adora2a or Adora1 disrupting G-protein coupling; a gain-of-function allele in Slc29a1 (ENT1); a stabilized complex I subunit (e.g., Ndufs4) mimicking tighter coupling; or a nonsense mutation in Ptgds." .... it also says: "A microdeletion affecting the 5' regulatory region or a non-critical exon of ADK might lead to a benign, inherited suppression of sleep pressure, causing minimal systemic disruption while significantly reducing brain adenosine accumulation." but I thought adenosine kinase was used everywhere? maybe not?

• sleep duration - PAX8, VRK2 (vaccinia related kinase 2) (rs62158211, rs17190618, rs1380703), rs3768984

• GNB3 - rs1047776 A allele and the rs2238114 C allele

• ARNTL - rs10766071 "has been associated with shorter sleep duration"

• ABCC9 - rs11046205 - A K(ATP) channel gene effect on sleep duration: from genome-wide association studies to function in Drosophila "rs11046205 explains ~5% of the variation in sleep duration. The A allele was associated with longer sleep duration, while the G allele was associated with shorter sleep duration"

• ADA - rs73598374 (higher quality sleep)

• CLOCK - rs12649507

• FTO - rs9939609 - something about short sleep duration and weight gain in children?

• morning person / "morningness": rs12736689 near RGS16, rs9479402 near VIP, rs55694368 near PER2, rs35833281 near HCRTR2, rs11545787 near RASD1, rs11121022 near PER3, rs9565309 near FBXL3; others reported in GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person ..

• insomnia - ref

• there are various optogenetic studies for "sleep neuron" stimulation but none so far seem to immediately cause sleep? Compared to systemic anesthesia, a targeted and localized stimulation that causes immediate sleep (or wakefulness) might be valuable. Some neurons trigger SWS but unclear if non-sleep SWS activity has any beneficial biological effect. GABAergic/galanin neurons in the ventrolateral preoptic area (VLPO) is a classic "sleep-promoting" hypothalamus area. Optogenetic or chemogenetic stimulation of GABA/galanin neurons in VLPO can cause rapid NREM sleep induction. (unclear on what timescale that works at)

• TODO: increase the total duration of usable wakefulness, rather than reducing the amount of high-quality sleep.

• TODO: evaluate sleepiness genetics

Social status

in mice:

Pas1 is a regulator of social dominance, ref

certain mutation of Shank2 increases social dominance but impairs other social interactions.

Hedonistic imperative david pearce stuff

David Pearce specifically proposed:

• modify pain sensitivity or insensitivity, see other notes on this page. david pearce is a big fan of SCN9A deletion or modification.
• in Hedonistic Imperative david pearce argues for enlarging mesolimbic dopamine circuitry, selectively boosting mu-opioid and serotonin pathway function, and disabling several countervailing inhibitory feedback processes (e.g., auto-receptors located on the same surface of the same neuron that released the neurotransmitter it responds to, often acting as a built-in inhibitory brake such as by inhibiting further synthesis or release of the neurotransmitter, a form of negative-feedback control over neuronal signaling) to raise hedonic set-points.
• remove dynorphin (aversive/kappa system) from reward circuits
• remove pro-aversive peptides (or peptidergic inputs) such as bradykinin, nociceptin/orphanin FQ, and substance P -- these are related to genes or receptors such as BDKRB1/2, OPRL1/PNOC, and TAC1/NK1R
• polygenic tuning of mood, personality, pro-social tone, hedonic set-point: consider modifications or changes related to COMT, SLC6A4 (SERT), FAAH, ADRA2B (often called the “ADRA2B deletion variant”), and OXTR.

reference table: dynorphin–κ system (PDYN/OPRK1) (stress/ahedonia), bradykinin (BDKRB1/2), nociceptin (PNOC/OPRL1), substance P (TAC1/NK1R)

polygenic hedonic tuning (human alleles): COMT, SLC6A4, FAAH, ADRA2B, OXTR.

mouse and related studies, not necessarily referenced by david pearce hedonistic imperative:

• dynorphin–κ-opioid system modification: reduce dysphoria/anhedonia, produce anti-stress anti-depressant like effects in rodents
• OPRM1 copy number affects social reward
• endogenous enkephalins naturally inhibit anxiety, and preproenkephalin (PENK) knockout increases fear/anxiety. increase mu-opiod receptor targeted signaling, more enkephalin signaling.
• FAAH -/- mice show reduced anxiety and reduced depression-like phenotype
• DAT -/- or DAT knockdown rodents are hyperdopaminergic and hyperactive, hyperlocomotive, more willing to work for rewards
• ΔFosB overexpression in nucleus accumbens heightens sensitivity to rewards (including natural rewards like sucrose/sex); CREB in NAc often shows the opposite (blunting reward; pro-depressant when high).

Reward system tweaks

Reinforcement feedback

Dopamine neurons create Pavlovian conditioned stimuli with circuit-defined motivational properties

or target somatosensory cortex to train mice to fire a single neuron in motor cortex (ref)

"We bypassed dopamine signaling itself and tested how optogenetic activation of dopamine D1 or D2 receptor–expressing striatal projection neurons influenced reinforcement learning in mice."

well we could just optogenetically inhibit various mu opioid receptors or neurons in nucleus acumbens.

Various operant conditioning and classical conditioning tasks have been achieved by direct optogenetic activation or inhibition of neurons in the nucleus accumbens or striatum neurons. Encoding these optogenetic receptors into the germline could enable greater real-time control over learning, motivational circuits, etc.

Mania, euphoria, and heightened reward

dopamine transporter (DAT) reduction or knockdown: hyperdopaminergic mice show mania-relevant behavior and high reward sensitivity.

ClockΔ19 mutant (circadian gene): hyperactivity, mania, reduced anxiety, reduced depression, greater reward sensitivity.

Antidepressant effect

TREK-1 (Kcnk2) knockout mice are more resistant to depression across various assays

ΔFosB overexpression in nucleus accumbens increases responsiveness to natural rewards and promotes stress resilience

beta-catenin upregulation in nucleus accumbens (D2-MSNs) - increases resilience after stress; pro-resilient, anxiolytic effects. (ref)

VMAT2 overexpression: more vesicular monoamine storage/release with reduced depressive-like behaviors and improved affective readouts.

more antidepressant-like effects: p11 (S100A10) overexpression, BDNF overexpression (forebrain/CaMKIIα lines), purinergic receptor deletion via P2X7 receptor knockout, FAAH knockout or inhibition, Kv7/KCNQ channel boosting or overexpression in dopamine-producing neurons located in the ventral tegmental area, ...

Positive motivation

D2 receptor overexpression in nucleus accumbens increases willingness to expend effort for goals (ref)

downregulation, blockage or reduction of κ-opioid receptor (Oprk1) reduces negative affect or aversion

don't knock out μ-opioid receptor (Oprm1) because it's necessary for expression of social and food reward

Partner preference

in voles: Vasopressin V1a receptor (Avpr1a) gene transfer via AAV-V1aR overexpression in ventral pallidum converts non-monogamous meadow voles into partner-preferring animals (ref)

in voles: oxytocin receptor upregulation in nucleus accumbens (NAc), part of the ventral (limbic) striatum, enhances alloparental behavior and partner preference formation (ref)

Brain uploading (prepatory)

Full connectome recording via synaptic barcoding and its in vivo reconstruction

Summary: Use RNA barcodes inside neurons and synapses such that at the synapse two RNA neurons are combined. Later the structure of the connectome can be extracted by DNA sequencing. By encoding this into the genome, the number of neurons or synapses that get tagged this way can be vastly improved compared to AAV delivery of connectome-seq genomic material.

Cell lineage tracing and barcoding techniques like brainbow, MAPseq ("Multiplexed Analysis of Projections by Sequencing"), the in situ sequencing variant BARseq, or Connectome-seq use genetic programs to decorate neurons and synapses throughout the brain so that the connectivity (connectome) can be recovered by DNA sequencing instead of electron microscopy brain imaging for brain uploading. To some extent this is often achieved by lentivral or AAV delivery of genetic payload into adult brain to target some of the neurons. intraparenchymal delivery of AAV is undoubtedly helpful for this. However the information is, at this time, only recovered postmortem. (In fact, it is plausible that postmortem AAV or microinjection may (for a short period of time postmortem) be able to do some amount of barcoding). Future versions might be able to emit SYNseq or synaptic barcoding information via exosome export of DNA or something.. but for now it is a postmortem procedure.

Germline compared to AAV synaptic cartography can achieve significantly better distribution and coverage (namely 100% coverage) of cells and neurons in the brain can be achieved via germline genetic engineering of brainbow-style or synaptic barcoding schemes. The effect of this is to grow a human brain that is "extra prepared" for brain uploading via DNA sequencing as opposed to requiring neural anatomy reconstruction via scanning electron microscopy.

In the future it may be possible to deliver genomically encoded full neural network topology information such that a molecular biology program can reconstruct the original neuronal topology or connectome. See also https://gnusha.org/logs/2025-09-30.log for more speculation about what this kind of multi-cellular genetic program would require. It very likely would be in vitro neural circuit reconstruction long before it is ever in vivo human reconstruction... if ever.

Other speculative neuronal enhancements to assist with brain uploading

These are mostly fanciful ideas that should be validated in an animal model first.

Organelle- or compartment-specific tags (e.g. mitochondria, dendritic spines, axon terminals): Improve automated segmentation by giving EM-visible landmarks or fluorescent anchors.

Membrane-tethered reporters: Aid in delineating neuronal boundaries for optical microscopy or electron microscopy.

EM-detectable tags (e.g. APEX2, miniSOG, HRP-fusion proteins): Enable correlative light and electron microscopy, helping bridge genetic labeling with ultrastructural reconstruction.

Add various GFP or fluorescent indicators to neurons. Fluorescent voltage indicators and other fluorescent indicators are available.

Use the oscillatory waves cell identity visualization trick and couple it to barcoding information somehow.

DNA ticker tape memory for calcium spike recording, action potential spike recording, or intracellular protein recorders. Needs to be coupled with cellular export into bloodstream, or maybe only activate it shortly before death. It is unclear what level of information can be recorded or retrieved from this. Similarly with the fluorescent indicators, it may not be wise to express them throughout life and instead wait to activate them until later or maybe during cell death programs.

Various genomically encoded nanobodies can be expressed for antibody-based tagging and staining.

Consider anything that would help with postmortem expansion microscopy for brain imaging.

review PRISM for any other changes that would be beneficial to genomically encode, such as their GFP-fused "protein bits" that space-fill each neuron with a random neural barcode driven by Cre-lox (or polylox barcoding or CRISPR-based barcoding) lineage randomization. It would be interesting if the "protein bits" could be combined with connectome-seq migration of pre-synaptic and post-synaptic RNA barcodes into the synaptic junction for connectome recovery via sequencing. The combination could be achieved, possibly, by having some sort of relationship between the RNA barcode and the abstract bit-vector from the set of "protein bits" expressed by that neuron.

Longevity

Dsup from tardigrades for chromatin/DNA radiation resistance, and also for longevity via impeding mitochondrial respiration and lowering ROS damage.

Tardigrade Dsup extends C. elegans life span by impeding mitochondrial respiration and promoting oxidative stress resistance -- tardigrade Ramazzottius varieornatus damage suppressor (Dsup) gene when expressed in the nematode Caenorhabditis elegans caused tolerance to "x-ray exposure and oxidative stress without apparent toxicity and exhibited a notable extension of life span. This effect was independent of the canonical DAF-2/DAF-16 longevity pathway and mitochondrial dynamics. Instead, Dsup expression markedly reduced mitochondrial respiration, providing a plausible mechanism for enhanced oxidative stress resistance and extended longevity." Dsup is largely unstructured but binds nucleosomes to shield DNA from damage. Dsup binding causes chromatin compaction and chromatin condensation, which affects transcription of nuclear-encoded mitochondrial genes, causing a reduced expression of respiratory chain components, lower oxygen consumption (decreased mitochondrial respiration), and therefore cuasing less electron transport (meaning fewer reactive oxygen species). Probably transcription factors or histone chaperones or other processes, using ATP etc, are trivially able to bypass Dsup on the chromatin and get access to the actual genetic material when needed. Dsup binds to chromatin and DNA, but not so strongly that it never dissociates.

Here is where Dsup could be useful in human biology:

• Oocytes and mature eggs: Reproductive germ cells experience chronic low-level oxidative stress and have relatively low basal metabolic rates compared to somatic tissues. Dsup could shield their DNA from age-related damage, potentially preserving fertility and embryonic viability, similar to its protective role in tardigrade anhydrobiosis.
• Resting or quiescent stem cells (e.g., hematopoietic stem cells in bone marrow): These cells rely on glycolysis more than oxidative phosphorylation for energy during dormancy and are vulnerable to ROS-induced mutations. Mild mitochondrial suppression by Dsup might promote self-renewal and longevity while reducing mutagenic risk, without compromising their occasional bursts of activity.
• Astrocytes
• avoid use of Dsup in cardiac myocytes, skeletal fast-twitch muscle fibers, cortical or hippocampal neurons, hepatocytes, spermatocytes, or other cells that have high energy demands.

Other longevity interventions:

• rs2149954-T (EBF1 gene?) and APOE rs4420638-G (see "Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age" -- which includes other allele recommendations), however note that rs4420638 (near the TOMM40/APOE/APOC1 locus) has been associated with "poorer delayed recall performance". And the rs2149954-T alle has been associated with low blood pressure in middle age, and decreased cardiovascular mortality risk, independent of blood pressure.

  • MTR or RYR2 rs1625040-A
  • SYT16 rs2784505-G
  • PDE5A or MAD2L1 rs13114426-T
  • MARCH10 or TANC2 rs2109265-A
  • AOAH or ELMO1 rs11977641-C

• Bayesian association scan reveals loci associated with human lifespan and linked biomarkers -- "A recent extreme longevity study[18] found four novel associated protective alleles near CDKN2B/ANRIL (rs4977756-G), SH2B3/ATXN2 (rs3184504-G), ABO (rs514659-A) and HLA (rs3763305-A). Remarkably, the first two variants replicated in our analysis with (one-sided) P values P=4.34 × 10^−6, P=1.08 × 10^−3, P=0.03, P=0.51, respectively."

• Senescent-resistant human mesenchymal progenitor cells counter aging in primates -- "isogenic biallelic FOXO3-engineered human embryonic stem cells (hESCs) with targeted knockin mutations to replace two phosphorylation sites of FOXO3, Ser253 and Ser315, with alanine residues (FOXO32SA/2SA hESCs). When differentiated into MPCs with the FOXO32SA/2SA genetic signature, these cells exhibit enhanced senescence resistance, environmental resilience, and self-renewal capacity, enabling sustained tissue persistence in rodents (and now primates)."

• just load up on lots of senescoprotective or geroprotective alleles

mutations in:

• KLOTHO

• FOXO3 and FOXO3A

  • FOXO3A centenarian SNPs rs3800231, rs9400239, rs479744 (German cohort) - dominant longevity effect, stronger in centenarians than nonagenarians. (ref)
  • FOXO3A SNP rs2802288 ? (ref)

• TOMM40 rs2075650 (see ref)

Some apolipoprotein changes...

• APOC1 rs4420638
• APOB rs1801703, rs12713450, rs12720854
• APOE rs429358-C is bad for longevity
• ApoE ε2 rs7412-T is pro-longevity. The ε2 isoform has reduced affinity for LDL‑receptor family, leading to altered lipoprotein metabolism; associated with lower plasma LDL‑C, and reduced Alzheimer's diease risk.
• APOE3 Christchurch R136S and RELN-COLBOS: rare protective alleles that delay onset by years to decades even in autosomal-dominant Alzheimer's disease.
• APOE - avoid rs429358-C (0.9 years decrease in lifespan or parental lifespan?); rs429358-T (the non‑ε4 allele) should be preferred.

ApoE is a lipid-binding apolipoprotein that transports cholesterol and other lipids. In the brain ApoE is the principal cholesterol carrier, moving lipids from astrocytes to neurons via LDL-receptor-family receptors; in peripheral tissues it mediates lipoprotein clearance and cholesterol metabolism.

The following mutations are from a (2019 longevity GWAS study):

• GPR78/ADGRG8 rs7676745-G (the common allele) is more longevity-conferring.
• FOXO3 rs2802292-G, rs10457180-G
• CDKN2A-AS1 (ANRIL, regulates CDKN2A/p16INK4a & CDKN2B/p15INK4b) - rs4977756-G (mentioned elsewhere on this page)
• CDKN2B-AS1 (ANRIL) rs1556516-G
• LPA (Lipoprotein(a)) rs10455872-A; LPA encodes apolipoprotein(a); assembles Lp(a) lipoprotein. Elevated Lp(a) promotes thrombosis/CVD. A allele lowers Lp(a) levels, reducing cardiovascular mortality.
• SH2B3 (LNK) / ATXN2 rs3184504-G; SH2B3: Adapter protein inhibiting cytokine/JAK-STAT signaling, regulates hematopoiesis/inflammation. ATXN2: RNA-binding protein in stress granules/endocytosis. G allele lowers inflammation/CVD risk.
• ATXN2 / BRAP (SH2B3 nearby) rs11065979-C
• HTT (Huntingtin) rs61348208-T; multifunctional protein involved in vesicle trafficking, autophagy, transcription. CAG expansions cause Huntington's; T allele may optimize HTT function, protecting against neurodegeneration.
• LDLR (LDL receptor) rs142158911-A; clears LDL-cholesterol from blood. A allele enhances LDL uptake, lowering hypercholesterolemia/CVD risk.
• IL6 (interluekin-6) rs2069837-A
• GRIK2 (glutamate‑receptor‑ion‑channel K2) rs1416280-C
• RAD50/IL13 (damage‑repair protein RAD50 / Interleukin‑13) rs2706372-T
• GRHL1 (grainy‑head‑like transcription factor 1) rs2008465-A

Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances:

• MAGI3 (membrane-associated guanylate-kinase-like protein 3) rs1230666-G -- Scaffold protein that links membrane receptors to intracellular signaling pathways, influencing cell polarity and growth
• KCNK3 (potassium channel subfamily K, member 3) rs1275922-G -- A two-pore-domain K⁺ channel that sets resting membrane potential and regulates vascular tone and endothelial function
• HLA-DQA1 (MHC class II DQα1) rs34967069-T -- Component of the HLA-DR/DQ heterodimer that presents antigenic peptides to CD4⁺ T-cells, shaping adaptive immunity
• CHRNA3/5 (nicotinic acetylcholine receptor α3/α5 subunits) rs8042849-T -- Subunits of the neuronal nicotinic receptor that mediate cholinergic signaling and influence smoking behavior
• FURIN / FES rs6224-G -- Furin processes precursor proteins into their active forms; FES is a tyrosine kinase involved in cell-differentiation signaling
• HP (haptoglobin) rs12924886-A -- Acute-phase plasma protein that binds free hemoglobin, preventing oxidative damage and modulating inflammation
• CELSR2 / PSRC1 rs4970836-G -- CELSR2 participates in planar cell polarity; PSRC1 influences lipid metabolism and atherosclerosis risk
• TMEM18 (transmembrane protein 18) rs6744653-A -- Small membrane protein linked to regulation of body-mass index and adipocyte biology
• GBX2 / ASB18 rs10211471-C -- GBX2 is a transcription factor critical for early brain development; ASB18 mediates ubiquitin-ligase activity
• IGF2R (insulin-like growth factor 2 receptor) rs111333005-G -- Mannose-6-phosphate receptor that clears circulating IGF2, thereby modulating growth signaling and cellular senescence
• POM121C (nucleoporin 121 C) rs113160991-G -- Structural component of the nuclear pore complex, influencing nucleocytoplasmic transport
• ZC3HC1 (zinc-finger C3HC-type containing 1) rs56179563-A -- Regulates the cell-cycle inhibitor p21ᴄᴅᴋᴺ¹ and is implicated in coronary artery disease susceptibility
• ABO (blood-group transferase) rs2519093-C -- Glycosyltransferase that determines ABO blood group; variation influences plasma levels of inflammatory and coagulation factors
• some items already on this page:
  • HTT (huntingtin) rs61348208-T -- Large cytoplasmic protein required for neuronal development and intracellular transport; poly-Q expansions cause Huntington disease
  • LPA (lipoprotein(a) – apolipoprotein(a) gene) rs10455872-A -- Encodes apolipoprotein(a), a structural component of lipoprotein(a) that modulates plasma lipid levels and cardiovascular risk
  • CDKN2B-AS1 (antisense RNA at the CDKN2B locus) rs1556516-G -- Long-non-coding RNA that modulates expression of the CDKN2B tumor-suppressor locus, influencing cell-cycle arrest and senescence
  • ATXN2 / BRAP rs11065979-C -- ATXN2 is involved in RNA metabolism and neurodegeneration; BRAP regulates MAPK signaling and ubiquitination
  • LDLR (low-density lipoprotein receptor) rs142158911-A -- Cell-surface receptor that mediates endocytosis of LDL particles, central to cholesterol homeostasis
  • APOE (apolipoprotein E) rs429358-T -- Lipid-transport protein that regulates plasma cholesterol and triglyceride levels; the T allele corresponds to the ε2 (protective) variant

maybe:

• PPARGC1A rs148144750
• NRG1 rs62497784 (and NRG1 rs35753505 is associated with intelligence)
• RAD52 rs35278212
• NCOR1 rs61753150
• RAD51 rs191297852
• ADCY5 rs61734561

• HLA-DRB5 rs71549220

• PMS2

• GABRR3

• Various frameshift indels in TET2 and DNMT3A, and high levels of granulocytes in blood. "Both TET2 and DNMT3A are factors [28,29] and are thought to silence hematopoietic stem cell self-renewal to permit efficient hematopoietic differentiation [30,31]. Therefore, loss of functionality in these genes is likely to underlie an enhanced self-renewal leading to the observed age-related myeloid lineage bias. This skewing towards the myeloid lineage is assumed to have adverse effects on immune functionality in normal healthy individuals, but in the oldest old the increase of the myeloid compartment might be compensative for the age-related decrease in naive T-cells, known as immuno-senescence. Hence on condition that the enhanced self-renewal, instigated by somatic disruptive mutations in TET2 and DNMT3A, leads to increased levels of competent immune cells, be it of the myeloid lineage though, might partly compensate for the age-related loss of immuno-capacity of the lymphoid compartment." (from "Germ line and somatic characteristics of the long-lived genome")

Maybe also mutations in:

• GSK3B (healthy aging index)
• NOTCH1 (diastolic blood pressure)
• TP53 (serum HDL)
• CETP (cholesteryl ester transfer protein) - "A functional longevity-associated allele rs5882 in the cholesteryl ester transfer protein (CETP) gene, I405V, is also significantly associated with slower memory decline and lower risk for dementia and Alzheimer's disease (Barzilai et al., 2006; Sanders et al., 2010)." (CETP is a lipid shuttle glycoprotein that moves cholesteryl esters and triglycerides between lipoproteins. CETP is structured as an elongated, hydrophobic tunnel, allowing it to bind and transfer neutral lipids. CETP influences HDL levels, lipid exchange, and reverse cholesterol transport.) CETP 405V/V is associated with a favorable lipid profile (higher HDL, larger lipoproteins, downregulation of CETP). However, the benefits of CETP I405V might be Ashkenazi-only. This might be a statistical artifact in the analysis pointing to CETP I405V or it might be due to the Ashkenazi lipoprotein phenotype (unusually large HDL and LDL particles, higher apoA-I levels, higher HDL2b fraction (bouyant HDL), low triglyceride-rich remnant burden, lower prevalence of small dense LDL). But in other populations (with higher triglycerides, more insulin resistance, or more small dense LDL), turning down or reducing CETP may worsen lipoprotein remodeling pathways such as by impeding reverse cholesterol transport, and CETP inhibition in that lipid context might produce dysfunctional HDL or impair cholesterol efflux. See https://gnusha.org/logs/2025-11-24.log for more information about the lipoprotein architecture theory of intelligence and neuron membrane maintenance.
• ZNF562

... see "Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study".

According to ref (table 2), maybe mutations in: AKAP9, ATG7, C1QTNF2, C9orf96/STKLD1, DSC2, EFEMP2, FCGBP, FGA, GP5, HEMK1, IQCK, KIAA1614, KLKB1, MNT, MYO16, MYOF, PLTP, PRL, RAD51AP1, RXFP4, STK31, SUPV3L1, WDR87, ZNF233.

• rs2069837-A (IL6) and rs2440012 (ANKRD20A9P) and others from "Novel loci and pathways significantly associated with longevity"

• rs35715456 on chromosome 18 (see "Genome-wide association study of parental life span"); other longevity candidate genes: APOE, MINIPP1, FOXO3, EBF1, CAMKIV, and OTOL1; EBF1 gene region rs17056207.

• "Human longevity is influenced by many genetic variants: evidence from 75,000 UK Biobank participants" -- "In GWAS, a nicotine receptor locus (CHRNA3, previously associated with increased smoking and lung cancer) was associated with fathers' survival ... Offspring of longer lived parents had more protective alleles for coronary artery disease, systolic blood pressure, body mass index, cholesterol and triglyceride levels, type-1 diabetes, inflammatory bowel disease and Alzheimer's disease."

• SNPs near ZNF704 on chromsome 8q21.13 may be a candidate, see ref. See also ZNF562 alleles?

cognitive aging: "Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum" -- MLST8, DHX57 -- see rs6723868 and "surrounding 25 SNPs"; and rs30986 -- "Within 20 kb of rs30986 are six genes: MLST8, PGP, E4F1, ECI1, DNASE1L2, and BRICD5"... and rs26840, rs27709, rs27648.

cognitive aging: TMEM106B and GRN alleles (ref)

skin aging: MC1R alleles have been found to add/subtract 2 years from one's youthful appearance. See rs34265416, rs4785704, rs34714188, rs12924124, rs35026726, rs12931267, rs75570604, MERGED_DEL_2_86235, 16:89913406:D, rs1805007, rs112556696, etc. Also see CALN1 rs10259553 and CORO2A rs35480968. (MC1R V92M is also associated with Alzheimer's disease risk)

skin aging: "Genetic variants associated with skin aging in the Chinese Han population" -- "Our candidate study found a significant association between SNP rs2066853 in exon 10 of the aryl hydrocarbon receptor gene AHR and crow’s feet. In addition, we found a significant association between SNP rs10733310 in intron 5 of BNC2 and pigment spots on the arms, and between SNP rs11979919, 3 kb downstream of COL1A2, and laxity of eyelids. Our results identified genetic risk factors for signs of skin aging (pigmentation, wrinkles or laxity) in Han Chinese."

• Speculative longevity improvements: slow metabolism; and whatever metformin is doing.

• gwas longevity results (click associations, sort by p-value)

• longevity - APOE, APOC1, APOC1P1, CHRNA3, IREB2, CDKN2B-AS1, RPS10P26, TLK2, LPA, PLG, TOMM40, MFRP, C1QTNF5, ATXN2, HYKK, CHRNA5, BRAP, MYL2, SLC22A3, LPAL2, ALDH2, TRAFD1, HECTD4, PTPN11, NAA25, ECHS1...

• The Gerontology Research Group has an interest in the following candidate genes, mostly involved in DNA repair and metabolic pathways related to aging and lifespan: RAD54L, LCE3D, AGBL5, BOLA3, VWA3B, C2orf69, OGG1, WDR6, FAM19A1, PLCXD2, SST, SNCA, LARP1B, FBXW7, SUB1, SYCP2L, RNF8, GRIK2, AHR, NEUROD6, ST7, TRIQK, C9orf85, CTNNA3, TCF7L2, LRP5, C11orf1, CAB39L, ASPHD1, DDX19B, VAMP2, ALDOC, HOXB6, TOB1, CCDC102B, CD226, TSHZ1, ADNP2, RAB4B, SALL4, CLIC6, PLP1.

• SERPINE1 null mutation confers 7 year increase in average lifespan among Berne Amish (ref), see also ref

CBP2/TAFI (carboxypeptidase B2) SNP -438A/A (rs2146881) from Reiner 2015 "was found to have extended healthy lifespan by 1.1 years (and overall lifespan by 0.9 years) in men (2224 subjects)." (reddit)

IL6R (rs2228145/Asp358Ala): reduced IL-6 signaling associates with longer parental lifespan (anti-inflammatory angle)

thymus rejuvenation: in old age, or senescent thymus, consider upregulating FOXN1 (thymic epithelial transcription factor).

Mice that are homozygous or heterozygous for deletion of Dlx5/6 in GABAergic neurons show 33% improvement in life expectancy. This reduction also improves socialization and vocalizations (see the language/speech section of this doc).

anti-dementia? Pathological HK1 (Hexokinase 1) aggregation or seeding is the abnormal self‑assembly of HK1 into stable, amyloid‑like oligomers or fibrils that can nucleate further misfolding of native HK1 molecules, propagating protein‑misfolding cascades implicated in neurodegenerative or metabolic disorders. A mutation in Hexokinase 1 (HK1) might be able to phenocopy the action of ezetimibe by preventing pathological HK1 aggregation seeding yet preserving catalytic glucose phosphorylation, providing some neuroprotection against dementia-like proteinopathy and amyloid burden.

IF1 overexpression (blog post) based on the concept of F1F0‑ATP‑hydrolysis as a heat production engine across species: Species with higher IF1 expression per unit mass inhibit more ATP‑hydrolysis, produce less heat, have lower sBMR, lower ROS and therefore live longer. Also consider other ATP hydrolysis inhibitors. Cancer cells exploit the ATP‑hydrolysis‑driven proton‑leak to maintain a hyper‑polarised mitochondrial membrane that supports the Warburg phenotype. Selective inhibition of hydrolysis therefore hits cancer metabolism without harming normal cells which can compensate with ambient heat. Consider a shorter but still functional human IF1 protein fragment using residues 42-58 and using a mitochondrial import sequence, and also a cell penetrating peptide sequence. There are also small molecule selective F1F0‑ATP‑hydrolysis inhibitors. Another idea is to make a gain-of-function IF1 protein mutant that is pH-insensitive that provides more hydrolysis blocking. Selective delivery of IF1 protein to mitochondria (or a better mitochondrial import sequence?). The paper argues that combating ROS generation (by throttling the ATP‑hydrolysis heat engine) is a more powerful and safer way to lower ROS than trying to mop up ROS after they form. Cosmetical or dermal delivery of IF1 peptide can provide localized inhibition which may significantly reduce ROS in the skin (where photo-damage is abundant) without affecting whole‑body temperature. Possibly useful to target to specific tissues genomically instead of whole body? ROS is merely a symptom and excess heat‑producing ATP hydrolysis is the source of the damage. (IF1 structure and slop)

Some other IF1 gain of function mutations to consider: reduce N‑terminal proteolysis by matrix peptidases; increase rigidity and reduce unfolding‑induced proteolysis; more resistance to denaturation; fusion to a mitochondrial‑stable scaffold (e.g., COX8A‑targeting peptide + sfGFP) to make it less prone to aggregation; increase long-term stability. Multiple pH insensitivity mutations are possible. Add tandem repeat core to increase number of inhibitory helices. Multimerization, trimerization or dimerization via leucine‑zipper trimer fused to IF1-core? Use an antibody or nanobody to increase binding affinity to a ride-along target? "covalent dimer via split-intein after mitochondrial import" nah... Better mitochondrial targeting sequence or mitochondrial import sequence. Better cell penetrating peptide sequence. tether to a mitochondrial chaperonin?

Both DNP (dinitrophenol) and IF1 protein influence the mitochondrial proton gradient, but DNP does it by adding a non‑specific proton conduit, whereas IF1 acts as a brake on the reverse activity of ATP synthase. Consequently, DNP raises basal metabolism, while IF1 lowers basal metabolism.

AOX (alternative oxidase) expression selectively in astrocytes (or other tissues) to suppress Complex III (CIII)-derived mtROS without affecting basal respiration or ATP. "AOX is a mitochondrial enzyme not normally expressed in mammals, but when ectopically expressed, it localizes to the inner-mitochondrial membrane and consumes oxygen through the oxidation of ubiquinol, the substrate required for CIII ROS production. By shunting ubiquinol, AOX suppresses CIII ROS33 and other ubiquinol-dependent ROS production sites, including CI. Therefore, AOX can phenocopy SELs under contexts where one or more mtROS sites are active." "Mitochondrial complex III-derived ROS amplify immunometabolic changes in astrocytes and promote dementia pathology" (2025) -- Aldh1l1-Cre-driven astrocytic AOX (a plant/fungi-derived mitochondrial enzyme) shunts ubiquinol away from the CIII Qo-site (major mtROS source), reducing stimulus-induced mtROS (IL-1α or oAβ). No change in basal mtROS/ATP. Downstream effects: blunts cysteine oxidation (redox proteomics), STAT3 phosphorylation, and neuroinflammatory gene expression (Cxcl5, Rsad2, C3). CIII-ROS has a causal role in astrocyte immunometabolism and tauopathy progression. Related small-molecule CIII-ROS suppressor S3QEL2 given chronically extended PS19 tau mouse survival. AOX phenocopies S3QEL in acute assays, suggesting similar therapeutic potential. Mechanism: stimuli → NCLX/Ca²⁺ → ΔΨₘ hyperpolarization → ubiquinol buildup → CIII-ROS burst → oxidative stress/inflammation; AOX drains ubiquinol, intercepting ROS without proton-pumping/ATP cost. For longevity: Tissue-specific AOX (e.g., astrocyte Aldh1l1-Cre, neuronal Syn1-Cre, or microglia Cx3cr1-Cre) to curb brain mtROS in aging/AD/PD without systemic metabolic drag. Ubiquitous expression risky (may impair ETC efficiency under stress)? Test in worms/mice for lifespan. Gain-of-function: codon-optimize for mammals, fuse to strong mito IMS-targeting sequence (e.g., COX8), multimerize for higher QH₂ flux. Pair with NRF2/PGC-1α for biogenesis compensation. Small-molecule alternatives like S3QEL2 already validated for survival. Unlike IF1 (F1FO brake), AOX acts upstream at Q-cycle without raising proton gradient/heat.

TODO: incorporate 2025 supercentenerian GWAS exceptional longevity associations from supplement 11, like mutations found in (ZNF214, ZNF534, ESPL1, CDK11, MDM1, PRIM2, ERCC5, PDE4DIP, OR4C3, OR4C5, MAP2K3, KCNJ12, MUC3A, PRAMEF22, GPRIN2, TIMM23B) and others. ERCC5 is interesting as a endonuclease used in nucleotide excision repair that cleaves damaged DNA during repair of bulky lesions.

short sleeper phenotypes may cause increased lifespan: dec2 P384R mutation in drosophila "live significantly longer"

COX7RP overexpression causes modest lifespan extension in mice -- COX7RP is a mitochondrial respiratory supercomplex assembly factor. ".. COX7RP is an important regulatory factor for metabolic homeostasis along with promoting mitochondrial respiratory supercomplex assembly, which enhances ATP synthesis and suppresses ROS production." and COX7RP overexpression is associated with "... lower expression of senescence-associated genes".

Improved memory in aging

Improve memory in aging via conditional ferritin light chain 1 (FTL1) knockout in aged brain or a FTL1 hypomorph or FTL1 +/- het. This knockout improves memory in aged brain. Elevated neuronal ferritin‑light chain (FTL1) in the aged hippocampus drives cognitive decline by disturbing iron homeostasis and downstream metabolic competence. Age‑related up‑regulation of FTL1 increases the pool of oxidized (Fe3+) labile iron, which impairs mitochondrial electron‑transport efficiency and lowers proton‑motive‑force‑driven ATP synthesis. The resulting ATP shortfall compromises the expression and trafficking of synaptic proteins (e.g., PSD95, NMDA‑R, AMPA‑R, synapsin) and reduces both excitatory and inhibitory synapse density, leading to weakened long‑term potentiation and memory deficits. Knocking out FTL1 restores the Fe3+/Fe2+ balance, re‑activates oxidative‑phosphorylation genes (Sdhb, Atp5 subunits, Ndufa10), rescues mitochondrial ATP production, and reinstates synaptic protein levels and synapse numbers, thereby normalising hippocampal plasticity and improving performance. FTL1 inhibition ameliorates age‑associated cognitive impairment by correcting iron‑induced metabolic dysfunction and revitalising synaptic integrity.

GNAQ gain of function significantly improves memory in aging mice, worms and neurons. -- "The cAMP element binding protein (CREB) transcription factor, whose expression and function decline with age, activates the plasticity mechanisms necessary for long-term memory consolidation in vertebrates and invertebrates. Activation of CREB through rejuvenation methods, such as exercise and parabiosis, or CREB overexpression, improves synaptic plasticity and memory with age. EGL-30/Gαq is a guanine nucleotide-binding protein G(q) subunit α (Gαq) that regulates pre-synaptic transmission and other neuronal functions in C. elegans. Its constitutive activation (EGL-30 [Q205L and V180M]) extends memory through activation of CREB. Like EGL-30(Q205L), the constitutively active form of the highly conserved mammalian GNAQ(Q209L) leads to reduced GTPase activity and continued activation of downstream Gαq signaling. Therefore, we wondered if Gnaq(gf), like egl-30(gf), could improve memory and slow cognitive decline in aged mammals and, if so, whether the downstream molecular mechanisms are similarly well conserved across species. We found that the analogous activating mutation in GNAQ rejuvenates memory in very old mice through well-conserved neuronal molecular mechanisms."

yamanaka OSKM gene therapy improves hippocampal memory in aged brain - maybe express these factors linked to an in vivo aging sensor? or systemic administration activation?

Mammals

Many of the following longevity interventions or results are from studies of transgenic mice.

GH/IGF signaling & nutrient sensing

• IGF1 receptor (IGF1R) haploinsufficiency (Igf1r+/-), longevity effect especially strong in female PubMed
• consider other insulin/IGF receptor mutations, like lowering IGF1R signaling to de-repress FOXO, or age-gated IGF1 or IGF1R so that there is high IGF1 signaling in early life, and low IGF signaling later in advanced age (reduced cancer and improved stress resistance). Most of the benefit will probably come from late-life IGF1R reduction or IGF1 signaling reduction.
• idea: IGF1R deficiency can be mimicked by something like, say, hyperactive SOCS1 gain-of-function allele responsive to accumulating senescent cell signals (via SASP cytokines) to preserve IGF1 receptor activity for early fitness while triggering receptor degradation in advanced age to boost FOXO/DAF-16 nuclear activity and lifespan extension.
• idea: maybe a mutation in PTP1B to tie its enhanced dephosphorylation of IGF1R to age-related telomere shortening via a telomeric repeat-binding factor interaction, maintaining early-life growth signaling but progressively inhibiting it for late-life stress resistance.
• growth hormone receptor knockout (GHRKO) ("Laron" model) Wiley Online Library
• IRS1 knockout (Irs1-/-), sex-biased though PubMed -- "insulin receptor substrate 1" (IRS1)
• S6K1 knockout (S6k1-/-; mTOR axis) (ref), especially strong effect in females PubMed; Rps6kb1 knockout. This mimics a selective block of the mTORC1-S6k1 axis, which is a major target of rapamycin. Results from hepatic S6k1 deletion indicates partial contribution of liver S6K1 to whole-body aging.
• AKT1 haploinsufficiency (Akt1+/-), longer lifespan with metabolic shifts related to mTOR and autophagy PLOS
• FGF21 transgenic overexpression, lifespan extension via GH/IGF modulation PMC, or adipocyte-specific FGF21

sirtuins & stress response

• SIRT6 overexpression (whole-body), also shown to reduce frailty in B6 mice. Nature; Also consider using SIRT6 from whale instead.
• use a human centenarian SIRT6 variant with increased double-strand break repair and LINE-1 suppression (SIRT6 N308K and A313S)
• brain-specific SIRT1 overexpression (BRASTO mice), increase median and max lifespans, via hypothalamic mechanism PMC. SRT2104 is a SIRT1 activator in clinical trial. SIRT1 deacetylates FOXO3, p53, PGC-1α, NF-κB, etc., generally shifting cells toward stress resistance, mitochondrial biogenesis, and lower inflammatory tone. It interacts with AMPK (mutual activation) and indirectly influences mTOR signaling through nutrient-sensing pathways. Chronically cranking SIRT1 with high NAD+ might have trade-offs (e.g. interplay with PARP1 and DNA repair). Besides SIRT1 activation, hyperactivating FOXO3 deacetylation can be achieved by stimulating other HDACs like HDAC3 that target FOXO3 or inhibiting acetyltransferases such as p300/CBP to reduce FOXO3 acetylation.
• SIRT1, SIRT6, and SIRT7 are predominantly nuclear sirtuins, while SIRT3, SIRT4, and SIRT5 are mitochondrial family members. (ref: sirtuins)
• LINE1 repression (i don't understand this?)
• what happened to "Sirtis Pharmaceuticals" anyway?

oxidative stress & mitochondria

• mitochondrial catalase transgenic (MCAT), increase of median and max lifespan, downregulates oxidative damage. PubMed
• selegiline (L-deprenyl) is an irreversible, selective MAO-B inhibitor whose longevity-relevant biology is mostly about lowering mitochondria-derived oxidative stress and switching on pro-survival gene programs (antioxidant, anti-apoptotic, and neurotrophic. Knoll rat experiments reported lifespan extension with chronic low-dose deprenyl (ref). reddit.
• MAOB expression rises with age, but is this a cause or an effect or both?
• selegiline expression where, everywhere? or certain localized tissues?
• reminder that phenylethylamine+selegiline is essentially meth (combo TAAR1 agonist plus MOA-B antagonist) and should be approached with extreme caution

KLOTHO

• KLOTHO overexpression (KlTg): improved lifespan, endocrine effects on insulin/IGF signaling. ref: Suppression of aging in mice by the hormone Klotho See also ref and this 2016 klotho review, and cognitive ref
• possibly you want KLOTHO heterozygosity?

Klotho acts like a systemic longevity hormone, regulating mineral metabolism, oxidative stress, and multiple growth pathways. Klotho directly influences phosphate homeostasis by acting as an obligate co-receptor for fibroblast growth factor 23 (FGF23), facilitating its binding to the FGFR1c receptor to activate downstream ERK signaling that suppresses renal phosphate reabsorption via downregulation of NaPi-IIa cotransporters and inhibits 1α-hydroxylase to reduce active vitamin D synthesis. Overexpression of Klotho influences FGF23 / phosphate / vitamin D homeostasis, insulin/IGF1 and Wnt signaling, and oxidative stress resistance and some autophagy/proteostasis pathways.

Alternative ideas instead of specifically targeting or overexpressing Klotho:

• gain-of-function mutation in the FGFR1c receptor that enhances its affinity for FGF23 independently of Klotho, thereby activating ERK signaling to suppress renal phosphate reabsorption and vitamin D synthesis, mimicking Klotho's endocrine effects on mineral homeostasis.
• overexpress a constitutively active form of ERK1/2 specifically in renal proximal tubule cells to directly downregulate NaPi-IIa cotransporters and 1α-hydroxylase, replicating Klotho's phosphate-lowering without relying on the Klotho-FGF23 co-receptor complex.
• alterations in the insulin/IGF1 receptor pathway, such as a dominant-negative IRS-1 variant, to attenuate downstream PI3K/Akt signaling and enhance longevity through reduced anabolic signaling, paralleling Klotho's inhibitory effects on insulin/IGF pathways via alternative endocrine modulation.

Myc & growth control

• reduced Myc expression (haploinsufficiency): longer healthy lifespan with broad protection PMC

p66Shc (ROS signaling adaptor) knockout: ref, PMC ref. p66Shc has pro-apoptotic activity upon oxidative stress. -- "One unexpected pathway involves p66Shc in mitochondria ROS production. In higher organisms about 20% of fibroblast p66Shc is localized to mitochondria and, in response to oxidative stress, part of the cytosolic pool of p66Shc translocates to mitochondria. Within mitochondria p66Shc then binds cytochrome c and acts as an oxidoreductase, shuttling electrons from cytochrome c to molecular oxygen. The redox activity of p66Shc is likely to be the explanation of the increase in ROS production caused by the recombinant expression of p66Shc, and the decrease in ROS levels typical of p66Shc knockout cells. ... ROS production in mitochondria is regulated by metabolic activity, substrate supply, and mitochondrial membrane potential. Interestingly, p66Shc−/− fibroblasts have altered mitochondrial bio-energetic properties. In particular, p66Shc−/− cells have a reduction in both their resting and maximal oxidative capacity, suggesting that the ablation of p66Shc may extend life span by repartitioning metabolic energy conversion away from oxidative and toward glycolytic pathways. One interpretation of the data is that p66Shc mediates deleterious triggering of apoptosis, and its ablation induces a significant expansion of the lifespan."

senescent-cell clearance (genetic "senolysis")

• INK-ATTAC transgene (drug-inducible ablation of p16Ink4a+ cells) PMC

telomeres

• Telomerase (TERT) overexpression: delayed aging and increased longevity without extra cancer in treated cohorts (AAV gene therapy of wildtype mice in this study) PubMed
• TERT overexpression in cancer-resistant mice (extra tumor suppressors) delays aging and extends lifespan (ref)
• mTERT overexpression
• idea: a mutation increasing TERT's stability by disrupting ubiquitin-mediated degradation signals would prolong telomerase half-life, ensuring sustained telomere maintenance during organismal aging without risking oncogenic overactivity.
• idea: engineer a variant in TERT's RNA-binding motif to improve affinity for TERC, boost holoenzyme assembly and activity.
• idea: a mutation altering TERT's nuclear import signals to enhance localization efficiency might increase telomerase availability at chromosome ends.
• exogenously transiently inducible TERT activity instead of endless runaway extension. don't use the effector when dealing with acute cancer.
• negative feedback to TERT to maintain telomere lengths in a narrow distribution around the target length.
  • potential negative feedback telomere length sensors: TRF1 Myb domain, POT1 OB fold, {ATM/ATR, γH2AX, and 53BP1 TIFs}, TERRA (telomeric repeat-containing RNA).
  • a shelterin‑occupancy readout (low TRF1/POT1 occupancy) AND a telomere‑localized DDR signal (TIFs) gives telomere specificity, reduces false positives from general DNA damage
• if you have very long telomeres, then invest in additional anti-cancer pathway enhancement
• background: Two faces of p53: aging and tumor suppression
• background: DNA damage responses and p53 in the aging process
  • "While DDR prevents tumorigenesis, its constitutive activation, such as that in hyperactive p53 mutants, accelerates the aging process. The continuous activation of DDR arises by genetic mutations that augment DDR and can also result from DNA lesions that are not repaired and thus persist. For instance, critically shortened and thus unprotected telomeres are recognized as DNA DSBs. Indeed, the inability of telomerase to maintain the telomere length causes premature aging through activating the DDR and p53. Mice that are lacking the catalytic subunit or the RNA component of telomerase have shorter lifespans with early onset of aging phenotypes, even though in mice these phenotypes require several generations of defective telomere extension to arrive at critical telomere shortening, which precipitates the progeroid pathologies. Premature replicative senescence also shortens lifespan in Ku80−/−-mutant mice that lack functional NHEJ. Intriguingly, the accelerated aging phenotypes of both animal models can be alleviated by the loss of p53, again underlining the pivotal role of p53 in DDR-mediated premature aging."
• "Short telomeres generate chronic, non-repairable DDR signalling that keeps p53 transcriptionally active indefinitely."
• DCAF4 -- avoid rs2535913-A; keep G because A is associated with lower leukocyte telomere lengths. TERC rs16847897-C is consistently associated with shorter telomere lengths in leukocytes, prefer GG trait.
• TERT rs2736100-C has been associated with longer telomere length (ref); consider also TERC rs12696304-G and TERC rs16847897-C.
• TERT rs7726159-AA is associated with longer telomere length (ref)
• TERC rs10936599-C, NAF1 rs7675998-G, OBFC1 rs9420907-C, ZNF208 rs8105767-G, RTEL1 rs755017-G, ACYP2 rs11125529-A is associated with longer telomere length, maybe MPHOSPH6 rs2967374-A (ref)
• CTC rs30272341 rs3027234-C for longer telomere lengths
• OBFC1 (STN1) (telomere maintenance), rs77987791 rs7925084 -- "OBFC1, also known as STN1, is a critical component of the CST (CTC1-STN1-TEN1) complex that plays an essential role in regulating telomere maintenance. The CST complex functions primarily as a terminator of telomerase action, helping to limit excessive telomere elongation by competing with telomerase for access to the telomeric 3' overhang. OBFC1/STN1 specifically facilitates the recruitment of DNA polymerase α-primase to telomeres, which is necessary for C-strand fill-in synthesis following telomerase-mediated G-strand extension. This fill-in synthesis converts the extended single-stranded overhang into double-stranded telomeric DNA, completing the telomere replication process. Both excessively short and excessively long telomeres can cause problems. Short telomere syndromes, collectively known as telomeropathies, include conditions like dyskeratosis congenita, idiopathic pulmonary fibrosis, aplastic anemia, and liver cirrhosis, which result from critically short telomeres causing cellular senescence and stem cell exhaustion in high-turnover tissues. However, abnormally long telomeres also carry risks, particularly an increased susceptibility to certain cancers including melanoma, glioma, and lung cancer, because extended telomeres allow cells to continue dividing beyond normal limits, potentially accumulating mutations and evading the tumor-suppressive mechanism that telomere shortening provides." however, you can upregulate other anti-cancer pathways if you allow for longer telomeres. OBFC1 is a component of the CST (CTC1-STN1-TEN1) complex involved in telomere maintenance and DNA replication. The protein contains an N-terminal OB (oligonucleotide/oligosaccharide-binding) fold domain that facilitates single-stranded DNA binding, followed by a winged helix-turn-helix domain in its C-terminal region; structurally, it adopts a compact globular architecture that enables it to interact with both CTC1 and TEN1 partners while engaging telomeric DNA."
• probably you want to do a GWAS for longer telomere length, in general, and do polygenic selection on this basis.
• TODO: process more telomerase-related longevity interventions from the hplusroadmap logs and here and here.

During aging and runaway aging, the genome loses copies of ribosomal RNA (rRNA) because of excision, DNA damage repair, etc. rRNA is apparently stored on 13p12, 14p12, 15p12, 21p12, 22p12. There are several hundred copies in a healthy non-aged adult genome. One obvious thing to do would be to add extra copies of rRNA genes throughout the genome in different locations, and ensure that if needed they can be used (not under heterochromatin silencing or the silencing can be turned off when the cell needs these other rRNA copies).

Other things get lost from the genome and could be given more redundancy or more consideration:

• mitochondrial DNA (mtDNA): Large-scale deletions in the circular mtDNA genome accumulate in post-mitotic tissues like muscle and brain, impairing electron transport chain function and increasing reactive oxygen species production, which exacerbates aging phenotypes. To fix, consider adding more mtDNA or more copies of mitochondrial genes, and consider better mtDNA DNA damage repair mechanisms or other gain-of-function related to DNA damage repair.
• segmental duplications (low-copy repeats): These near-identical genomic blocks (~5% of the human genome) undergo unequal recombination, resulting in net copy number loss over time, which disrupts gene dosage balance and increases susceptibility to age-related genomic instability and neurological decline. (ref, ref) To fix, consider optimizing recombination mechanisms in vitro and adding back in the modified enzymes.
• long and short tandem repeats (STRs) in regulatory regions: Contractions or deletions in these microsatellites (2–6 bp motifs) occur via replication slippage, reducing enhancer/promoter activity and gene expression variability, thereby promoting age-related diseases. (ref, ref, ref, ref) To fix, consider optimization of replication enzymes in vitro to reduce incidents of slippage.
• copy number variations that get changed due to error-prone non-allelic homologous recombination, or other reasons.
• copies of ribosomal rRNA
• see Causality of aging hallmarks, TRCS critical analysis
• idea: overexpression of UBF (upstream binding factor) or SL1/TBP variants with enhanced rDNA promoter affinity to boost rDNA transcription from remaining copies,
• idea: CRISPR-based engineering of rDNA "magnification" machinery, e.g., ectopic expression of ribosomal DNA polymerase I enhancers or Pop1 endonuclease inhibitors to reduce excision rates and stabilize copy number during replication.
• rDNA stability GWAS hits: prioritize alleles like RPO1-1 rs2293832-T (associated with longer leukocyte rDNA arrays)
• idea: physically extend telomere length to be longer using DNA synthesis or direct editing using Cas9, recombinases, or whatever else you want.
• idea: targeted duplication of aging-vulnerable SD blocks (e.g., 15q11-q13 Prader-Willi/Angelman region or 17q21 MAPT locus)
• idea: overexpression of RAD51 or DMC1 recombinase variants tuned to favor intra-chromosomal over ectopic recombination, minimizing NAHR-driven losses.
• idea: transgenic expression of high-fidelity DNA polymerase epsilon (POLE) mutants (e.g., pol2-M644G equivalent) to reduce replication slippage in microsatellite-rich promoters/enhancers.
• idea: extra copies of contraction-prone STRs in key longevity genes (e.g., DMNT3L or FOXO3 regulatory repeats) inserted upstream of native loci to buffer age-related activity loss.
• if engineering long telomeres/rDNA, co-express hypermorphic TP53 or PPM1D variants for fine-tuned DDR
• idea: genomic integration of Tornado-circRNA cassette for constitutive TERT expression in stem cells, maybe under inducible expression to trigger repeat dosing. (ref)
• idea: Tornado-circTFAM or circPOLG for mitochondrial genome maintenance, delivering nuclear-encoded factors with MTS (mitochondrial targeting signals) to repair large-scale mtDNA deletions in post-mitotic tissues; superior persistence over mRNA for sustained ETC function and ROS reduction, inspired by circTERT's mitochondrial benefits in HGPS.

and:

• idea: transgenic upregulation of TFAM (mitochondrial transcription factor A) or POLG (mtDNA polymerase gamma) proofreading mutants to enhance mtDNA replication fidelity and repair, countering large-scale deletions in post-mitotic tissues.
• idea: allotopic expression of all 13 mtDNA-encoded OXPHOS genes as nuclear transgenes with mitochondrial targeting signals, providing redundancy against age-accumulating mtDNA deletions; combine with ANT1/PGC1α overexpression for improved import and biogenesis. reduce ROS.

See also DNA damage repair.

Brain / hypothalamus (neuron-focused)

• brain-specific SIRT1 overexpression (already mentioned)
• inhibiting hypothalamic IKKβ/NF-κB slows whole-body aging and extended lifespan, via central neuro-immune axis PMC
• some sort of role played by hypothalamic neural stem/progenitor cells, where ablation accelerates aging, and transplantation or stem-cell exosomes slows aging and extends lifespan PMC

Adipose / endocrine adipokines

• fat-specific insulin receptor knockout (FIRKO) produces a lean phenotype with increased lifespan via different adipose insulin signaling. PubMed
• adiponectin overexpression (ΔGly Tg): healthier aging with a median lifespan increase, knockout shortens lifespan. eLife

Liver-driven endocrine signals

• FGF21 transgenic (liver-secreted "starvation" hormone) PMC

Vasculature / endothelium

• endothelium-targeted Sirt7 gene therapy (ICAM2 promoter) PMC
• counteracting age-related VEGF insufficiency (vascular rejuvenation) PubMed

Skeletal muscle (myokine/autophagy axis)

• muscle-specific TFEB overexpression, causing improved muscle proteostasis and reduced brain neuroinflammation PMC

Heart (cardiomyocytes)

• cardiac-specific catalase overexpression PubMed

Mitochondria and longevity

• mitochondria-targeted catalase overexpression increases mouse lifespan (15-20% median increase) and reduces age-associated oxidative damage.
• Mclk1/Coq7 haploinsufficiency (Mclk1 +/-): decreasing ubiquinone-biosynthesis enzyme activity produces long-lived mice across backgrounds; mechanisms include altered mitochondrial ROS/signaling with preserved respiration.
• SURF1 knockout
• hMTH1/NUDT1 overexpression clears 8-oxo-dGTP from the nucleotide pool, lowers oxidative nucleic-acid damage, and extends lifespan.
• OPA1 overexpression (inner-membrane fusion/cristae integrity) preserves cristae architecture, improves respiratory-chain efficiency.
• ATG5 overexpression to increase mitophagy increases mouse lifespan.
• Parkin (PARK2) overexpression for more mitophagy.
• mtOGG1 (mitochondria-targeted 8-oxoguanine DNA glycosylase) overexpression to improve mtDNA base-excision repair.
• PRDX3 (mitochondrial peroxiredoxin) overexpression to lower mitochonrial H2O2 (? unclear if this is effective)

mitochondrion membrane "peroxidizability" is lower in long-lived species. Across mammals (incl. humans) and birds, mitochondrial phospholipids have fewer highly polyunsaturated fatty acids (esp. DHA) → membranes are harder to oxidize, lipid peroxidation is lower, and mitochondria age more slowly. Humans fall on the "low peroxidizability" end vs mice. Naked mole-rats and many birds are extreme examples

mtDNA mutations scale with lifespan. get good at mtDNA repair or mitophagy. or mitochondrial replacement therapies somehow.

antioxidant/repair capacity or location may track longevity better than raw ROS production. (ref)

bats have enhanced mitophagy/DNA-damage responses and a dampened NLRP3 inflammasome, reducing mito-inflammation during stress (flight). (ref)

human mitochondria have lower PUFA content and a lower peroxidation index than mice.

naked mole rats mitochondrial membranes are unusually resistant to peroxidation (very low DHA in phospholipids).

human oocyte mitochondria seem to be uniquely protected. (ref)

TODO: look for human mitochondrial longevity mutations in the literature.

mtDNA copy number (mtDNA-CN) should be increased (ref)

MitoSENS: mitochondria DNA mutations need to be bypassed (MitoSENS) by moving mtDNA genes to the nucleus (allotopic expression) and import the proteins back into mitochondria to maintain cellular respiration. Allotopic expression of mitochondrial genes into the nucleus will require recoding for cytosolic translation and also mitochondrial targeting sequences. Mitochondrial-targeted nucleases could be used to eliminate mutant genomes. Therapeutic mitochondrial transplantation or progenitor cell transfer. Engineer enhanced mitochondrial import machinery. Add mitochondrial-targeted DNA repair systems. Overexpress mitochondrial biogenesis factors (PGC-1α, NRF1/2).

dec2P384R enhances mitochondrial respiratory capacity in Drosophila flies and HEK293 cells (ref)

BAM15: Restricting bioenergetic efficiency enhances longevity and mitochondrial redox capacity in Drosophila melanogaster

mitochondrial uncouplers sometimes also have a pro-longevity effect.

Mitrix Bio is investigating the direct intravenous infusion or tissue injection of youthful bioreactor-grown mitochondria. These exogenous organelles can be taken up by cells to restore bioenergetics, bypassing the need to repair widely mutated endogenous mtDNA.

See also mitochondria.

Strategies for engineered negligible senescence

Aubrey de Grey proposed "Strategies for Engineered Negligible Senescence" which includes the following:

https://sens.org/

Strategies for Engineered Negligible Senescence is a repair-based approach to aging. It consists of seven categories of molecular and cellular damage that accumulate with age and proposes targeted adult interventions to keep their levels below the threshold that causes pathology. While SENS is primarily focused on adult aging, many of the concepts can be used to inform human germline genetic engineering for anti-aging.

• cell loss (like from non-dividing cells) and atrophy requires replacement (RepleniSens) via tissue engineering and stem cell therapies to restore cell numbers and function. Stimulation or proliferation of resident progenitors to replace lost cells.
• death-resistant (senescent) cells must be removed (ApoptoSens) via targeted ablation such as through senolytic drugs or via immune/CAR-T approaches. p16-activated caspase, senolytic small molecule therapy (dasatinib, quercetin, navitoclax), immune-mediated clearance of senescent cells (CAR-NK cells, vaccination against senescent antigens).
• extracellular aggregates require immunoclearance (AmyloSENS): use vaccination/antibody therapies to tag and remove amyloids such as Aβ or transthyretin in tissue spaces. Active or passive immunization to tag aggregates for microglia/macrophage uptake. Use catalytic monoclonal antibodies or nanobodies that enhance proteolysis. Use engineered proteases like neprilysin or MMP variants. See neprilysin overexpression. Enhance endogenous clearance pathways. alagebrium (ALT-711) analogue expression during thymic negative selection.
• intracellular aggregates should be digested by better lysosomes (LysoSENS) by introducing novel lysosomal enzymes (like those sourced from microbes) to digest stubborn junk like oxidized cholesterol adducts and lipofuscin that materially clog lysosomes. Genomically encode modified enzymes with better trafficking and activity, like bacterial or fungal hydrolases. Transcriptional upregulation of TFEB (master lysosomal biogenesis factor) or TFEB overexpression. Engineer pH-optimized variants of existing lysosomal enzymes. Overexpress other autophagy/lysosomal biogenesis factors. ATG5 overexpression. Beclin-1(Becn1) F121A knock-in to boost autophagy. reverse proteotoxic pathology and lipofuscin via upregulation of lysosome and TFEB programs.
• extracellular crosslinks require the matrix to be replaced or broken (GlycoSENS) via development of crosslink-brakers (such as glucosepane) or refresh extracellular matrix to restore tissue elasticity, especially in arteries. Glyoxalase-1 (Glo1) overexpression.
• mitochondria DNA mutations need to be bypassed (MitoSENS) by moving mtDNA genes to the nucleus (allotopic expression) and import the proteins back into mitochondria to maintain cellular respiration. Allotopic expression of mitochondrial genes into the nucleus will require recoding for cytosolic translation and also mitochondrial targeting sequences. Mitochondrial-targeted nucleases could be used to eliminate mutant genomes. Therapeutic mitochondrial transplantation or progenitor cell transfer. Engineer enhanced mitochondrial import machinery. Add mitochondrial-targeted DNA repair systems. Overexpress mitochondrial biogenesis factors (PGC-1α, NRF1/2).
• oncogenic nuclear (epi)mutations to pre-empt cancer (OncoSENS) by the "widespread interruption of lengthening of telomeres" to prevent lethal tumor overgrowth, in addition to periodic stem cell reseeding throughout the body; CRISPR/dCas9-based targeted demethylation or histone acetylation to restore youthful gene expression; possibly some epigenetic rejuvenation via transient yamanaka-factor expression for partial reprogramming but i am skeptical. tumor-suppressor genes must not be silenced, in fact they must be unsilenced, and chromatin remodeling errors must be fixed or be made to trigger apoptosis. Immune surveillance to kill pre-cancerous cells. Engineer more robust tumor suppressor networks. Add novel DNA damage sensors and response pathways. Super p53 with added extra Ink4/Arf (s-Arf/p53 mice) produced significantly longer lifespan and delayed aging.

Some of the SENS opportunities can be met via germline engineering:

• design redundant metabolic pathways to prevent single points of failure
• create "damage-proof" protein variants less prone to aggregation/oxidation
• dramatically upregulate proteostasis networks
• engineer enhanced DNA proofreading and repair machinery, like double-strand break sensor, detection, and repair, or go into apoptosis
• look for better bacterial/archaeal DNA repair systems from other organisms
• metabolic optimization: engineer more efficient electron transport chains with less ROS production
• add alternative respiratory pathways (like those in long-lived animals)
• optimize NAD+ synthesis and utilization pathways
• engineer telomerase regulation for optimal telomere maintenance
• create enhanced stem cell reserves and regenerative capacity
• import longevity genes from extremely long-lived species (bowhead whales, Greenland sharks, naked mole rats)
• add extremophile stress resistance genes
• integrate plant/bacterial antioxidant systems
• damage-resistant proteins? metabolically optimized protein encodings?
• place "stemness" genes (PAX7, LGR5, SOX2, MYC, TERT) under endogenous or synthetic stress-inducible promoters
• maintain larger stem cell pools and create a "progenitor bias" in every tissue, possibly with FOXO3 modifications or upregulation
• probably significantly more opportunities that have long been overlooked.

Other aging intervention

This is based on a "how aging works" outline from.. many years ago.

mitochondria-targeted catalase overexpression increases mouse lifespan and reduces age-associated oxidative damage.

MnSOD (Sod2) modest overexpression to buffer superoxide without fully flattening redox signals.

GPx4 or Prdx3 mitochondrial-targeted overexpression for lipid peroxides/H2O2 control. GPx4 overexpression reduces age-related pathology; Prdx3 guards mitochondrial redox.

Nox2 (Cybb) loss-of-function or p47phox (Ncf1) hypomorph, curbs AngII/PKC-driven ROS amplification and vascular remodeling.

p47phox phosphorylation-site mutants that reduce PKC-to-NOX docking. preserve baseline NOX but lower "gain" to H2O2 bursts. (ref)

Agtr1a (AT1A) heterozygous knockout or hypomorph: AT1A loss extends lifespan, lowers oxidative damage, increases mitochondria and Sirt3 and Nampt.

klotho knock-in

something for the mTOR axis like S6k1 -/-?? (ref) -- "Caloric restriction (CR) protects against aging and disease but the mechanisms by which this affects mammalian lifespan are unclear. We show in mice that deletion of the nutrient-responsive mTOR (mammalian target of rapamycin) signaling pathway component ribosomal S6 protein kinase 1 (S6K1) led to increased lifespan and resistance to age-related pathologies such as bone, immune and motor dysfunction and loss of insulin sensitivity. Deletion of S6K1 induced gene expression patterns similar to those seen in CR or with pharmacological activation of adenosine monophosphate (AMP)-activated protein kinase (AMPK), a conserved regulator of the metabolic response to CR. Our results demonstrate that S6K1 influences healthy mammalian lifespan, and suggest therapeutic manipulation of S6K1 and AMPK might mimic CR and provide broad protection against diseases of aging."

S6K1 knockout (Rps6kb1−/−): deletion of ribosomal S6 kinase 1, a downstream effector of mTORC1, causing lifespan extension in Drosophila. -- "We identified the Drosophila fat body as an essential organ for suppression of S6K to extend lifespan. TORC1 inhibition by rapamycin treatment repressed enlarged, multilamellar lysosomes in the Drosophila fat body, and this effect was blocked by elevating S6K activity. We identified Syntaxin 13 (Syx13), a SNARE family protein that mediates endomembrane function, as a downstream mediator of TORC1–S6K signaling. Repressing Syx13 in the fat body by double-stranded RNA interference (RNAi) induced the enlarged multilamellar lysosomes, while overexpressing Syx13 suppressed them. Further, suppression of TORC1–S6K–Syx13 signaling reduced age-associated chronic inflammation, reduced the decline in ability to clear bacteria and extended lifespan via the endolysosomal control of regulatory PGRP-LC isoform. Moreover, repression of inflammation in mid-adulthood, by knocking down the Drosophila NF-κB like transcription factor Relish in the fat body, enhanced bacterial clearance and increased fly lifespan."

preserve nuclear FOXO stress-resilience without chronic overactivation?

SIRT6 overexpression, previously mentioned.

fix inflammatory aging feedback loops: 1) Ager (RAGE) loss-of-function or sRAGE-favored knock-in, 2) TLR4 hypomorph rather than TLR4 null, to attenuate inflammaging, get less adipose inflammation, and better glucose tolerance.

p38α (Mapk14) activity-dampening allele in stem-cell compartments (HSC/MuSC-biased regulatory elements), or Dusp/Mkp-1 enhancer knock-in. p38 drives HSC/MuSC aging; partial inhibition rejuvenates engraftment. complete p38 loss is deleterious.

mitochondrial biogenesis: moderate Pgc-1α enhancer knock-in, or modest overexpression of Parkin/Pink1. Restore biogenesis/mitophagy where it declines with age; avoid cardiac overexpression toxicity.

Many redox/antioxidant overexpressions fail to extend lifespan unless mitochondria-targeted (mCAT is the exception).

Longevity in other animals

• C. elegans: daf-2 (insulin/IGF receptor) mutants PMC
• C. elegans: age-1 (PI3K); upstream of DAF-16/FOXO PubMed
• C. elegans: intestine-specific degradation of insulin/IGF receptor DAF-2 nearly doubled lifespan; neuronal/hypodermal knockdown gave smaller gains. Nature
• Drosophila FOXO/dFOXO activation shows improved lifespan with adipose-like tissue-specific expression. Fight Aging!, Science

Elephants have many extra copies of p53 (TP53) + hyper-responsive DNA-damage signaling. Elephants carry ~20 TP53 retrogenes. Elephant cells trigger apoptosis at lower damage thresholds. (ref). "Zombie" pro-apoptotic gene LIF6. A re-functionalized LIF pseudogene (LIF6) is directly upregulated by TP53 after DNA damage and triggers mitochondrial apoptosis, as a second independent tumor-suppression layer (ref).

bowhead whales: DNA repair & replication factors under selection/duplication. Comparative genomics found bowhead-specific changes in ERCC1 and duplication/lineage-specific changes in PCNA, plus shifts in pathways tied to DNA repair/cell cycle and cancer resistance. (ref) However, whale does not seem to have more p53.

Evidence for improved DNA repair in long-lived bowhead whale - "bowhead whale cells exhibited enhanced DNA double-strand break repair capacity and fidelity, and lower mutation rates than cells of other mammals. We found the cold-inducible RNA-binding protein CIRBP to be highly expressed in bowhead fibroblasts and tissues. Bowhead whale CIRBP enhanced both non-homologous end joining and homologous recombination repair in human cells, reduced micronuclei formation, promoted DNA end protection, and stimulated end joining in vitro. CIRBP overexpression in Drosophila extended lifespan and improved resistance to irradiation. These findings provide evidence supporting the hypothesis that, rather than relying on additional tumour suppressor genes to prevent oncogenesis, the bowhead whale maintains genome integrity through enhanced DNA repair." See other DNA repair suggestions on this page.

whales and dolphins: upgrades in tumor suppression. tumor-suppressor genes show positive selection and faster turnover. higher cancer resistance. (ref)

naked mole rats: cancer resistance via extracellular matrix and secretion of very high-molecular-mass hyaluronan (HMM-HA). Mechanism ties to p16^INK4a–mediated early contact inhibition. better proteostasis, protein homeostasis, and stress resistance. Make a ultra-high-activity hyaluronic acid synthase (HAS2) or take it from naked mole rat. Should the HA-degrading enzyme HYAL2 be deleted? This super-sized hyaluronic acid binds CD44 receptors, suppresses the senescence-associated secretory phenotype, keeps the extracellular matrix densely hydrated and elastic, sequesters reactive oxygen species, and antagonizes NF-κB–driven inflammation, thereby maintaining tissue integrity, delaying cellular senescence, and contributes to the naked mole rat's long lifespan. Generally this page needs more hyaluronic acid content.

naked mole rats: A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging

bats: reduced growth signaling via GHR/IGF14. telomere maintenance without age-related shortening. Inflammation braking as a longevity strategy: bats have dampened cytosolic DNA sensing (loss of PYHIN genes; STING S358 change), curbing chronic inflammation that drives aging.

rockfishes: positive selection in DNA-repair pathways. (ref)

galapagos tortoise: DNA repair, mitochondrial homeostasis, enhanced immune pathways. XRC6 variant.

Longevity TODO

• rapamycin informed: hypomorphic mTOR increases longevity (ref) -- "We analyzed aging parameters using a mechanistic target of rapamycin (mTOR) hypomorphic mouse model. Mice with two hypomorphic (mTORΔ/Δ) alleles are viable but express mTOR at approximately 25% of wild-type levels. These animals demonstrate reduced mTORC1 and mTORC2 activity and exhibit an approximately 20% increase in median survival. While mTORΔ/Δ mice are smaller than wild-type mice, these animals do not demonstrate any alterations in normalized food intake, glucose homeostasis, or metabolic rate. Consistent with their increased lifespan, mTORΔ/Δ mice exhibited a reduction in a number of aging tissue biomarkers. Functional assessment suggested that, as mTORΔ/Δ mice age, they exhibit a marked functional preservation in many, but not all, organ systems. Thus, in a mammalian model, while reducing mTOR expression markedly increases overall lifespan, it affects the age-dependent decline in tissue and organ function in a segmental fashion."
• Raptor (RPTOR) haploinsufficiency: mimics rapamycin administration by lowering anabolic signaling, enhancing autophagy, and shifting metabolism toward cellular maintenance. Reduces raptor-dependent mTORC1 activity.
• rapamycin informed: mitochondrial target of rapamycin (mTOR), mTOR inhibitors, etc...
• KAT7 inactivation in the liver to increase lifespan (a histone acetyltransferase). KAT7 is a driver of cellular senescence.
• IL-11 blockade: Inhibition of IL-11 signalling extends mammalian healthspan and lifespan -- both genomic deletion of IL-11 and also IL-11 antibody administered in aging mice shows an improvement in longevity. Consider either deletion of IL-11 from the genome, a hypomorph mutation, heterozygosity, or simply encoding an antibody or nanobody against IL-11 to be expressed throughout life or later in life (maybe triggered by some other activator such as systemic administration or local sensing).
• endocrine niches broadcast longevity or aging signals; you don't need every cell to change, instead targeting key "broadcast" cell types can move systemic aging (fat, endothelium, hypothalamus, skeletal muscle).
• TODO: chemical activators of telomerase
• TODO: calorie restriction mimetics (rapamycin, metformin, NAD⁺ precursors).
• overexpression of antioxidant enzymes (SOD1, SOD2, GPx, etc) by themselves generally do not extend lifespan, despite sometimes improving resistance to acute oxidative stress. MCAT or catalase overexpression targeted to the mitochondria is an interesting exception to this (see elsewhere in this doc).
• late-life cardiac-targeted Cisd2 overexpression gives mice an extended median and maximum lifespan, and delayed cardiac aging. It is not clear if extra Cisd2 expression earlier in life would be beneficial, so consider coupling extra Cisd2 to an inducible expression system.
• conditional IGF‑1R down‑regulation in adulthood: age-gated weakening of GH/IGF1 axis (high early‑life activity, low late‑life activity). Would taking antibodies against IGF1, GH, etc, be sufficient?
• TODO: AMPK activation or overexpression needs to be studied in a mammalian model as a longevity intervention.
• metformin mimetic: liver-specific overexpression of a constitutively active AMPKγ1 (R70Q) subunit (or gain-of-function with R531G), combined with heterozygous knockdown of mitochondrial complex I subunit Ndufs4, would genetically mimic metformin's dual mechanism of AMPK activation and complex I inhibition. Metformin activates AMP-activated protein kinase (AMPK) and inhibits mitochondrial complex I, leading to reduced oxidative stress, decreased inflammation, improved insulin sensitivity, and activation of autophagy pathways that collectively may slow cellular aging processes. Or PRKAA1/2 hyperactivation.
  • tunable AMPK activation: Liver and intestine-specific expression of a constitutively active AMPKγ1 (R70Q) subunit, or gain-of-function AMPKα with T172D phosphomimetic (PRKAA1/2 hyperactivation). Critical: use adult-onset inducible expression with degron/destabilization domain for dose-like control. Strong constitutive AMPK GoF produces artifacts (growth/behavior/energy balance issues, compensations) that metformin doesn't cause. Captures: metabolic shift toward catabolism, mTORC1 suppression, increased autophagy, improved insulin sensitivity, reduced inflammation, stress-response transcription (FOXO, PGC-1α). Misses: mitochondrial redox effects of complex I inhibition, gut-mediated signaling (GDF15, microbiome), hormetic ROS signaling.
  • secondary target - partial Complex I inhibition: Heterozygous knockdown of mitochondrial complex I subunit Ndufs4, or mild hypomorphic alleles of Ndufs subunits (tissue-restricted, inducible). This mimics metformin's primary trigger (a slight inhibition of Complex I) and activates AMPK endogenously through hormetic energy stress. Narrow therapeutic window; developmental lethality if not inducible.
  • mild mTORC1 suppression: Raptor (RPTOR) haploinsufficiency or overexpression of TSC1/TSC2. Mimics rapamycin-like effects by lowering anabolic signaling, enhancing autophagy, and shifting metabolism toward cellular maintenance. mTOR suppression alone often causes growth defects, immune suppression, or glucose intolerance if not finely tuned.
  • tissue prioritization for metformin mimicry: (1) Intestinal epithelium - metformin's strongest first contact; gut perturbations reproduce large systemic phenotypes. (2) Liver hepatocytes - classic metabolic control center for insulin/IGF tone, gluconeogenesis. (3) Myeloid lineage (monocytes/macrophages) - inflammaging is a major aging benefit readout; myeloid cells shape tissue inflammation across organs.
  • Intestine + liver mild tunable AMPK bias (adult-onset) + feedback controller preventing overactivation (keeps AMPK/mTOR in narrow band) + epistasis toggles (Complex I bypass to test upstream necessity, tissue-specific AMPK LOF to test downstream necessity). A closed-loop controller maintaining target state of mild energetic stress across diets, ages, and circadian variation most closely approximates metformin's weak, chronic, context-sensitive perturbation.
• TODO: dehydroepiandrosterone (DHEA) overexpression?
• TODO: 5′-deiodinase (DIO1/DIO2) hypomorphic alleles ?
• TODO: thyroid-hormone receptor β (THRβ) antagonism, or THRβ made to dampen TH nuclear signaling and negative feedback on TSH/TRH.
• TODO: estrogen receptor gain-of-function (ERα/ERβ/GPER1) to enhance estradiol signaling.
• TODO: growth-hormone-releasing hormone (GHRH) pathway modulation.
• from reviewing my old longevity notes:
  • TODO: GSK3β inhibition to improve aging and memory (ref, ref)
  • TODO: dietary supplementation with a PI3K inhibitor (targeting p110α) extended median and maximal lifespan (ref). What transgenic intervention would mimic this effect? PI3Kγ or PI3k gamma hypomorph?
  • PEPCK-C overexpression has a positive impact on longevity, not just muscle function
  • chondroitinase ABC and longevity
  • PKCε inhibition (ROS-amplifier blockade)
  • MTHFR phosphorylation-site mutants (homocysteine-driven redox control)
  • EphA4 knockout
  • Δ6-desaturase down-regulation (membrane peroxidation index)
  • Δ6-desaturase low-activity alleles (long-lived species mimic)
  • mGSTA4 disruption (Nrf2 hormesis, 4-HNE stress)
  • Nrf2 ARE-boosting small molecules / Keap1 inhibitors
  • ATM lysosome-anchored mTOR super-complex modulation
  • ATM kinase inhibition for senescence rescue
  • Caveolin-1 down-regulation
  • Caveolin-1 interacting peptide mimetics
  • p16 mRNA decay enhancement via AUF1 or HuR manipulation
  • p16 mRNA stabilizing mutations (senescence delay)
  • p16 3′UTR stem-loop targeting antisense oligos
• TODO: mouse longevity loci
• TODO: Epigenetic aging can be decelerated by improved proteostasis (NHLRC1), dampened methylation turnover (TPMT), nutrient-sensing down-regulation (SESN1), or restrained ROS/inflammation signalling (FLOT1, NFKB1, HDGF). These all lower the rate of or presence of methylation changes. (ref) The study has supplementary data that could be used to find mutations that provide a protective effect against epigenetic aging.
• TODO: incorporate missing items from fightaging.org's longevity genetics wish list
• TODO: process weird longevity ideas from Gerontology Research Group in IRC logs here and here and here
• ribosomal hyperaccuracy for better protein synthesis at lower error rate in old age (RPS23 hyperaccuracy mutations from a microbe)
• better proteostasis
• endoplasmic reticulum improvements https://gnusha.org/logs/2026-01-06.log like XBP1 overexpression or SKN-1A/Nrf1 overexpression; or EDEM overexpression (ERAD-enhancing mannosidase-like proteins); or: IRE1 knockout in mouse brain accelerates senescent cell accumulation and cognitive decline - the S-nitrosylation of IRE1 increases with age, inhibiting its RNase activity (SNO-IRE1), so de-nitrosylation might be a target.
• duplicate key proteostasis genes to have extra copies, including folding chaperones but probably also other chaperones, to have extra copies of chaperones in case of genome DNA damage.
• TODO: process gerontology research group (GRG) retrieval augmented generation (RAG) results
• TODO: estrogen, estrogen receptors, estrogen signaling, pathways downstream of estrogen.
• adiponectin ADIPOQ promoter SNP rs17300539-A (ref) -- "genetic variants in ADIPOQ that influence adiponectin levels may contribute to this rare phenotype of exceptional longevity"
• Sardinian centenarian G6PD (glucose-6-phosphate dehydrogenase) deficiency doesn't seem to be highly associated with longevity based on recent studies, although was previously reported as a positive association.
• dNsun5 RNAi improves lifespan (ref, PMC version) re: NSUN5. yeast Rcm1 (NSUN5 ortholog) methylates C2278 in 25S (LSU) rRNA. Loss of that methylation changes ribosome structure near the LSU catalytic core and shifts which mRNAs are efficiently translated, enriching oxidative-stress programs. NSUN5 is an RNA cytosine-5 methyltransferase (SAM-dependent) that targets a single conserved cytosine in large-subunit rRNA, namely NSUN5. There are many other rRNA base methyltransferases like NSUN5, DIMT1, BUD23, and METTL5. Most 2′-O-methylation and pseudouridylation in eukaryotic rRNA is guided by snoRNAs via large RNP machines (not one enzyme per site). When NSUN5 activity is reduced, ribosomes lack one specific m⁵C mark in large-subunit rRNA. Those ribosomes translate most housekeeping mRNAs slightly worse but translate stress-response and redox-maintenance mRNAs disproportionately better. The result is a proteome biased toward maintenance rather than growth. Reduce NSUN5 activity, but do not eliminate. Switch from ribosomal speed towards ribosomal accuracy even if slower, but only after development or adolescence.
• look at snoRNA knockout or otherwise managing nucleolus hypertrophy somehow?
• TODO: hypermorph NOP56 to counter age-related ribosome biogenesis decline?
• TODO: hypomorph MYBBP1A to reduce nucleolar stress signaling?
• TODO: intermittent MG132 (proteasome inhibitor) to clear nucleolar aggregates?
• TODO: hypothetical nucleolar transfer via cell therapy to deliver healthy nucleolus?
• HLA-DQB1 (major histocompatibility complex, class II, DQ beta 1) rs41542812 rs1049107 rs1049100 rs3891176 (ref). "HLA-DQB1 contained 5 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular protein domains, exon 4 encodes the transmembrane domain, and exon 5 encodes the cyto-plasmic tail. All four novel variants in HLA-DQB1 are functional missense mutations. These four variants, rs41542812 (Gln158His), rs1049107 (Gly157Ser) and rs1049100 (Val148Ile), lays in β chain of HLA-DQB1. Variety in β chain may change the binding site for special antigen, which plays a key role in maintaining internal homeostasis in vivo, such as lipid homeostasis. In addition, rs3891176 (Ala29Ser), located in exon 1, may change the function of the leader peptide and transform the signal that HLA-DQB1 received. ... We speculated that the HLA-DQB1 variants decreased the expression and/or antigen binding function of the HLA Class II antigen DQ protein β chain on the Antigen Presenting Cell (i.e., the macrophage), reduces the cytokines released by T-lymphocytes, thus reducing liver cell synthesis and release of cholesterol, to maintain the balance of cholesterol metabolism in vivo. This theory remains to be studied more in depth to obtain the corresponding evidence."
• maybe but uncertain - HLA-DRB5 rs71549220 (ref)
• TODO: process Exome sequencing of three cases of familial exceptional longevity (2014)
• TODO: Insights from Brazilian supercentenarians (2026)

Overexpression of SIRT3 in cell culture reduces oxidative stress, enhances respiration, and increases expression of beneficial regulators like FOXO3A. However, SIRT3 transgenic mice are not longer-lived but are more resilient to stress like mitochondrial acetylation challenges.

overexpression of OPA1 shows extended lifespan (ref) and resistance to oxidative stress (ref)

The localization of polymerase theta (Polθ) to mitochondria increases with oxidative damage. Polθ may be involved in facilitating mtDNA replication under oxidative stress but this process is error prone. Can we make a version of polymerase theta that is less error prone? Can mtDNA be repaired or replicated without polymerase theta (can we safely knock it out)?

CD38 knockout mice maintain higher tissue NAD+ levels with age compared to wild-type, with improved mitochondrial respiratory rates and preserved metabolic function during aging. Genetic deletion of Cd38 reduced ovarian aging markers, enhanced NAD+ levels in ovarian tissue, preserved follicle reserve, and extended reproductive lifespan in mice.

NAMPT overexpression increases NAD+ levels, enhances SIRT1 activity, reduces p53 acetylation, and improves resistance to oxidative stress (ref)

USP30 knockout for better mitophagy?

Big mice die young but large animals live longer

human eunuchs live 14-19 years longer especially when castrated young. castration delays epigenetic aging and feminizes DNA methylation patterns. Sterilization and contraception increase lifespan across vertebrates .

Comparative biology of maximum lifespan

from ref:

Number of species	Taxa	Technique	Discovery	Reference
98	vertebrates	Molecular	Telomere length declines with age in vertebrates, but the relationships are weak and variable across taxonomic classes	112
44	vertebrates	Molecular	Immune function generally declines with age in mammals and birds	57
193	vertebrates	Genomics	Genes related to the cell cycle, immune response, DNA repair and transcription are important for cancer resistance	143
65	fish	Genomics	Positive correlation between MLS and the ratio of tumor suppressor to oncogene copy number	161
88	rockfish	Genomics	Positive selection of DNA double-strand break repair pathways and increased CpG to TpG mutations in long-lived rockfish	5
34	rockfish	Genomics	Negative correlation between MLS and the mitochondrial mutation rate	129
23	rockfish	Genomics	Insulin signaling and aryl-hydrocarbon metabolism modulate longevity	32
67	mammals	Experimental	Longer-lived species are more resistant to protein oxidation.	131
16	mammals	Experimental	Positive correlation between MLS and ROS resistance	35
6	mammals	Experimental	Positive correlation between MLS and cellular senescence upon DNA damage induction	109
28	mammals	Molecular	Positive correlation between MLS and red blood cell lifespan	111
10	mammals	Molecular	Positive correlation between MLS and NRF2 signaling activity	135
8	mammals	Molecular	Negative correlation between MLS and telomere shortening	122
8	mammals	Molecular	Power law between MLS and the telomere shortening rate	123
8	mammals	Molecular	Mitochondria of long-lived species have lower protein abundance of complex I subunits and reduced levels of voltage-dependent anion channels	125
8	mammals	Molecular	Positive correlation between MLS and mitochondrial base excision repair	126
6	mammals	Molecular	Long-lived species have increased levels of macroautophagy and heat shock proteins	102
168	mammals	Genomics	Negative correlation between MLS and methionine usage in mitochondrial DNA-encoded proteins	124
63	mammals	Genomics	Naked mole-rats have the highest number of cancer gene copies in their genomes	160
36	mammals	Genomics	Insulin/IGF-1 signaling, immune response-related pathways and cancer resistance are associated with longevity	31
36	mammals	Genomics	Genes related to DNA damage, lipid metabolism and the ubiquitin–proteasome system show evolutionary patterns associated with longevity	28
25	mammals	Genomics	Genes involved in lipid metabolism and collagen-associated vitamin C binding show strong levels of amino-acid conservation in long-lived species.	29
16	mammals	Genomics	Inverse scaling of somatic mutation rates with lifespan	70
5	mammals	Genomics	Negative correlation between MLS and mutation frequency	71
125	Mammals, 90 dog breeds	Epigenomics	Reciprocal relationships between MLS and the average rate of change in methylation in bivalent promoters	88
24	mammals	Epigenomics	Association between MLS and the rate of DNA methylation drift	87
6	mammals	Epigenomics	Negative association between longevity and the rate of DNA methylation changes at age-associated sites	84
4	mammals	Epigenomics	Faster accumulation of epigenetic disorders in short-lived species compared to long-lived species	85
103	mammals	Transcriptomics	Pathways related to translation fidelity and the expression of methionine restriction-related genes correlate with longevity	95
41	mammals	Transcriptomics, metabolomics	Positive correlation between MLS and the expression of genes related to translation and base excision; negative correlation between MLS and the expression of genes related to the TCA cycle, oxidative phosphorylation, insulin processing and ubiquitin‑mediated proteolysis	36
41	mammals	Transcriptomics	Identification of genes and pathways correlated with MLS	37
33	mammals	Transcriptomics	Negative correlation between MLS and mitochondrial, fat and amino-acid metabolism in the liver, as well as inositol and calcium signaling in the brain	41
29	mammals, 26 rodents	Transcriptomics	A significant portion of aging-related changes in gene expression is beneficial for longevity	42
8	mammals	Transcriptomics, proteomics, metabolomics	Long-lived species downregulate mTORC1 activity	103
8	mammals	Transcriptomics	Positive correlation between MLS and DNA maintenance/repair and ubiquitination pathways	34
4	mammals	Transcriptomics	Long-lived species have higher PCBP1 levels in immune cells, protecting them from free iron and ROS	60
12	mammals	Proteomics	Negative correlation between MLS and proteome turnover	98
26	mammals	Metabolomics, lipidomics	Long-lived species have low levels of polyunsaturated triacylglycerols, low levels of tryptophan degradation products, low levels of brain amino acids, high levels of sphingomyelin and a high urate to allantoin ratio	4
11	mammals	Metabolomics	Long-lived species have reduced plasma levels of methionine, cystathionine and choline; increased levels of nonpolar amino acids; reduced levels of succinate and malate; and increased levels of carnitine	46
7	mammals	Metabolomics	Long-lived species have low concentrations of methionine and its derivatives, a low amino-acid pool and a low concentration of choline	45
35	mammals	Lipidomics	Higher saturation of sphingolipids may protect long-lived species from oxidative damage	54
191	mammals	Observational	Carnivorous mammals have increased cancer-related mortality	16
110	dog breeds	Molecular, genomics	Positive correlation between MLS and mitochondrial efficiency	128
864	dogs	Epigenomics	Short-lived giant dogs exhibit a faster loss of DNA methylation at LINE1s	92
12	bats	Experimental, genomics	Amino acid changes in MYD88 dampen the TLR2-dependent inflammatory response	68
4	bats	Molecular	Bats show telomerase activity in fibroblasts and tissues	115
37	bats	Genomics	Gene loss of epithelial α and β defensins, NKG2D ligands and the PYHIN gene family in bats	66
6	bats	Genomics	Loss of pro-inflammatory NF-κB regulators and expansion of antiviral APOBEC3 genes in bats	67
26	bats	Epigenomics	Negative association between longevity and the rate of DNA methylation changes at age-associated sites	86
18	rodents	Experimental	Long-lived species have improved DNA double-strand break repair mediated by SIRT6	73
18	rodents	Experimental	Long-lived species and species with a larger BM require more oncogenic hits to form tumors	144
17	rodents	Molecular	Negative correlation between MLS and the frequency of amino-acid misincorporation at the first and second codon positions	96
8	rodents	Molecular	Positive correlation between MLS and the heat shock factors HSP25 and HSF1, as well as the autophagy factors ATG7 and ATG3	101
16	rodents	Molecular	Negative correlation between MLS and IGF-1R levels in the brain	106
15	rodents	Molecular	Negative correlation between BM and telomerase activity	116
15	rodents	Molecular	Large, long-lived rodents use replicative senescence as an anticancer mechanism, and small, long-lived rodents use alternative mechanisms	117
4	rodents	Molecular	No decline in telomere length with age in the naked mole-rat	118
26	rodents	Transcriptomics	Longevity genes are regulated by pluripotency factors and are upregulated during reprogramming, and genes that are down-regulated in long-lived species are controlled by the circadian network	38
13	primates	Molecular	No correlation between MLS and ROS production	133
12	primates	Molecular	Positive correlation between MLS and immunoproteasome expression	100
35	birds	Experimental	Long-lived birds are more resistant to stress	130
78	birds	Molecular	Long-lived birds have higher antioxidant levels and lower ROS levels	139
30	birds	Molecular	Change in telomere length, but not absolute telomere length, is correlated with MLS	120
19	birds	Molecular	Negative correlation between MLS and the telomere rate of change per year	119
7	birds	Molecular	Long-lived birds have longer telomeres and are resistant to ROS	121
23	birds	Genomics	Genes related to telomerase, DNA repair, cell cycle progression, RNA splicing and processing, and oxidative stress pathways have high levels of sequence substitutions in long-lived birds	30
107	birds	Lipidomics	Longer-lived birds have longer fatty acid chains and a higher content of monounsaturated fatty acids	53

MLS = maximum life span

The following ideas were generated from the above table about comparative biology of longevity. Not all of these should be overexpressed-- maybe other changes would be more warranted; still the following ideas could provide a place from which to start future work. Note however that the following is only items that were missing from the rest of the longevity page; there are other items that conform to the table that are already elsewhere on the page.

DNA repair machinery overexpression:

• ATM overexpression: ATM kinase coordinates the DNA double-strand break response, phosphorylating downstream targets including p53, BRCA1, and CHK2. Enhancement should improve DSB detection and checkpoint activation. ATM haploinsufficiency accelerates aging phenotypes; extra ATM may improve damage surveillance.
• ATR overexpression: ATR kinase responds to replication stress and single-stranded DNA. Modest overexpression might improve handling of stalled replication forks, a major source of genomic instability during aging.
• BRCA1 overexpression: BRCA1 promotes homologous recombination repair of DSBs and maintains genome stability. Enhancement should improve high-fidelity DSB repair capacity.
• MRE11-RAD50-NBN (MRN complex) overexpression: the MRN complex senses DSB ends and recruits ATM for checkpoint signaling. Enhancement should improve initial DSB recognition and processing.
• XRCC5 (Ku80), XRCC6 (Ku70), PRKDC (DNA-PKcs) overexpression for NHEJ: these proteins form the core non-homologous end joining machinery. Enhancement may reduce DSB persistence, though NHEJ is error-prone compared to HR.
• MUTYH overexpression: MUTYH is a base excision repair glycosylase that removes adenines mispaired with 8-oxoguanine, preventing G:C to T:A transversions from oxidative damage.
• APEX1 overexpression: APEX1 (APE1) is the major apurinic/apyrimidinic endonuclease in base excision repair, processing abasic sites generated by DNA glycosylases.

Proteostasis and chaperone machinery:

• HSF1 overexpression: HSF1 is the master transcription factor for the heat shock response, driving expression of chaperones (HSP70, HSP90, small HSPs) under stress. Enhancement should improve proteotoxic stress resistance, though HSF1 also supports cancer cell proteostasis.
• HSPA1A (HSP70) overexpression: HSP70 is a major ATP-dependent chaperone that prevents protein aggregation and assists refolding. Overexpression has shown benefits in specific stress and disease models.
• HSPB1 (HSP25/HSP27) overexpression: small heat shock proteins act as ATP-independent holdases that prevent irreversible aggregation. Cytoprotective effects demonstrated in multiple contexts.
• STUB1/CHIP overexpression: CHIP (C-terminus of HSP70-interacting protein) is an E3 ubiquitin ligase that triages terminally misfolded proteins from chaperones to the proteasome. Connects chaperone and degradation systems; loss accelerates aging phenotypes.
• LAMP2A overexpression: LAMP2A is the lysosomal receptor for chaperone-mediated autophagy (CMA), which selectively degrades KFERQ-motif proteins. CMA declines with age; LAMP2A maintenance in liver extends healthspan markers. ref
• PSMB8 (immunoproteasome) overexpression in immune cells: immunoproteasome subunits (LMP7/PSMB8) improve antigen presentation and may have broader proteostasis roles in immune aging. Long-lived species show higher immunoproteasome expression.

Mitophagy receptors:

• BNIP3 and BNIP3L (NIX) overexpression: alternative mitophagy receptors that directly recruit autophagosomes to mitochondria independent of PINK1-Parkin. Important for hypoxia-induced and developmental mitophagy. Tissue-specific expression may be optimal (cardiac vs skeletal muscle vs neurons have different requirements).

Inflammaging dampers:

• TNFAIP3 (A20) overexpression: A20 is a deubiquitinase and ubiquitin ligase that terminates NF-κB signaling through negative feedback. Loss causes severe autoinflammation. Enhancement should dampen chronic NF-κB activation while preserving acute inflammatory responses.
• NFKBIA (IκBα) stabilization or overexpression: IκBα sequesters NF-κB in the cytoplasm. Stabilizing IκBα (e.g., by removing phosphorylation sites that trigger degradation) should reduce basal NF-κB tone without eliminating acute responses.
• cGAS (MB21D1) knockdown or STING (TMEM173) knockdown: cGAS-STING senses cytosolic DNA from damaged mitochondria, micronuclei, and retroelements, driving type I interferon and inflammatory cytokine production. Chronic activation contributes to sterile inflammation of aging. Partial dampening (not elimination) may reduce inflammaging while preserving antiviral capacity. Bats show dampened STING signaling via amino acid changes.
• MYD88 partial dampening (hypomorph or specific amino acid changes): MYD88 mediates TLR and IL-1R signaling. Complete loss causes immunodeficiency, but bats show specific MYD88 amino acid changes that modulate inflammatory output without eliminating signaling. A hypomorphic allele or bat-like substitutions could reduce inflammaging while preserving pathogen responses.

Epigenetic maintenance and transposon silencing:

• DNMT1 overexpression: DNMT1 maintains CpG methylation patterns during DNA replication. Age-related decline in DNMT1 fidelity contributes to epigenetic drift. Enhancement should improve maintenance methylation fidelity, though excessive DNMT1 could cause hypermethylation.
• TRIM28 (KAP1) and SETDB1 overexpression: TRIM28-SETDB1 complex deposits H3K9me3 at retroelements and maintains heterochromatin. Loss causes transposable element derepression. Enhancement should maintain TE silencing and heterochromatin stability during aging.
• CBX5 (HP1α) overexpression: HP1α reads H3K9me3 marks and maintains heterochromatin structure. Age-related HP1 decline contributes to heterochromatin erosion and TE activation.
• UHRF1 overexpression: UHRF1 recognizes hemimethylated DNA at replication forks and recruits DNMT1. Critical for maintenance methylation; enhancement should improve methylation inheritance fidelity.

Ferroptosis resistance and membrane protection:

• AIFM2 (FSP1) overexpression: FSP1 (ferroptosis suppressor protein 1) provides GPX4-independent ferroptosis resistance by reducing CoQ10 to trap lipid radicals. Dual enhancement of GPX4 and FSP1 would be synergistic for membrane protection.
• SLC7A11 (xCT) overexpression: xCT is the cystine/glutamate antiporter that provides cysteine for glutathione synthesis, which is required for GPX4 function. Enhancement increases ferroptosis resistance by boosting the glutathione pool.
• ACSL4 knockdown or reduction: ACSL4 incorporates polyunsaturated fatty acids into membrane phospholipids, creating ferroptosis substrates. ACSL4-deficient cells are highly ferroptosis-resistant. This is a "remove the fuel" strategy for reducing membrane peroxidation vulnerability.
• SCD1 overexpression (tissue-targeted): SCD1 (stearoyl-CoA desaturase) produces monounsaturated fatty acids, which are more resistant to peroxidation than PUFAs. Shifting the MUFA:PUFA ratio could reduce membrane vulnerability. Tissue-targeting is essential as SCD1 overexpression has complex metabolic effects.

More mice and murine studies

• TODO: incorporate Murne models of lifespan extension (2004)
• TODO: incorporate Key proteins and pathways that regulate lifespan (2017)
• TODO: incorporate Somatic growth, aging, and longevity (2017)

macrophage migration inhibitory factor knockout (Mif−/−): global deletion of MIF, a pro-inflammatory cytokine. These mice live longer, have reduced systemic inflammation, less hemangiosarcoma, but more amyloidosis.

arginase-II knockout (Arg2−/−) extends lifespan in female mice but not male mice. This Arg2 knockout is a deletion of arginase-II, a mitochondrial enzyme involved in arginine metabolism. Associated with reduced expression of p16INK4a, p66Shc, and S6K1.

GH / IGF-1 / insulin axis (somatotropic signaling)

• Pit1 (Pou1f1) loss-of-function in Snell dwarf mice: global pituitary transcription factor deficiency causing severe GH/PRL/TSH hypoplasia, lifespan extension, reduced IGF-1, enhanced stress resistance.
• Prop1 hypomorphic in Ames dwarf mice: pituitary hypoplasia with reduced GH/PRL/TSH, lifespan increase, lower IGF-1.
• Ghrh knockout in lit/lit mice: defective GH-releasing hormone, decreased GH/IGF-1 secretion, reduced body size, lower cancer.
• Ghr null in Laron dwarf mice (Ghr-/-): complete GH resistance, low systemic IGF-1, lifespan extension.
• Liver-specific Igf1 knockout (L-Igf1 KO): ablation of main circulating IGF-1 source.
• Muscle-specific Igf1r haploinsufficiency (M-Igf1r+/-): reduced IGF-1 signaling in skeletal muscle.
• Adult-onset Igf1r conditional knockdown using tet-off system post-maturity: late-life IGF-1R reduction.
• Igfbp2 overexpression

Crazy longevity ideas

• senscent cell killswitch by designer drugs, "INK-ATTAC and p16::3MR, to allow for drug-inducible suicide genes to selectively eliminate p16ink4a-positive senescence at any time" ref (anti-aging/longevity)

Reproductive systems

Fertility

the following is mostly mouse science:

• BAX knockout (-/-) causes a greater follicular endowmnet and oocyte endowment
• BCL-2 overexpression in oocytes increases the primordial follicular endowment by birth; transgenic bcl-2 mice were generated that overexpress human bcl-2 in an effort to reduce prenatal oocyte loss. The later stage follicular pruning still occurs, of course.
• PUMA (BBC3) knockout: increases germ cell and primordial follicle numbers in embryonic and early postnatal ovaries.
• caspase-2 knockout or inhibition: reduces oocyte apoptosis; knockout mice show increased oocyte survival and larger ovarian reserves in experimental settings.
• increase primordial germ cells (PGCs) founder cell count via time-tuned BMP/WNT priming of the posterior epiblast. BMP4 from extraembryonic ectoderm and WNT3 give epiblast cells competence to become PGCs and induce the core specifiers PRDM1/BLIMP1, PRDM14, TFAP2C. Note that biphasic BMP4 or conditional BMP4 happloinsufficiency or Noggin expression may be necessary to preserve PGC pool size.
• epiblast-restricted overexpression (Sox2-CreERT2) of Prdm1/Prdm14/Tfap2c during the competence window should increase the fraction of cells choosing the PGC fate.
• strengthen chemoattraction, chemotaxis and survival cues during the migration and colonization phase via KITL-KIT upregulation in gonadal ridge or along the migration path, for motility and survival; gonad- or mesentery-restricted CXCL12 overexpression or boosted CXCR4 in PGCs might increase capture efficiency; improve beta1-integrin-ECM engagement via PGC-specific ITGB1 gain-of-function or gonadal fibronectin/laminin overexpression. Note that migration cues and integrins are pleiotropic, so it's important to use cell-type-restricted enhancers or drivers to gate these genetic programs.
• oogonia expansion and meiotic entry timing - extend the mitotic window before meiosis during fetal development: delay STRA8 induction via transient Cyp26b1 expression in the fetal ovary or oocyte-restricted dampening of RA/STRA8 signaling, which could allow for extra mitoses to occur, then there are more oogonia available to be enclosed into primordial follicles.
• oogonia expansion and meiotic entry timing - cell-cyle acceleration in oogonia: drive CDK4/6–Cyclin D activity or lower p21/p27 in germ cells to increase symmetric divisions before meiotic S-phase, ideally paired with enhanced DNA repair.
• follicle assembly and perinatal survival - expand the somatic niche (pregranulosa supply) - cortical Lgr5+ pregranulosa cells (stimulated by RSPO1–WNT4–β-catenin) proliferate (upregulate?) to provide the granulosa pool. RSPO1 overexpression or stabilized beta-catenin in ovarian surface epithelium/Lgr5+ lineages could enlarge the scaffold that encloses more oocytes into follicles.
• follicle assembly and perinatal survival - nudge Notch to improve cyst resolution and produce more one-oocyte follicles - oocyte JAG1 upregulation or granulosa Notch sensitization might increase efficient enclosure and reduce multi-oocyte follicles or follicular atresia.
• follicle assembly and perinatal survival - brief prepubertal YAP1 activation in pregranulosa could enlarge early follicle support without prematurely activating the pool.
• Review: primordial pool of follicles and nest breakdown in mammalian ovaries (2009)
• oocyte apoptosis occurs around fetal/perinatal life when the germline cyst breaks down and only a subset of germ cells become oocytes.
• some oocyte apoptosis is related to DNA damage such as double-strand breaks (oocyte DNA damage checkpoint), and this should probably not be blocked, except to the extent that we can upregulate DNA damage repair (although in pools of millions of oocytes it is unclear if DNA damage repair is an important component to maintaining a large supply). Trp63 (TAp63) loss or Chek2 loss protects primordial oocytes from elimination after irradiation/chemo, if you want to preserve oocytes even with damaged DNA. There might be good reasons to want to preserve mature oocytes with damaged DNA, such as for ooplasm donation or oocyte enucleaton.
• oogonia expansion and meiotic entry timing - raise DNA repair capacity to prevent checkpoint-mediated culling: BRCA1 deficiency shrinks the oocyte reserve, while RAD51 activity promotes survival. transgenic RAD51 or BRCA1 up-tuning (oocyte-restricted, perinatal) could reduce DNA damage response (DDR)-triggered losses during/leaving meiotic prophase.
• during cyst breakdown, many nurse-like germ cells die via a non-apoptotic PCD program (acidification). acidification can be blocked pharmacologically (bafilomycin/concanamycin). In mouse perinatal ovaries, many cyst sister cells behave as nurse cells and die via a non-apoptotic, lysosome/acidification-driven PCD aided by pre-granulosa cells (V-ATPase/cathepsin–dependent).
• autophagy supports oocyte survival: germ cell–specific ATG7 knockout causes major primordial-follicle loss (primary ovarian insufficiency phenotype).
• in growing follicles, granulosa-cell apoptosis is central to atresia. Consider altering granulosa cell apoptosis programs (Fas/FasL system, caspase-3).
• evidence for non-apoptotic RCD (autophagy, pyroptosis, ferroptosis) in the ovary in somatic (granulosa) cells.
• CHK1-dependent elimination (checkpoint-1): CHK1 works semi-redundantly with CHK2 to cull oocytes that carry unrepaired meiotic DNA double-strand breaks (DSBs). In Chk2-/- neonatal ovaries, CHK1 turns on after birth and continues the culling. Inhibiting CHK1 in vitro (see LY2603618) rescues oocyte number in Chk2-/- ovaries but also slows cyst breakdown and slows primordial follicle formation.
• Hippo-YAP/TAZ controls ovarian somatic proliferation and ovary organ scaling; granulosa YAP activity promotes growth, while LATS1/2 restrain it.
• larger ovaries and follicles via growth hormone
• upregulate IGF1 for size, also IGF1 increases ovulated oocyte number

• yamanaka OSKM in hypothalamus prolongs fertility and ovulation in rats -- maybe a way to use systemic administration to activate a OSKM expression program in old age?

• protect the ovary during adolescence and pre-puberty ("anti-burnout") via AMH and mTOR inhibitors and AS101 reduces "burnout" (ref); consider low dose persistent AMH or mTOR inhibition (perhaps targeted to the ovary)

• physiologic fetal pruning needs to be aborted or mitigated somehow, possibly via S1P pathway agonism (ref) or S1P pathway protection

Artificial twinning or genetic predisposition to twinning

• (genomically encoded) AMH antibody to reduce circulating AMH such that FSH can recruit more follicles but potentially accelerating ovarian aging and accelerating menopause.
• increased ovarian sensitivity to FSH (via SMAD3 (TGF-β signaling mediator which tunes the ovary's sensitivity to gonadotropin and biasing towards hyperovulation) and oocyte factors).
• dosage of GDF9 (oocyte-derived growth factor) and BMP15 profoundly controls ovulation rate.
• FSHB) (FSH β–subunit promoter/nearby region) variants are repeatedly associated with having dizygotic twins. Mechanistically, FSHB variants modulate circulating FSH and menstrual-cycle dynamics, plausibly increasing the chance of multiple dominant follicles and therefore two ovulations in one cycle.

Monozygotic twinning rates are increased when the zona pellucida is thinned/breached or with specific culture conditions (such as blastocyst culture, other conditions), pointing to abnormal hatching or delayed splitting as triggers. This ties the mechanism to blastocyst dynamics and zona integrity, not to known maternal alleles. There is also a mechanical method for splitting the human embryo into two separate monozygotic embryos from a published study in the 1990s that a research society censored and demanded that all research data be deleted. oh also he resigned :(.

Fertility goals

• increase fertility
• ovarian hypertrophy, larger ovaries
• more oocytes, more eggs, more primordial follicles, enhanced ovarian reserves, more activated follicles
• more oocyte survival during gestation and pre-pubertal culling
• better DNA DSB repair inside oocytes
• extra ovaries, supernumerary ovaries, access ovaries
• more mature oocytes even with some amount of DNA DSBs or other problems, to use the mature eggs for oocyte donation, ooplasm donation, or oocyte enucleation
• enable further germline genetic engineering
• deliver young mitochondria to aging oocytes, or otherwise optimize mitochondria for 50+ years of support in a cell-cycle-arrested oocyte.
• minimize follicular atrophy, hypoxia, or oxidative stress

Fertility TODO

• somehow cause a pool of mitotically-active oogonial stem cells to survive and persist throughout life (prevent meiotic entry, maintain pluripotency, suppress further differentiation cues, interfere with basement-membrane assembly to keep germ cell nests open and not compartmentalized by follicles, engineer somatic ovarian stroma to express GDNF (glial-cell-line-derived neurotrophic factor) and CXCL12 (two niche factors that maintain spermatogonial stem cells in mammalian testes and are absent in the fetal ovary), impose epigenetic breaks on differentiation, inhibit histone-demethylase KDM4B, and then suppression of TAp63 isoforms or up-regulation of anti-apoptotic BCL2 in the OSC sub-lineage would let extra oogonia survive.)
• for very long lived oocytes, consider amphibian or xenopus oocyte DNA DSB or DDR detection and repair genes and mutations
• could we convert spermatogonial sperm cells into mitotically-active oogonial stem cells to produce oocytes instead of sperm? what about the female imprint pattern?
• add Dsup into human oocytes to protect chromatin and protect from DNA damage (see elsewhere on this page for information about Dsup)
• oocyte-specific deletion of Petn to cause premature follicular activation
• disable Hippo to allow for multiple oocyte activation
• look closer at Hippo in the context of ovarian fragmentation techniques
• FSH overexpression to increase fertility
• disable AMH to increase fertility
• FOXO3 overexpression for enhanced ovarian reserves
• enable or increase human postnatal oogenesis (a controversial subject in fertility science)
• speculation that PCOS (polycystic ovary syndrome) may be related to a larger ovarian follicle pool?
• TODO: consider antibody targets for any of the above, including folliculogenesis, oocyte differentiation, maturation, AMH, follicular atresia, etc.
• TODO: what causes the pre-pubertal drop in follice count or oocyte pool?
• consider GFP expression in oocytes to assist with finding oocytes during future medical procedures
• cortical stroma is largely avascular and has no direct blood supply: arteries penetrate the hilus, branch in the medulla, and then form a fine network that stops at the cortico-medullal border. from there, oxygen, nutrients and drugs must diffuse through the cortical stroma to reach primordial follicles. large animals (sow, cow, ewe) have a thick cortex; the inner third is therefore the most hypoxic and most dependent on follicle-derived VEGF for local neovascularization. cortical stroma itself remains virtually capillary-free until follicles are recruited and secrete angiogenic factors.
• dolphin ovary cortical stroma is very thick. significant hypoxia adaptation. Lactate dehydrogenase isoforms are shifted to the anaerobic LDH-5 form, indicating metabolic reliance on glycolysis rather than oxidative phosphorylation. Antioxidant enzyme activities (SOD, catalase, GPx) in dolphin cortical stroma are low and comparable to values measured in cow, and they decline with age, so the same ROS vulnerability exists.
• PCOS may alter stromal vascularity or vascularization.
• programmed or permanent infertility (you'd be making a bet on the development of assisted reproduction technologies in the future, such as creating sperm or eggs from skin cells) (many infertility-causing mutations are known); there are various longevity benefits from certain kinds of eunuch.
• ADAMTS14 rs144724107 is associated with ~10% increased likelihood of female offspring (offspring sex ratio bias)

• anti-aneuploidy:

  • upregulation of CCDC66 might decrease aneuploidy in oocytes (ref)
  • spindle assembly checkpoint (SAC) kinase BubR1 (BUB1B) upregulation protects against aneuploidy, cancer, and extends healthy lifespan

• in mice: Hdac6 overexpression causes older mice to continue to produce larger litters.

• PEPCK-Cmus mice (overexpression of cytosolic PEPCK in skeletal muscle) show a longer window of remaining reproductively active

• ventromedial hypothalamus circuits are essential for female mating behavior

• inhibition of hypothalamic AgRP neurons rescues fertility of diet induced obesity female mice (ref)

Certain genetic changes could be beneficial for the production of human oocytes that are usable for human cloning, ooplasm donation, somatic cell nuclear transfer, in vitro fertilization, etc: more mitochondria, larger oocytes, more ooplasm, various cell cycle intervention "hooks", ..

Crazy ideas for more fertility

• fetal ovarian donation either from clones or fetal ovarian/oocyte donation from an aborted fetus
• extra ovaries, this is genetically difficult to implement.

Pregnancy

TODO: increase predisposition to twinning or maternal-utero compatibility with pregnancies of multiples. see also fertility upregulation in the TODO section below. see also in vitro fertilization (WIP).

Reduced morning sickness during pregnancy

• heightened morning sickness and vomiting: rs1891246, rs790899 -- see Genetic analysis of hyperemesis gravidarum reveals association with intracellular calcium release channel (RYR2)
• "Genetic variants influencing the human chorionic gonadotrophin hormone, serotonin and autoimmune functioning have been proposed as candidates for nausea and vomiting during pregnancy (NVP). It has also been proposed that there is a higher frequency of severe NVP in patients with disorders in taste sensation, in the glycoprotein hormone receptor or in fatty acid transport." from ref

Puberty and sexual characteristics

• age at first sexual intercourse: mutations near or related to ESR1, CADM2 (CADM2 polymorphisms are also associated with information processing speed)

• number of sexual partners: mutations near or related to CADM2

• risk taking behavior (MDFIC)

• gay gene? low p value found via GWAS, but they put it into mice anyway..

Puberty

MKRN3 H420Q precocious/early puberty

puberty timing, check near: MAPK3, PXMP3, VGLL3, ADCY3-POMC, LIN28B

rs246185 near MKL2 on chromosome 16p13.12 might be associated with 2.1 weeks earlier menarche, arrests early puberty, also impacts male genital development

puberty block: global kisspeptin (kiss1) knockout, global GPR54 (Kiss1R) knockout, conditional (targeted to ARC or APV neuron) Kiss1 deletion or suppression (ref), dicer ablation in Kiss1 neurons

delayed puberty via suppression of GnRH neurons before puberty

for each year of delayed puberty there is a +9 month longevity boost

turn off GnRH neurons (or have them dedifferentiate or change identity) via dominant negative FGFR expression? (ref); or beta1-integrin ablation in GnRH neurons? targeted ablation of GnRH neurons via cell-type-specific expression of diphtheria toxin receptor (DTR) or caspase?

block pituitary response to GnRH via GnRH receptor (GnRHR) knockout

GnRH1 knockout - direct elimination of the primary GnRH peptide.

other possibilities:

• Neurokinin B (NKB/TAC3) knockout: remove the upstream signal for GnRH expression.

• pituitary hormone disruption: eliminate and knockout LH beta subunit (LHB), or FSH beta subunit (FSHB); common glycoprotein alpha subunit (CGA) knockout (to affect both LH and FSH); or pituitary-specific transcription factor knockouts (SF1, PROP1, POU1F1).

• gonadal steroidgenesis blocking (testosterone, estradiol, steroidogenesis regulators, etc..), not entirely recommended.. was the goal eunuch? see separate eunuch section.

• anti-mullerian hormone (AMH) overexpression can suppress gonadal function

• gonadal development: gonadotropin receptor knockouts (LHCGR (LH/hCG receptor), FSHR (FSH receptor))

• germline-specific ablation or apoptosis etc.

• synthetic transcriptional repressors or designer proteins to silence pubertal gene networks

Puberty blockers can also be used to make "perma puppies" that don't go through puberty or mature into adulthood.

TODO: make puberty optional or subject to a master control switch via inducible expression techniques. Let the child trigger puberty whenever they want: wait 5 more years? wait 20 years?

Delay puberty by a substantial amount: look at mutations in/around ZNF483, GPR83 (a G protein‐coupled receptor) related to GnRH neurons (GPR83 seems to modulate signaling of MC3R, which is known to sense nutritional signals). Also LIN28B, MKRN3, KISS1, rs364663 at the LIN28B locus (effect ≈ 0.089 years per allele). Delayed puberty has been found in families with mutations in or around FGFR1, GNRHR. Mutant HS6ST1. Familial delayed puberty via disruption of GnRH neuronal migration during embryonic development and IGSF10 from a Finnish family.

Menstruation and menstruation pain (dysmenorrhea)

reduce pain in the uterus (dysmenorrhea) via NaV1.7 (SCN9A) congenital pain insensitivity modifications targeted to the uterus? conditional expression based on systemic drug to activate it? It would be interesting to be able to re-activate the SCN9A nociceptors in the uterus during pregnancy.

TRPV1-lineage primary afferents drive pelvic tactile allodynia in endometriosis and VEGF-driven uterine pain models; maybe TRPV1 antagonism or neuron-specific manipulation could blunt uterine pain?

maybe an oxytocin-linked contractility pathway is responsible for some of the pain? (ref) Consider uterus-targeted COX-2 inhibition, knockout, or reduction.

reduce or disable dysmenorrhea (primary locus might be NGF, IL1A, and IL1B). pain severity seems to be associated with nerve growth factor (NGF) mutations (ref).

Another way to reduce mensturation pain is to surgical (but could possibly be replicated by genetics): ovarian denervation for dysmenorrhoea, presacral neurectomy but high risk of complications including constipation and urinary dysfunction, laproscopic uterine nerve ablation is another option but has not been found to eliminate the pain suggesting that the source of menstrual pain may have multiple origins. Also the laproscopic uterine nerve ablation apparently only offers short-term pain relief (12 months) (ref)??

TODO: disable menstruation by switching human biology to estrus instead of menstruation. This will be difficult. Separately, menstruation can be disabled by exogenous systemic oral contraceptives (Lybrel, Seasonique), progestin-only methods (hormonal IUD, depot medroxyprogesterone acetate (Depo-Provera), etonogestrel implant, and we could express the hormone endogenously if we want to add that. Direct physical endometrial ablation or hysterectomy is an alternative option.

Menopause

delayed age of menopause: rs13196892 located between genes TXNDC5 and MUTED is associated with delayed age of menopause, and rs6467223 in TNPO3 is also associated with delayed age of menopause.

TODO: age of menopause mutations (ref, ref, ref). While most of these are regarding premature menopause, it may be possible to find some mutations in these data sets related to delayed or older menopause and even extended fertility windows.

maybe: optional or delayed menopause, such as through ovarian time travel where you cryopreserve one of the ovaries early in life and then implant it 50 years later to use your younger ovary later. This is not a genetic change.

See also puberty blocking genetics.

Sexual characteristics

mammary and breast size: http://www.snpedia.com/index.php/Breast_size and ref - see rs7816345, rs4849887, rs17625845, rs12173570, rs7089814, rs12371778, rs62314947, rs7089814(C;C), rs4665972(C;C), rs4849887(C;C), rs2819348(T;T), rs17356907(A;A), rs34479159(T;T), rs10488023(A;A), rs61159171(C;C), rs61280460(A;T), rs4820792(C;C), rs7837045(A;C), rs17625845(T;T), rs1529102(C;T), rs7102705(A;G), rs7104745(A;A), rs12585963(A;A), rs62314947(C;T)

erectile dysfunction risk - rs57989773 near 6q16.3 between MCHR2 and SIM1 (ref)

rs193536 - might impact male genitals and TF binding

The embryonic genital tubercle is the shared primordium of penis/clitoris. Sonic hedgehog SHH from urethral epithelium maintains a proliferative mesenchymal progenitor pool; loss shrinks the organ by ~75% via lengthened cell cycle. WNT5A also drives outgrowth and urethral tubulogenesis. HOXA13/HOXD13 dosage is essential for genital tubercle formation. Androgen signaling (androgen receptor signaling via SRD5A2-mediated DHT) masculinizes the genital tubercle. Androgen receptor loss (Tfm) (such as AR knockout) yields female-typical external genitalia. In mouse, SRD5A2 loss can be partly buffered by testosterone. Androgen biosynthesis plays some role in addition to androgen receptors.

in mice: (1) genital tubercle outgrowth via SHH, beta-catenin, WNT signaling, (2) masculinization.

Regulation of external genitalia development (2019)

mouse - Delineating a conserved genetic casette promoting outgrowth of body appendages. Note that the genital tubercle is larger in the AER-R26Fgf8-GOF (gain of function) embryos which also show excessive limb development. There is also in one figure a postaxial extra digit in the forelimb. "To compare the function of FGF8 in the limb and GT, we mated the R26Fgf8 allele with a transgenic Msx2-Cre line [35], which confers Cre expression in the forming and mature AER and the ventral limb ectoderm. As expected, the AER-R26Fgf8-GOF mutants exhibited excessive limb growth and developed extra digits (asterisk in Figure 3J), an enlarged calcaneus bone (arrowhead in Figure 3K), and ectopic skeletal elements (arrows in Figure 3J–3K, and Figure S4G) in both forelimbs and hindlimbs. These overgrowth phenotypes are similar but more severe than what has been observed in the AER-Fgf4-GOF embryos, and further support the concept that FGF8 plays a pivotal role in promoting the outgrowth of both appendages."

prostate volume - rs11736129 (ref), SYN3 locus.

in mice, prostate size is determined by prolactin and the MYC/miR-32 axis. ejaculate volume possibly driven by FGF3 overexpression (enlarged seminal vesicles and other accessory glands). See this review of mouse male reproductive phenotypes of genetically altered mice.

finger length / finger digit ratio SNPs:

• rs314277 LIN28B
• rs7759968 LIN28B ??
• rs2332175
• rs4902759 upstream of SMOC1

Muscle

Muscle hypertrophy

Muscle hypertrophy can be achieved through myostatin inhibition or knockout of myostatin.

There are a number of options here, but with germline modification, a muscle-specific knockout of ACVR2B or myostatin are good choices.

Also follistatin overexpression in muscle.

myostatin and follistatin and muscle hypertrophy, downregulation of activin type II receptor (ActRIIA/B) (targeted by bimagrumab).

Muscle hyperplasia

As an alternative to muscle hypertrophy, you could instead increase muscle cell progenitors and increase the number of myocytes in the limbs or certain muscle groups (muscular hyperplasia).

TEAD1 (Hippo pathway effector complex partner): myofiber-specific TEAD1 overexpression drives a dramatic satellite-cell hyperplasia (many more Pax7+ cells) without increasing muscle size at baseline. This primes tissue for larger regenerative output because there are more myoblasts available to form new fibers.

Fn14 Tnfrsf12a (TWEAK receptor) in satellite cells increases satellite cell proliferation/self-renewal during injury.

beta-catenin activity is critical for determining myofiber number during myogenesis in embryogenesis.

Tcf4+ fibroblasts / PDGFRα+ FAPs regulate myogenesis and can bias fiber formation during development and regeneration. (ref)

A missense mutant myostatin causes hyperplasia without hypertrophy in the mouse muscle (2002) (myostatin C313Y)

Note: in both muscular hypertrophy and muscular hyperplasia, it is important to check what happens to the heart, or to specifically exclude the heart from targeting.

Muscle strength

muscle-targeted IGF1 overexpression (various promoters: mIGF-1, α-actin, MCK) increases postnatal muscle mass and strength; multiple lines report larger fibers and higher tetanic force, and protection from age-related weakness. Mechanistically linked to AKT/mTOR.

FOXO family (muscle catabolism gatekeepers): FoxO1/3/4 triple knockout mice maintain or increase strength into aging by suppressing atrophy programs (UPS/autophagy genes). Earlier work shows FoxO loss protects from muscle loss.

inducible/conditional muscle AKT1 activation causes fiber hypertrophy and higher strength, especially in fast glycolytic fibers. myr-AKT1 models show increased grip/peak force and IIb fiber growth.

enhancing ACTN3 (α-actinin-3 "power gene") function or maintaining fast-fiber identity is pro-strength.

conditional Ctnnb1 (beta-catenin) studies show it's critical for fetal myogenic progenitor number and eventual myofiber output, which will secondarily set attainable strength.

in human:

• power/strength markers: ACE Alu I/D (rs4646994) (called ACE D); ACTN3 Arg577; AMPD1 Gln12; HIF1A 582Ser; MTHFR rs1801131 C; NOS3 rs2070744 T; PPARG 12Ala;
• rs2854464 AA individuals were ~2% stronger than G-allele carriers (ref)
• muscular strength - https://www.biorxiv.org/content/early/2017/10/10/201020 - mutations near FTO, SLC39A8, TFAP2B, TGFA, CELF1, TCF4, BDNF, FOXP1, KIF1B, ANTXR2, etc.
• better knee extension strength (see table 2) in age 60 years or older:
  • TACC2 rs10749438-G
  • ADIPOR1 rs141279361-C
  • FSHR/NRXN1 rs77607073-G
  • CRBN/LRRN1 rs147964289-A
  • CBLB rs141616911-C
  • IQCJ/IQCJ-SCHIP1 rs138068168-T
  • CCDC149 rs11942832-T
  • KLHL5/WDR19 rs118050709-C
  • LINC02057/ZSWIM6 rs1289351462-A
  • F2RL1 rs2243036-A
  • FER rs61093400-G
  • MAML2 rs6483495-G
  • TBX3/MED13L rs182016826-T
  • SERTM1/RFXAP rs117436582-A
  • EGLN3/SPTSSA rs76373752-C
  • CHTF8 rs3743680-C
  • GTSCR1/LINC01541 rs148814682-T
  • DMD rs1718047-A

Muscle (hyper)innervation

Note that muscles naturally pull in more innervation on its own when growing, although only to a point. Myostatin null mice show more total axons and more motor axon innervation. By comparison, muscle IGF1 increases muscle mass but not innervation.

• hyperinnervation via muscle GDNF overexpression but no behavior changes reported.
• LRP4 overexpression in muscle improves neuromuscular junction (NMJ) structure/innervation. increased grip strength, hanging time, and running distance.
• DOK7 overexpression enlarges neuromuscular junctions, increases innervation, improves motor function. improved rotarod performance and plantarflexion torque. enhanced motor activity and extended lifespan.
• PGC-1α remodels NMJ morphology to look more "training-like" phenotype (PGC-1α isoform induced by resistance training regulates skeletal muscle hypertrophy)
• high MuSK overexpression in muscle (HSA::MuSK transgene): leads to ectopic AChR clusters and synapses throughout the muscle; motor axons branch to contact these sites, and synapses form even without agrin, rescuing lethality in agrin mutants (i.e., more synapses than normal patterning would allow
• more neuromuscular junction formation via muscle-wide secretion of transgenic "mini-agrin"
• excessive phrenic nerve branching and innervation of ectopic diaphragm muscle via motor neuron Neuropilin-1 (Npn-1) loss
• Pten deletion in motor neurons: hypertrophic axons/nerve and accelerated recovery of axon numbers after facial nerve injury; baseline terminals enlarged (a sprouting-prone phenotype).

Early in development, each endplate is initially polyneuronal but undergoes synapse elimination to end up mono-innervated. Is this necessary? Can it be eliminated?

Muscle metabolism

PEPCK-C overexpression: In muscle, this allows greatly improved metabolism and endurance (see "mighty mice"). Synergistic effect with myostatin inhibition is untested.

Sprinting vs endurance

• alpha-actin-3 (actinin) for endurance and increased power in sprinters (Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation) ("The results showed that the skeletal muscle of people lacking α-aktinin-3 had a greater proportion of slow-twitch fibers. When they were in the process of cooling, these people were able to maintain their body temperature in a more energy-efficient way. People who lack α-aktinin-3 rarely succeed in sports requiring strength and explosiveness, while a tendency towards greater capacity has been observed in these people in endurance sports.")
• ACTN3 - sprinting vs endurance - rs1815739
• ACTN3 - could we make sprinting vs endurance changes in ACTN3 something that could be genetically switchable in adult if delivered as a germline alteration?
• endurance: ACE Alu I/D (rs4646994) (called ACE I); ACTN3 577X; PPARA rs4253778 G; PPARGC1A Gly482;
• endurance: ERRγ overexpression increases running endurance, robust angiogenic program and neovascularization, strong induction of genes for fat metabolism, mitochondrial respiration. -- "How type I skeletal muscle inherently maintains high oxidative and vascular capacity in the absence of exercise is unclear. We show that nuclear receptor ERRγ is highly expressed in type I muscle and, when transgenically expressed in anaerobic type II muscles (ERRGO mice), dually induces metabolic and vascular transformation in the absence of exercise. ERRGO mice show increased expression of genes promoting fat metabolism, mitochondrial respiration, and type I fiber specification. Muscles in ERRGO mice also display an activated angiogenic program marked by myofibrillar induction and secretion of proangiogenic factors, neovascularization, and a 100% increase in running endurance. Surprisingly, the induction of type I muscle properties by ERRγ does not involve PGC-1α. Instead, ERRγ genetically activates the energy sensor AMPK in mediating the metabovascular changes in ERRGO mice. Therefore, ERRγ represents a previously unrecognized determinant that specifies intrinsic vascular and oxidative metabolic features that distinguish type I from type II muscle." ERRγ promotes robust AMPK activation in the absence of exercise. ERRγ transgenesis confers running endurance and resistance to diet-induced obesity.
• "Regulation of muscle fiber type and running endurance by PPARδ (PPARdelta)" -- "We describe the engineering of a mouse capable of continuous running of up to twice the distance of a wild-type littermate. This was achieved by targeted expression of an activated form of peroxisome proliferator-activated receptor δ (PPARδ) in skeletal muscle, which induces a switch to form increased numbers of type I muscle fibers. Treatment of wild-type mice with PPARδ agonist elicits a similar type I fiber gene expression profile in muscle. Moreover, these genetically generated fibers confer resistance to obesity with improved metabolic profiles, even in the absence of exercise."; there are even pharmaceutical PPARd agonists. AMPK agonists are also exercise mimetics.

Muscle TODO

• MCK-PPARβ/δ mice are known to have enhanced exercise performance; MCK = muscle creatine kinase; PPAR = the nuclear receptors peroxisome proliferator-activated receptor α. "lactate dehydrogenase b (Ldhb)/Ldha gene expression ratio is increased in MCK-PPARβ/δ muscle, an isoenzyme shift that diverts pyruvate into the mitochondrion for the final steps of glucose oxidation. ... MCK-PPARβ/δ muscle was shown to have high glycogen stores, increased levels of GLUT4, and augmented capacity for mitochondrial pyruvate oxidation, suggesting a broad reprogramming of glucose utilization pathways. Lastly, exercise studies demonstrated that MCK-PPARβ/δ mice persistently oxidized glucose compared with nontransgenic controls, while exhibiting supranormal performance." (additional ref 2015)
• hormone targeting
• muscle injury repair and satellite cells
• creatine metabolism?
• muscle recruitment stuff
• genomically encoded exercise mimetics
• NCoR1 suppresses oxidative metabolism and mitochondrial biogenesis in muscles. Muscle-specific NCoR1 knockout increases muscle mass, shifts toward a more oxidative program, and increases mitochondrial number/activity with improved exercise endurance (ref, ref).

target gain-of-function or overexpression of MCT4 (SLC16A3) for lactate export from glycolytic tissues (fast-twitch muscles). In some cancers, SLC16A3 is upregulated possibly helping cancerous cells to export lactate.

gain-of-function of COX7RP is assumed to enhance exercise endurance in mice and humans (ref)

Some of the following proposals are based on findings from this study: Metabolic GWAS of elite athletes reveals novel genetically-influenced metabolites associated with athletic performance

TGR5 overexpression in skeletal muscle: Transgenic muscle-specific overexpression or knock-in of a constitutively active TGR5 (bile acid receptor) variant could enhance muscle differentiation and hypertrophy. TGR5 is exercise-inducible, and its activation improves skeletal muscle function while improving cardiac adaptability to hemodynamic stress. Constitutive activation via transgenic approaches would bypass the need for endogenous bile acid ligands, potentially providing sustained anabolic signaling for increased power output and muscular hypertrophy. Ileal FXR or FGF15/19 expression: Intestine-specific transgenic overexpression of FXR, or direct transgenic expression of FGF15 (murine)/FGF19 (human), could amplify bile acid metabolic signaling. Ileal FXR-FGF15/19 signaling activation improves skeletal muscle mass and strength in aged mice, demonstrated via the intestine-selective FXR agonist fexaramine. INcreases muscle protein synthesis and oxidative capacity.

UGT1A1 hypomorphic knock-in (engineered Gilbert syndrome): hypomorphic UGT1A1 variants (mimicking the promoter polymorphisms seen in Gilbert syndrome) could induce mild, controlled hyperbilirubinemia. Gilbert syndrome-like mice show protection from diet-induced obesity, insulin resistance, and fatty liver. Bilirubin and biliverdin are potent endogenous antioxidants; reviews explicitly propose that elevated bilirubin may enhance exercise performance, noting higher bilirubin prevalence in endurance athletes.

Creatine transporter (SLC6A8) or GAMT overexpression: Transgenic overexpression of SLC6A8 (creatine transporter) in skeletal muscle, or GAMT (guanidinoacetate methyltransferase) to enhance endogenous creatine synthesis, could amplify intramuscular creatine and phosphocreatine stores. Guanidinoacetic acid supplementation increases creatine and improves repeated-sprint ability by boosting phosphocreatine-mediated rapid ATP regeneration. The opposite intervention (β-GPA-induced phosphocreatine depletion) causes metabolic remodeling toward fatigue resistance and can induce torpor-like states, suggesting creatine metabolism transgenic modifications could be tuned for either explosive power or endurance phenotypes. GAMT is also involved in creatine by methylating GAA in the liver to create creatine.

AGAT produces guanidinoacetate (GAA) from arginine + glycine. Improving the function of AGAT may also improve creatine biology and muscle physiology. SLCO1B3/SLCO1B7 are hepatic uptake transporters that among other things transport guanidinoacetate into hepatocytes to make creatine from guanidinoacetate. Tweaking SLCO1B3/SLCO1B7 might also be warranted.

SCAD-deficient (Acads-/-) mice accumulate ethylmalonate and short-chain acyl-CoAs; paradoxically protected from diet-induced obesity with improved insulin sensitivity via altered mitochondrial energetics. Because ethylmalonate and the accumulated short‑chain acyl‑CoAs can serve as readily oxidizable anaplerotic fuels that boost mitochondrial respiratory capacity, enhance substrate‑level phosphorylation and stimulate AMPK‑mediated signaling for rapid energy turnover and improved muscle endurance, their elevated levels may give elite athletes a metabolic edge for high‑intensity, sustained performance.

GCPII/FOLH1 knockout mice have reduced NAAG peptidase activity and are protected against nerve injury and ischemic brain damage via reduced glutamate excitotoxicity. GCPII inhibitors increase brain NAAG, activate mGluR3, and improve motor and cognitive outcomes after TBI. GCPII inhibitor BCI-838 mimics the pro-neurogenic and cognitive benefits of physical exercise in AD mouse model, so it's a "exercise mimetic" via NAAG pathway.

KLKB1 (plasma kallikrein) knockout mice protected from thrombosis with altered BAT thermogenesis. Kinin B1 receptor signaling modulates mitochondrial activity during fasting and voluntary exercise, changing VO₂ and heat production. Kallikrein-kinin system tunes exercise hyperemia and vascular efficiency.

Humanized SLCO1B1 (OATP1B1) mice exist for drug disposition studies; bile acid transport affects metabolic signaling.

Steroid & nitrogen metabolism

Trans-chromosomic CYP3A-humanized mice carrying human CYP3A4/5/7/43 cluster recapitulate human fetal→adult expression patterns and human-like DHEA-S/steroid metabolism.

NAT8 overexpression: neuronal NAT8/ATase2 overexpression alters dendritic structure. The goal here would be modulation of metabolite pool. NAT8 is important in elite athlete metabolomics GWAS (N-acetyl-amino acids). Consider: muscle-specific Rosa26-LSL-NAT8 using MCK-Cre for nitrogen buffering?

NAT1/NAT2 double knockout mice show leaner, more insulin-sensitive phenotype with increased energy expenditure. NAT2 determines caffeine acetylator status.

Muscle membrane and recovery

FADS1/FADS2 knockouts show dramatically reduced arachidonic acid in phospholipids, altered eicosanoid/inflammatory profiles. Lower AA-phospholipids associated with elite athletes in GWAS.

S1P (sphingosine-1-phosphate) signaling regulates skeletal muscle regeneration: S1P receptors modulate satellite cell activation, muscle repair, and atrophy. SGPP1 (S1P phosphatase) knockout elevates tissue S1P. Hepatic SPTLC3 knockout depletes d16-sphingomyelins and alters metabolism; cardiac SPTLC3 affects Complex I activity. CERS4 controls ceramide chain-length composition critical for membrane integrity.

VNN1 (Vanin-1) knockout mice have elevated glutathione and enhanced oxidative stress protection.

Succinate biology

The following are some ideas for improving succinate biology. These ideas have not been fully evaluated; this is why these are in a TODO section.

• Overexpress ADAMTS19 in skeletal muscle to remodel the extracellular matrix, increasing interstitial porosity and enabling faster local succinate diffusion to SUCNR1‑expressing cells; this should sharpen succinate signaling and support better vascular and metabolic adaptation.
• Increase SEMA6D activity in endothelial cells to drive richer capillary networks, expanding the tissue sink for circulating succinate and improving oxygen delivery, which together can lower systemic succinate while boosting aerobic performance.
• Boost ATG10 expression in muscle fibers to heighten mitophagy and maintain high‑quality mitochondria; healthier mitochondria will process succinate more efficiently, supporting superior endurance and faster recovery from exercise stress.
• Introduce a hypomorphic reduction of NEK7 to temper NLRP3 inflammasome activation, curbing excessive succinate‑driven inflammation and thereby accelerating post‑exercise repair and enhancing training adaptations.
• Activate a muscle‑specific regulatory element that up‑regulates STK33 (or its downstream pathway) to modestly raise intracellular succinate production, providing stronger HIF‑1α‑mediated angiogenic and metabolic signaling during training.
• Elevate SUCNR1 (GPR91) levels in muscle or vascular endothelium to amplify succinate receptor signaling.
• Stabilize HIF‑1α in muscle by reducing PHD2 activity or expressing a degradation‑resistant HIF‑1α variant, thereby harnessing succinate‑induced hypoxic signaling to enhance glycolytic capacity, vascular growth.
• Modestly inhibit succinate dehydrogenase or increase succinate‑CoA ligase activity in muscle to raise intramuscular succinate concentrations, and then test whether higher succinate levels can act as an exercise‑mimetic signal to drive hypertrophy, angiogenesis, and improved endurance.

Sports-related enhancements

Candidate genes for sports doping

This is lifted from this table from "Gene doping: a review of performance-enhancing genetics" (2007).

Gene/product	System/organ targets	Gene product properties	Physiologic response
ACE	skeletal muscles	peptidyl dipeptidase	ACE-D is involved in fast twitch muscles.
ACTN3	skeletal muscles	actin-binding proteins related to dystrophin	Involved in fast-twitch muscles.
endorphins	central and peripheral nervous system	widely active peptides	pain modulation
EPO	hematopoietic system	glycoprotein hormone	Increases RBC mass and oxygen delivery.
HGH	endocrine system	191-amino acid protein	Increases muscle size, power, and recovery.
HIF	hematologic and immune systems	multisubunit protein	Regulates transcription at hypoxia response elements.
IGF1	endocrine/metabolic/skeletal muscle	70-amino acid protein	Increases muscle size, power, and recovery by increasing regulator cells.
myostatin (MSTN)	skeletal muscle	2-subunit protein	Regulates skeletal muscle. Inhibition increases muscle size, power, and recovery.
PPAR-delta	skeletal muscle and adipose tissue	nuclear hormone receptor protein	Promotes fat metabolism and increases number of slow twitch fibers. See also PPARδ upregulation.
VEGF	vascular endothelium	glyosylated disulfide-bonded homodimers	Induces development of new blood vessels.

Abbreviations: ACE, angiotensin-converting enzyme; ACTN3, actinin binding protein 3; EPO, erythropoetin; HGH, human growth factor; HIF, hypoxia inducible factor; IGF1, insulin-like growth factor; PPAR-delta, peroxisome proliferators-activated receptor (delta); VEGF, vascular endothelial growth factor.

Other genetic changes for sports

• glucagon-like peptide 1 to increase glucose in liver and reduce lactic acid buildups for athletes
• erythropoietin for red blood cell production
• insulin-like growth factor 1
• "an increase in synthesis of monoamines could improve the mood of athletes"
• preproenkephalin for pain reduction
• rs17822931 - dry earwax, sweat production, body odor. "rs17822931(T;T) individuals were at least 5-fold less likely to use deodorant, consistent with them being "genotypically nonodorous"".
• see muscle sections above.

"Elite athletes" GWAS (endurance)

from (Metabolic GWAS of elite athletes table 2 for endurance:

• SULT2A1 (rs10426201): intron variant associated with higher androstenediol (3alpha, 17alpha) monosulfate (2) (androgenic steroid).
• SLC22A16 (rs12210538): missense variant linked to lower dihomo-linoleoylcarnitine (C20:2) (fatty acid metabolism/acylcarnitine).
• SLC22A24 (rs75859219): upstream variant associated with higher etiocholanolone glucuronide (androgenic steroid).
• CYP3A7 (rs45446698): upstream variant tied to higher 16a-hydroxy DHEA 3-sulfate (androgenic steroid).

Theoretical "heterozygote advantages" genes

The principle here is that diseases such as sickle cell or Tay-Sachs, among many others, persist in a population because having one 'good' and one 'bad' copy of the gene offers a significant advantage - in disease resistance, intelligence, etc.

While it would be nice to find a point mutation that would mimic the benefits of heterozygosity, the most straightforward option would be to give someone both variants of the gene, with ~50% expression of each.

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9 -- there is at least one other technique for doing this, perhaps the other one wasn't co-authored by the ex-president of stanford (an independent panel found "manipulation and/or grossly inadequate data handling"? in other research).

Using heterozygous alleles is useful because we know several exact effects of +/- gene dosage, whereas it would take possibly substantial trial-and-error to figure out the exact expression profile to replicate via synthetic gene circuit for expression of that same gene. It's not necessarily "50% expression" merely because the effect is caused by heterozygosity..

It could be possible to program germline genomic programs that cause heterozygotic allele dosage depending on cell type or cell-specific expression throughout development or post-birth gene expression, instead of whole-body heterozygotic allele. So some cells or tissues or organs in the body can be homozygous for the allele while other cells can have different gene dosage and therefore different expression. In general it is probably better to have whole-body heterozyous programming for an allele because you can do upfront sequencing and quality control on the genome before making a fetus, whereas chromosome editing during development (or later in life) will have more moving parts that need to be more carefully quality controlled upfront.

While this document is mainly about germline genetic engineering for whole-body genetic modification, it would also be interesting to consider any beneficial impact from heterozygotic allele gene editing in different cell populations in the adult via adult gene therapy or cell therapy.

TODO: vitamin D linked heterozygotic advantage mutation that allows for escape from accelerated clearance. Causes lower risk of severe respiratory infections and better pregnancy outcomes at high latitude. GC1F/GC1S.

George Church's human genetic engineering wish list

George Church's human genetic engineering wish list

Multigenic traits can have single gene variants -- often rare in populations, (or synthetic alleles absent in nature) with large impacts. Synthetic gene circuits can also provide a monogenic effect.

Genotype: -/- means double-null for the gene (from both mother and father). +/- means one copy ok (+) and one broken (-) is sufficient to have a positive impact. The rest require very specific sequences to see the positive effect. For example E6V means that at position 6 an "E" (Glutamate amino acid codon GAG) is mutated into a "V" (Valine codon GTG).

Gene	Genotype	Protective, resilient or extreme effects	Potential Negatives:
LRP5	G171V/+	Extra-strong bones	Low Buoyancy
MSTN	-/-	Large, lean muscles, low atherosclerosis
FBXO32	-/-	Reduced muscle atrophy	-
MC1R	overprod.	UV radiation resistance	-
TRIM63	-/-	Reduced muscle atrophy	Hypertrophic cardiomyopathy
SCN9A	-/-	Pain insensitive	Unnoticed harm
FAAH-OUT	del/del	Pain insensitive	Unnoticed harm
NTRK1	del/del	Pain insensitive, no sweat	Unnoticed harm, hyperthermia
HSD17B13	+/TA(lof)	Low Chronic Liver Disease
HOXA11	unstated	Augmented manipulation ability with six-fingered hands
ABCC11	-/-	Low odor production
PRNP	G127V	Prion resistance
IFNL4	dG/TT	High Hepatitis C virus clearance
CCR5	-/-	HIV resistance	W.Nile Virus & flu; bone
FUT2	-/-	Norovirus resistance	Crohn's disease
IL23R	R381Q/+	IBD: Crohn's disease, Ulcerative colitis
HBB	E6V/+	Malaria resistance	Exertional rhabdomyolysis
PKU	+/-	Ochratoxin resistance?	Cognitive disability in -/-
CFTR	+/-	TB or other?	GI,Lung issues in -/-
HEXA	+/-	Mycobacteria resistance?	lethal by 4yo -/-
APOL1	+/-	Trypanosoma brucei	Kidney disease risk
APOA1	R173C/+	Low HDL & CVD
PCSK9	-/-	Low coronary disease	Diabetes, Low cognition
GHR,GH	-/-	Low cancer, stature
SLC30A8	-/+	Low T2 Diabetes
IFIH1 = MDA5	E627X/+	Low T1 Diabetes
ANGPTL3	-/+	Lipid and cardiac health
BDKRB2	a/g expression	Deep Diving
PDE10A	c/t incr thyroxine	Breath-hold diving
EGLN1	a/g	High altitude
EPAS1	3.4kb del	High altitude
MTHFR	A222V	High altitude
EPOR	W439X	High oxygen transport
BHLHE41 = DEC2	P385R/+	Less sleep
GRM1	R889W/+ or S458A/+	Less sleep
NPSR1	Y206H/+	Less sleep
ADRB1	A187V	Less sleep
APOE	E2/E2	Low Alzheimer's (E2=R112C, R158C)
APOE	R136S/R136S	Resilience to dominant Alzheimer's PSEN1-E280A
RELN	H3447R/+	Resilience to dominant Alzheimer's PSEN1-E280A
APP	A673T/+	Low Alzheimer's
GLUK4	del/+	Low bipolar, high cognitive
RIMS1	R844H/+	High cognitive	Late onset visual loss
BPIFB4	LAV:I229V/+	Healthspan, low CVD
CETP	I405V/I405V	exceptional longevity & cognitive
SIRT6	A313S or N308K	exceptional longevity
TPH2	g703t	Low aggressiveness / anxiety.
DRD4	exon3 VNTR	Low anxiety, high risk tolerance.
COMT	V158M	Low anxiety, high risk tolerance.	ADHD, headaches, etc
SLC6A4	43bp indel	Low stress, ADHD.	?
BDNF	M66V	Learning.
NR3C1	a>g	Low PTSD risk.
KO, Knock-in, gene therapy	Mice & other mammals
nmrHas2	overprod.	Low aging
CISD2	overprod.	Low aging
BUB1B	overprod.	Low aging
PAWR	overprod.	Low aging
PPARG	overprod.	Low aging
PTEN	overprod.	Low aging
SIRT1	overprod.	Low aging
SIRT6	overprod.	Low aging
SOST	-/-	Bone loss resistance
NPC1	+/-	Ebola resistance
CTNNB1	overprod.	Radiation resistance
TERT	overprod.	Low aging
CDKN2A	overprod.	Low cancer
TP53	overprod.	Low cancer
GRIN2B	overprod.	High learning & memory
NR2B	overprod.	Learning & memory enhancement
ARHGAP11B	human transgene in marmosets	Increased neocortex size & folding
MCPH1	human transgene in rhesus	Human-like brain neoteny
PDE4B	inhib.	Low anxiety, high problem solving
FOXP2	humanized	Learn stimulus-response associations faster
CCR5	-/- & +/-	Enhanced learning, low atherosclerosis, low hepatotox	Flavi- & Orthomyxo- viruses
NLGN3	R451C/Y	Enhanced spatial learning abilities	Impaired social (ASD)
KCNH3	-/- & +/-	Enhanced cognitive function
SP0535	transgenic	improved cognitive ability and working memory
SERPINE1	null/+	Median survival increase from 75 to 85 yr
KL=KLOTHO	gene therapy	Age-related diseases (review-2016)(cognitive-2023)
FGF21	gene therapy	Age-related
sTGFβR2	gene therapy	Age-related
OCT4+SOX2+KLF4	gene therapy	Optic nerve damage recovery
Cognition-related gene therapies
NGF	overprod.	(human) Low Alzheimer's
NEU1	overprod.	(mice) Low Alzheimer's
NGFR	overprod.	(mice) Low Alzheimer's
miR-29b	overprod.	(human cells) Low Alzheimer's
BACE1 siRNAs	overprod.	(mice) Low Alzheimer's
anti-amyloid antibodies	overprod.	(mice) Low Alzheimer's
APPsα	overprod.	(mice) Low Alzheimer's
Based on genome comparisons
Various	Alleles	Parrot longevity & cognition
CHRNA1	W187R	alpha-neurotoxin resistance in Mellivora, Erinaceus, Herpestes, Sus, Naja
NOTCH2NL	Overprod.	Human-specific modifiers of cortical size

Note: Some of the above studies need independent reproduction.

legend: Lower case a,c,g,t are nucleotide variants (typically regulatory), while uppercase indicated amino acid variants.

If you know of additional published or unpublished examples, or anyone who is exceptionally resistance to any disease, or strong familial hereditary traits, please let us know.

Resilience Project, HMS Fairbairn Family Lyme Research Initiative.

geochurch see also list

Longevity: GenAge Database of Ageing-Related Genes

LAV: 30 rare, protective, non-synon mitonuclear Longevity Associated Variants in 18 genes: ITPR1, LRPPRC, ALDOA, MFN2, SPTLC2, ACACB, SAMM50, FAR1, HARS2, ISCU, PMPCB, ATXN3, NDUFS2, ACADM, KIF1B, PRR5L, CYBB, DEPTOR

Height: ~9,500 SNPs explain ~29% of phenotypic variance

Pathogens: CFTR, NPC1, HEXA: Resistance to typhoid, cholera, mycotoxin abortions, enveloped viruses via MOGS, filoviruses, rabies via myasthenia gravis

Space: radiation, low gravity, etc.

geochurch thanklog

Thanks (in chronological order): Joao Pedro de Magalhaes (HAGR), Jason Bobe, Cory Smith, Luke Dabin, Mark Handle, David Thompson, Noah Davidsohn(6), Dimitrie Leustean, Sergiy Velychko, Christopher Schön(3), Chris Mason(3), Michael Shadpour for suggested additions. --GMC

geochurch changelog

26-Oct-2011 4 genes: MSTN, LRP5, PCSK9, CCR5

04-Apr-2012 5 genes: + FUT2

23-Oct-2013 6 genes: + APP

05-Feb-2014 11 genes.

10-Sep-2015 19 genes.

06-Sep-2017 28 genes.

24-Oct-2018 44 genes.

14-Aug-2019 51 genes.

09-Oct-2019 52 genes: + ADRB1

18-Oct-2019 54 genes: + NPSR1 + NTRK1

08-Nov-2019 55 genes: + APOA1

05-Jan-2022 59 genes: + MCPH1 + NOTCH2NL + ARHGAP11B + NR2B

23-Aug-2022 60 genes: + KCNH3

21-Nov-2022 67 genes: + Klotho + CHRNA1 + FGF21 + sTGFβR2 + OCT4 + SOX2 + KLF4

22-Nov-2022 74 genes: + CISD2 + BUB1B + PAWR + PPARG + PTEN + SIRT1 + SIRT6

03-Apr-2023 75 genes: + SP0535

24-Oct-2023 76 genes: + SERPINE1

22-Dec-2023 79 genes: + MC1R, FBXO32, TRIM63

12-Nov-2024 80 genes: + GRM1

07-Sep-2025 86 genes: + TPH2 + DRD4 + COMT + SLC6A4 + BDNF + NR3C1

geochurch space genetics

Space genetics: What if we cure aging and eliminate poverty and diseases of developing nations? We're going to have overpopulation, or at least some people say that. I don't think it's a great solution to say well we're not going to cure diseases of poverty or aging of the industrialized nation. One possibility is going to space. I don't mean this frivolously. It's a good idea for our species because we're at risk from supervolcanoes and asteroids. In space, we have a new set of problems including radiation and low gravity even on Mars. And then there's space genetics issues. We have a consortium on this and space colony challenges.

We have challenges like gravity, osteoporosis, neuro-behavioral issues, microbiome issues.

Kind of a quirky list here. These are rare protective alleles. They are things that make your bones extra strong which could result in something that could help in space, or on earth. Some that reduce pain sensitivity, which you might want to turn on and off, because if you have it off all the time then maybe you end up hurting yourself like kids chewing on their tongues. ABCC11 will give you low odor which might be helpful in space travel contexts. The good version is common in Asian populations.

There are some things that have been tested in animals, like low cancer and high cognitive ability.

What about radiation resistance? Here's a case in the literature where radiation resistance was improved 100,000-fold. 10-fold using e14-deletion. 50-fold using recA. 20-fold using yfjK. And 10-fold using dnaB. See Ecoli, Byrne et al, eLife 2014 ("Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair"). This only requires 4 mutations. There is a wide variation in natural organisms, but the only difference here is those 4 mutations.

Dsup from tardigrades for radiation resistance. Mentioned elsewhere on this page in the DNA damage resistance section as well as the longevity section.

Regeneration

Make a general embryological platform for regeneration. Salamanders achieve this through dedifferentiation but perhaps for human we can achieve this via in vivo maintenance of primordial pluripotent stem cells throughout adult life. There might be other ways to achieve this goal around healing.

Transient inactivation of Rb and ARF yields regenerative cells from postmitotic mammalian muscle

Lack of p21 expression links cell cycle control and appendage regeneration in mice

TODO: maintain primordial pluripotent stem cell pools throughout adult life.

TODO: look at salamander cell dedifferentiation capabilities, can we import that into human cells as a switchable capability?

Just saying "regeneration" is kind of ridiculous, it's like saying "let's add hiberation" -- okay good luck...

TODO

• Tetracycline response elements, i.e. tet-on and tet-off, can be used for transgenes where constant expression is undesirable. While a number of options for such inducible expression exist, the tet system is the most studied. It is left as an exercise to the reader to determine which genes would be suitable candidates [I will add some when I get around to it (editor's note: 13 years later.... Also DREADDs might allow for higher multiplexing or bandwidth?)].

• l-gulonolactone oxidase knock-in (re-enable human synthesis of vitamin C) http://www.anti-agingfirewalls.com/2018/03/11/double-gene-knockout-behind-obesity-epidemic/, or via GULO

• retinoid conversion: BCMO1

• Engineering into human genome the capability to synthesize essential amino acids, essential fatty acids and essential vitamins ("synthesizing a prototrophic human genome")

• refactor critical enzymes that use bizarre minerals or other uncommon elements to use more normal biology, by rational protein engineering and directed evolution to find highly active alternatives, while also possibly fixing any cross-dependency or mineral regulation strategies that were previously in place to regulate the unction of those enzymes using those minerals. This in effect will reduce dependency on multivitamins or other vitamin elements.

• for digestion, consider: add desaturase enzyme to convert from n-6 polyunsaturated fatty acid (PUFA) to n-3 PUFA (like DHA or other omega 3 fatty acid) (fat-1 pigs, fat-1 cattle, pigs with both fat1 and fat2 to handle more precursors, ...); keratinase, chitinase, uricase, better lysozymes, oxalate oxidase, ligninase, better proteases. Not all of these should be encoded into human germline due to inefficiency. Also, adding this to our food supply or gut microbiome is easier than adding it to human germline. Are there other digestion and metabolism modifications we should consider?

• optimize metabolism and nutrition for modern dietary demands (see here)

• human metabolism and weight loss and insulin stuff and kidney stuff, see http://gnusha.org/logs/2018-02-18.log

• hemoglobin from horses? can we just slap in a better myoglobin?

• add sickle cell hemoglobin for anti-malaria reasons

• for metabolism, consider ATP synthase re-engineering to remove more c-rings, or add more c-rings; differential expression of this ATP synthase based on which cell or tissue.

• reduce oxidative stress: enhance antioxidant defense, reduce ROS production, improve ROS detoxification, support redox homeostasis. Consider increasing expression of mitochondrial superoxide dismutase, glutathione peroxidases, catalase (target to peroxisomes or mitochondria), mitochondrial peroxiredoxins; for redox regulators: NRF2/NFE2L2 gain of function, FOXO3 overexpression to upregulate MnSOD/catalase/sestrin, PGC-1α to induce mitochondrial biogenesis and antioxidant enzymes (SOD2, GPX1); ROS producers - knockdown NADPH oxidases as a major source of ROS in many tissues, monoamine oxidase B, SDHA complex II, .... increase GCLC/GCLM to ratelimit glutathione synthesis; SLC7A11 overexpression to support GSH synthesis; thoredoxin reductase overexpression to regenerate reduced thioredoxin which is a key redox buffer. Careful about where these changes are expressed, in what cells or which tissues. This might be slop, consider systemic effects and oxidative homeostasis/respiration/etc.

• multi-virus resistance through recoding the genome to use an alternate codon mapping code so that virus genomes that use natty codon-AA mappings are unable to replicate inside cells that have their whole genome codon recoded. (belongs in immune section?)

• TODO: review human accelerated regions (segments of the human genome that are conserved throughout vertebrate evolution but are strikingly different in humans, especially compared to chimpanzees); and long non-coding RNAs (lncRNAs). See also "A high-resolution map of human evolutionary constraint using 29 mammals. Note also that thee are human-specific deletions compared to chimpanzees in otherwise conserved sequences. "A study examining intragenic clustering of human accelerated elements found that the transcription factor neuronal PAS domain-containing protein 3 (NPAS3) has the largest population of noncoding-accelerated regions. NPAS3 is active during mammalian brain development and the human accelerated elements within this locus predominantly appear to act as transcriptional enhancers."

• find areas of "accelerated evolution" in recent human genome; look at common mutations in the population; most mutations are probably detrimental or neutral. It's possible to figure out which genes (and alleles in particular) have been spreading rapidly throughout the population, so we should look at that information. Compare against neanderthal genome and other ancient human genomes that have been sequenced. Compare also to great ape genomes, chimpanzee, orangutan, macquee, etc. See also recent human adaptation (2024).

• "Partitioning heritability by functional annotation using genome-wide association summary statistics table 1 shows regions correlated with different conditions such as height (chondrogenic dif, H3K27ac), age at menarche (fetal brain tissue, H3K4me3), etc. Modifications in H3K4me3 in the angular gyrus correlate with years of education.

• in human vs apes, humans have 5 more copies of DRD5 than any other primate ref; and an increase in variable number of tandem repeats within the coding region of the third exon of the DRD4 gene (different gene).

• stomach size minimization or control

• organ duplication: multiple kidneys, multiple livers, multiple hearts (Doctor Who syndrome), functional polydactyly

• kidney/liver size increase, or supernumerary kidneys (extra kidneys), possibly through genetic modification but also possibly through cloning and etal surgery to add cloned liver (as an alternative to liver organoid transplant or liver organ donor transplant)

• sleep: reduced or zero perception of sleep pressure, anti-tiredness (might be a form of insomnia? might be adenosine metabolism related in brain neurons?) Stronger chemical or molecular control over sleep-related neurons.

• copy-paste some of the gene therapies from earonesty's list: https://web.archive.org/web/20150907230432/http://www.documentroot.com/2014/08/gene-therapies-i-want-to-see-developed.html

• incorporate proposed mutations and changes from Matthew McAteer's genetic modification wish list.

• gallstone disease - variants in ABCG8 and TRAF3 ref

• diving; large spleen - PDE10A mutations, thyroid hormone modulation; BDKRB2 - affects constriction of blood vessels in the extremities; FAM178B - related to carbon dioxide blood levels.

• alcohol stuff: ADH1B2 and ADH1B3 contribute to faster conversion of alcohol to acetaldehyde. ALDH1B1 contributes to faster clearance of acetaldehyde. ALDH22 common in asians is the alcohol flush reaction and is unable to break down acetaldehyde, a toxic byproduct of alcohol, so it's much easier to get alcohol poisoning.

• tay-sachs allele and IQ ? was this debunked or no?

• long COVID susceptibility: FOXP4 rs9367106-C, rs12660421-A (increases FOXP4 expression in lung), rs9381074, rs7741164, ...

• lifetime cannibis use: rs12673181 near metabotropic glutamate receptor 3 (GRM3), rs35827242 near CADM2 (risk taking?); for frequency of cannibis use, rs4856591 near CADM2.

• anti-depression: TYK2-P1104A knock-in (TYK2 hypomorph), TNFAIP3 (A20) overexpression (targeting NF-κB), NR3C2 brain-specific overexpression, CTLA4 duplication, SH2B3 overexpression. See anti-depression slop file.

• personality - see ref (?) This system is conserved across various mammalian species. SNORD copy number variations. "Particularly significant are SNORD115 and SNORD116_2. The latter is the variant that is predicted to bind to Ankrd11 exon X, while the possible target genes for the other two SNORD116 variants are not yet clear. These latter ones show generally only little copy number variation (Table 1). However, we note that the direction of the correlation is different between rodents and humans. In humans, the relatively higher anxiety group has the smaller number of copies, while it is the other way around in the three tested rodent species (see above)." -- regulation of behavioral variance using snoRNAs.

• disable human wisdom teeth aka third molar agenesis or M3 agenesis

  • PAX9 Ala240Pro Is Not Associated with Hypodondotia/Oligodontia or Cleft Lip/Palate but May Cause Congenitally Missing Third Molars.

    • other mutations in PAX9, and mutations in MSX1, AXIN2, ectodysplasin EDA/EDAR cause oligodontia?

  • GWAS third molar agenesis THSD7B, GRIN2B, LUZP2, ZBTB24, THYN1 are all probably bad targets

• gwern.net/Embryo-editing

• encode CRISPR-Cas9 or even dCas9 fusion proteins into the germline genome such that future payloads can rely on Cas9 or dCas9 availability for future genetic upgrade delivery into adults.

• disable germline transmission of certain modifications (germline editing is primarily required for zero mosaicism by modifying pre-conception or post-conception a single cell embryo, but this is only a delivery detail not something specifically related to desiring inheritance; long-term inheritance is a secondary goal that could be toggled on and off)

• if you can cause ancephalic (or anencephalic?) human fetal development via embryo engineering (such as for human cloning), then i wonder if you could introduce an engineered non-ancephalic neural cell line into the embryo (hybrid, mosaic or chimeric embryo) and have it develop the cortical neural tissues instead of the ancephalic cell line. this reduces concerns of non-brain pleitropy. The metabolic and other biological requirements in neurons is likely to be vastly different from the demands of the other cell types in the body; an increase in separation of concerns can reduce undesirable or unintended side effects including non-genomic other-tissue/other-organ "off-target effects".

• anti-sunburn, sunburn protection- see SOD pathway upregulation. additional radiation damage resistance, radiation damage repair, DNA damage repair pathway upregulate, ... Um, increase skin melanin content to protect against sunburns duh.

• reduce human skin attractiveness to mosquitos, possibly related to carboxylic acid secretions. Why can't we secrete nicer smelling odors or perfumes anyway.

• metabolic pathway optimization:

  • optimized glycolysis and ref, ref
  • lipid and fatty acid metabolism
  • mevalonate pathway
  • Targeting the electron transport system for enhanced longevity
  • acetyl-CoA flux optimization
  • gluconeogenesis
  • glutathione metabolism
  • reactive oxygen species (ROS) detoxification, ref
  • mitochondrial metabolism optimization
  • modeling: protein cost of metabolic flux, energy-based bond graph analysis of biomolecular pathways

• TODO: incorporate things about neochromosomes and human artificial chromosomes (HACs) from the IRC logs. sc2.0 had a neochromosome to store all their tRNA synthetases. you can knock out an essential gene on a natural chromosome and put it on the artificial one so the neochromosome doesn't get lost over time. (2026 news article)

• TODO: make a generic embryological platform for cell-specific expression and cell life cycle control during embryological development to target specific progenitor cell types or proliferators to increase their abundance, or otherwise regulate their proliferation or upregulate/downregulate, such that we can modularly plugin or swap out which cells we are targeting, based on cell lifecycle, rather than having to focus on unique genes related to those specific tissues or organs. Or will we have to edit specific to each tissue type due to quorum sensing and other growth limiting factors? Loss of CDK inhibitor p27Kip1 globally increases organ size and causes multiorgan hyperplasia. Consider CDK4/Cyclin-D1 overexpression. Generic proliferation effectors shown to scale progenitor pools during development.

• improved gyrification, sulcri, encephalization things, better brain anatomy, better white fiber tracts

• appearance, face genetics, symmetry, which parent does the child look like, etc

• anti-venom

• resistance to cryoprotectant toxicity for cryonics, cryovitrification, glutaraldehyde cross-linking, etc.

• TODO: make a document or system for GWAS variants, or alleles, or other mutations, indels, chromosomal microdeletions, etc, for which variants to avoid when making a germline genetically engineered human. Simply eliminating non-consensus genome mutations will substantially improve health and longevity, as Bram Cohen likes to point out. Did he not publish on this? there's no reference for this concept? There is also some additional value in intentionally avoiding known-harmful mutations or alterations.

• acromegaly-like targeted GH/IGF1 receptor improvement in hands to increase hand size?

• forearm muscle hypertrophy of flexor carpi radialis, flexor carpi ulnaris, extensor carpi radialis longus/brevis, extensor carpi ulnaris:

  • myostatin knockout or loss-of-function mutation, follistatin overexpression, IGF1 splice variants (knock-in of MGF mechano-growth factor targeted to these muscle tissues).
  • enhance anabolic signaling via mTORC1 pathway components such as constitutively active Rheb or TSC1/2 in muscle.
  • Pax7 overexpression (see elsewhere on this page regarding TEAD1 overexpression to drive satellite cell hyperplasia)
  • dominant negative receptor knock-in of myostatin receptor ACVR2B in these muscles.
  • enhanced mechanotransduction via FAK (PTK2) overexpression or constituitively active variant.
  • Titin (TTN) modification of PEVK or kinase domains to increase strain sensing.
  • PGC-1α4 overexpression in muscle to promote hypertrophy over oxidative phenotype.
  • Tbx5 is a forelimb-specific regulatory element or cell enhancer (targeter)

• better wound healing (TLN2 rs8031916, ZNF521 rs7236481, CSMD1 rs11136645, CSMD1 rs2449199, CSMD1 rs13279667, ...)

• supernumerary or extra cranial nerve roots or other spinal nerve fibers, with the expectation that they might be repurposed in the future for brain-computer interfaces or for reinnervation of muscles. Could be convenient to have some spare nerve fibers around that are already correctly wired into the brain. Might also help with surgical repair of brachial plexus injuries or other nerve fiber dissection injuries. With spare nerve fibers, the surgeon would have sufficient material to patch you back together. Are there any nerve fiber targeted genetic changes that could assist with PEG+chitin nerve fiber repair and healing?

• codon recoding: other than for multi-virus anti-virus resistance, check for poorly coded proteins in the human genome and recode for codon efficiency. Should we migrate proteins that use "rare codons" to use less rare codons (figure out how to achieve equivalent function with a non-rare codon)?

• whole body cell lineage tracing could be scientifically interesting, except that other than for brain uploading not sure if it has a practical use?

• TODO: figure out how to add electroreceptors to human biology. See https://gnusha.org/logs/2025-10-01.log for some ideas about converting primary sensory neurons in epidermis for the detection of microvolt electric field potentials on contact with (for example) someone else's head as a sort of EEG electrode and sensing strategy. With an adequate antennae or microvoltage sensor in the cortex, it may also be possible to do remote (steerable? steered?) sensing of distant entrainment without a direct axon inside of the brain.

• TODO: magnetoreception from birds? This should already be somewhere on this page. Don't know if it would work or if it has been added to mice yet.

• think hard about other outcomes that could be achieved with "immediate early genes" neural behavior cell-tagging techniques.

• TODO: pick good cell expansion, neuronal morphology modifications, electrophysiology tweaks, or optogenetic targets in the prefrontal cortex. These are classic sites for abstraction, rule representation, reasoning, and cognitive control. In primates, the caudate, nucleus accumbens, and dorsal striatum are heavily implicated in controlling rule switching and updating. More generally there are many other circuits in the brain worthy of consideration for either (1) germline cell growth control, (2) overexpression or other regulation of protein expression, and (3) encoding of optogenetic receptors, such as in regions such as thalamocortical, perceptual, direct somatosensory neuron activation, hippocampus, amygdala, basal ganglia, etc. Is it possible to pick certain neurons for optogenetic activation and use an out-of-band computer algorithm for the enhancement of learning rates, reasoning, abstraction, or other tasks? Does adding cells help? Does adding NMDA receptors help? more/less NMDA receptors? NR2B receptors? Direct control over cell-targeted synaptic plasticity under computer control via biofeedback and optogenetics? Consider targeting of association cortex or temporal cortex. What about online real-time stimulation changes for language/grammar learning?

• from https://gnusha.org/logs/2025-11-17.log -- "What about changing the human genome so that no single point mutation is able to significantly disrupt any particular vital protein residue function? In other words, re-encode all proteins etc so that important residues have redundant specification or function. We can also systematically test for mutations at any given point to ensure sufficient redundancy. For starters we can base that on which genetic diseases we see where only a small mutation is fatal even on one of the two alleles. Fatal mutations are often filtered out earlier in life like before week 10 of pregnancy, so they are harder to know about. Or even just extra backup copies of especially fragile genes or proteins at risk from single mutations."

• TODO: incorporate various weird ideas from https://gnusha.org/logs/2025-11-18.log like: 1) "Instead of presenting literal random peptides via MHC, cells present a compressed description of their internal state. T-cells would then fuzzy match these protein barcodes for an overall cell state degradation score to decision the cell. It’s like giving the immune system a diagnostic checksum for each cell's gene expression or metabolic state or other internal state." 2) "cryptography for secure cell-cell communication". and: "Application: Prevent metastatic mimicry. Cancer cells cannot replicate the precise signaling cryptographic key of authentic tissue. ... right, I guess you would want to send the whole genome or transcriptional state of the cell with each message so that your neighbor cells can verify your messages?" 4) "for intracellular barcode based memory systems, you could do intravenous delivery of small molecule timestamp peptides or oligonucleotides with a known sequence, have them get incorporated into growing barcode memory systems, and then you have a systemic timestamp or clock mechanism... kinda." It may also be the case that different sequences may be more resistant to mutation, so homozygosity could have a protective effect against certain kinds of mutational damage, regardless of whether there is any sort of functional effect from the heterozygosity.

• TODO: cell culture studies focused on cell-level improvements. Some of these results are likely to translate into whole animal. Many of the studies referenced in this document so far are based on transgenic animal studies, which are useful but an incomplete picture of the output of the institution of academic science. Or also cell-focused directed evolution studies (ref).

• TODO: Outline a more complete picture of different stages of life and what to systemically activate and when for stages such as neoteny, adolescence, adulthood, and senesence. It may be possible to prolong adulthood by manipulating IGF receptors while still maintaining IGFR functionality in very early life.

• TODO: consensus-based DNA damage repair specific to mtDNA, including known common mtDNA problems (like those mtDNA errors that can be fixed via restriction endonucleases in mitochondrial heteroplasmy). Implement mtDNA editors in the mitochondrial or nuclear genome to infrequently fix known/common mtDNA errors. Maybe link mtDNA mitophagy/autophagy or apoptosis to mtDNA error detection circuitry somehow? This could be useful for longevity/anti-aging in the sense of maintaining a healthy pool of youthful mitochondria.

• orthogonal DNA and amino acid system such that the nucleobases are less error-prone, or the oligonucleotides are more resistant to damage or degradation, etc. An entirely separate system can be constructed for alternative non-natural nucleic acids, and same with amino acids. Whether it would be entirely compatible with the existing genetic code, or require major refactoring and re-engineering of the whole genome and proteome remains to be seen.

• TODO: process "Genetic markers of stress, resilience and success at an elite military selection course" (2026) beyond rs3848874. "Genes associated with resilience and their functions included: tryptophan hydroxylase 2 (TPH2; serotonin synthesis); catechol-O-methyltransferase (COMT; catecholamine catabolism); corticotropin-releasing hormone receptor 1 gene (CRHR1; resilience to stress); Period3 (PER3; circadian rhythmicity); FK506 binding protein 5 (FKBP5; steroid receptor regulation). ... Cortisol, the most widely recognized marker of physiological stress, was associated with the CYP1A2 and FKBP5 genes. White Hispanic carriers of the minor allele of rs2069514 in CYP1A2 had significantly higher cortisol levels than major allele homozygotes. The CYP1A2 gene encodes a member of the cytochrome P450 enzyme family that metabolizes various substances, including caffeine. The rs2069514 variant is associated with decreased enzyme activity and accounts for some of the inter-individual variability in response to caffeine (Thorn et al., 2012, Tian et al., 2019, Al-Ahmad et al., 2017). In the Black race/ethnicity group, higher cortisol was associated with the presence of a minor allele in two variants (rs4713902 and rs7748266, in high linkage disequilibrium) of the FKBP5 gene. The gene FKBP5 is a cochaperone of the glucocorticoid receptor complex, which mediates cortisol's effects and plays a role in reducing the stress response of the brain (Mahon et al., 2013). While the CRHR1 protein is essential for the cortisol response to stress, FKBP5 is part of the negative feedback loop that inhibits glucocorticoid receptor activity. This gene has been associated with depression and anxiety, in addition to circulating cortisol concentrations (Scheur et al., 2016, Lahti et al, 2015, Rao, et al., 2016, Fan et al., 2021; Velders et al., 2011, Mahon et al., 2013). Mahon et al. also found that the minor allele of rs4713902 of FKBP5 was associated with higher baseline cortisol levels (Mahon et al., 2013)." Negative-feedback repression of cortisol signaling via weakening of FKBP5's inhibition of glucocorticoid-receptor complex would allow more efficient negative‑feedback repression of cortisol signaling and thus a more adaptive physiological stress response. There are other mutations of interest in the study as well, including psychological stress resilience.

Microbiome

• TODO: intracellular protein recorders inside gut microbiome to report on metabolism?
• TODO: something about endogenous K2 production

dental caries vaccine

wikipedia

a genetically modified strain of Streptococcus mutans called BCS3-L1, is incapable of producing lactic acid, which dissolves tooth enamel, and aggressively replaces native flora. In laboratory tests, rats who were given BCS3-L1 were conferred with a lifetime of protection against S. mutans. Dr. Jeffrey D. Hillman suggests that treatment with BCS3-L1 in humans could also provide a lifetime of protection, or, at worst, require occasional re-applications. He figures the treatment would be available in dentists' offices and "will probably cost less than $100.

paper: Genetically modified Streptococcus mutans for the prevention of dental caries

Neuronal enhancements for brain-computer interface

TODO: larger neurons on surface of brain for interface with brain-computer interfaces? are there any other genetic changes to facilitate interfacing with long-term electrode implants? or the vascular electrode (stentrode?) scheme? optogenetic control of neurons proximal to the surface of the neocortex or other brain cortex surfaces? what about inside grooves, gyri or sulcri? Optogenetics seems like one area to consider for brain-computer interfacing at least in the "write" direction. There are many optogenetics systems available for germline and in vivo stimulaton of freely moving/behaving animals with implants. Minimize astrocyte reactivity via reduction of glial fibrillary acidic protein expression for long term electrode compatibility. Coat brain implant electrodes with AAV for localized delivery and expression of anti-inflammatory factors, modulation of inflammatory response or pro-inflammatory cytokines, reduce microglial activation around implants. Integrin overexpression to enhance cell adhesion to electrode surfaces. ECM modifiers like fibronectin expression. Red-shifted opsins like ChrimsonR or Jaws for deeper tissue penetration in optogenetics, or two-photon responsive opsins. Are there any free-range animal BCI research projects using genetically encoded voltage indicators to transmit information to the BCI? Or fluorescent calcium indicators? or is it only via chronic window imaging? Ion channel overexpression and other electrophysiology shaping. Would larger dendiritc arbors be helpful? For stentrodes or vascular interface is there anything available to improve interfacing? Upconversion nanoparticles for even more distant neural stimulation via optogenetics. For long-term chronic implants consider LOX (lysyl oxidase) knockdown to reduce collagen crosslinking. BCI could deliver AAV with gene therapy for anti-apoptotic factors, neurotrophic support. Sonogenetic interfacial improvement via mechanosensitive ion channels. Check out magnetogenetics to see if magnetic field responsive ion channels are working or not (maybe something from birds). Neurons can report on their own activity via activity-dependent fluorophores or the oscillatory waves system.

Multiplex DREADDs for cell-type-specific retargeting of transient optogenetic receptor expression

With 46 unique DREADDs with zero cross-talk, you can systemically target every different cell type in the human body. With 92 bits you could get unique cell addressability (uh depending on diffusion and stuff), which seems less useful because you won't know which exact cell got which address? This scheme uses combinatorial ligand-AND addressing: each cell type is prewired with a unique subset of orthogonal DREADDs, and it is "armed" only when the correct delivery of ligands (a k-of-n code) is present over a sliding window period, triggering a synthetic transcriptional circuit that transiently expresses an optogenetic receptor equipped with self-limiting kinetics (e.g., degrons) so the receptor eventually gets recycled while transcriptional activity also decays with time. The opto-receptor can be tuned to cell-type-specific behavior for neurons or other cell types for GPCR style circuit triggering. The optogenetic element can be a receptor or it can be an azobenzene-controlled transcription factor inside the cell nucleus. GPCR per cell type can be hooked up to specific cell-type-specific genetic programming instead of universally expressing a single optogenetic receptor type. Further complicating matters there are also "optogenetic GPCRs" in the literature. Sonoporation mechanosensitive receptor types are available. Various chemogenetic receptors are available. Lots of options here.

Anyway, the result of this scheme is that you can reuse optogenetic receptor wavelengths over the lifetime of the human and use the same wavelengths (at different times) to trigger different kinds of neurons at different times (or other cell behaviors that were pre-engineered). You might also be able to scale via different optogenetic wavelength receptors for simultaneous stimulation or activation of different neuron types through this scheme.

For optogenetic receptors I think we only have a handful right now, maybe four or five? Double check.

And unfortunately the current record for DREADD multiplexing seems to be three or four ligands/receptors?? That's not very multiplexicative so far...

This technique could be combined with "immediate early genes" to specifically "tag" neurons for later re-activation. Maybe even in a "reusable" or "refreshable" way so that "immediate early gene" techniques can be used multiple times throughout the animal's life to target different neurons or different neural circuits.

This could also be used to facilitate better brain-computer interfaces, especially stimulation. Read-out could also be enhanced via fluorescence, optical oscillatory wave generation, luciferase, or other cell signal generation.

See also: Ligand-receptor promiscuity enables cellular addressing.

See also https://gnusha.org/logs/2025-10-02.log which is where the multiplex DREADD technique for optogenetic re-binding scheme was originally conceived or speculated.

TODO: Also think more about what could be done if we instead use 92 bits to uniquely address every cell in the body. The problem is that you don't know which cells correspond to which addresses. You might be able to localize it by randomly triggering different bits and then looking for some sort of fluorescent event throughout the body to identify the mapping between different bit-vectors and different cells. On second thought, you will need more than 92 bits because you cannot enforce that every cell has a unique address except by making it statistically improbable through the provision of more bits. How many more would you need?

And how would you learn which cells respond to which combinations of bits? How would you solve the search problem where you need to figure out the mapping between a bit-vector and a specific cell? You would want a way to query all the cells in the body and ask them to please fluoresce if they respond to bit n in the bit-vector and then you record that information. You sweep through all the bits and then you combine into a giant bitmask table to get the address of each cell that you were visually tracking.

possibly the cells could self-report via protein recording device that they make internally and export, or it's on a cilia on the external surface of the cell membrane and then detaches and is recoverable in the bloodstream. You could use connectome-seq style mapseq techniques to get a rough approximation of their location in the global graph of cell-cell adjoinancy matrix if not their exact location at least. You could then cartographically pinpoint some of the more popular or easily-identifiable nodes in the graph to track them to their exact location in the mammalian body, and use that to approximate the physical targeting of nearby adjacent cells.

Genomic Integrity and Error Correction Architectures

Motivation: DNA damage occurs continuously in all cells through endogenous sources (replication errors, reactive oxygen species from mitochondrial respiration, spontaneous hydrolysis, and replication fork collapse) and exogenous insults (ionizing radiation, ultraviolet light, and genotoxic chemicals), generating an estimated (REDACTED) lesions per cell per day including base modifications (8-oxoguanine, thymine glycol), single-strand breaks, double-strand breaks (DSBs), and inter-strand crosslinks. Cells deploy an interconnected network of repair pathways—base excision repair (BER) for oxidized/alkylated bases via glycosylases like OGG1 and APE1; nucleotide excision repair (NER) for bulky adducts via XPC-RAD23B recognition and ERCC1-XPF incision; mismatch repair (MMR) via MSH2-MSH6 mismatch recognition and MLH1-PMS2 strand discrimination; homologous recombination (HR) for error-free DSB repair via MRN complex end resection, RAD51-mediated strand invasion, and BRCA1/BRCA2 coordination; and non-homologous end joining (NHEJ) for rapid but error-prone DSB ligation via Ku70/Ku80 end binding, DNA-PKcs activation, and LIG4-XRCC4 ligation—all coordinated by upstream kinases ATM, ATR, and DNA-PKcs that phosphorylate hundreds of downstream effectors including CHK1, CHK2, and p53 to orchestrate cell cycle arrest, repair, or apoptosis.

The fundamental problem for longevity is that these repair pathways are themselves encoded in DNA and therefore subject to the same mutational processes they exist to correct: a somatic mutation in POLB (the gap-filling polymerase in BER) reduces repair fidelity, increasing the probability of subsequent mutations including in other repair genes like MSH2 or BRCA2, creating a positive feedback loop where repair capacity degrades faster than the background mutation rate would predict—this "doom loop" is compounded by the fact that many repair proteins function in complexes where stoichiometry matters (haploinsufficiency in MMR genes like MLH1 increases mutation rates), and by the observation that stem cell pools, which must maintain genomic integrity across decades, accumulate mutations at measurable rates (approximately 40 mutations per year in hematopoietic stem cells (pls double check this)) that eventually compromise the repair machinery itself, leading to the exponential increase in cancer incidence and tissue dysfunction observed in aging. The interventions cataloged here—from enhanced proofreading polymerases and upregulated repair enzymes to architectural solutions like consensus-based networks to transfer high-integrity genetic information, protected stem cell niches with hardened Weismann barriers, intrinsic error-correcting codes embedded in DNA structure, and exogenous restoration of verified genomic state—represent a systematic attempt to break this doom loop by transitioning from reactive damage repair (which cannot distinguish information-theoretic drift from structural damage without a reference template) to proactive integrity maintenance (which treats the genome as a verified dataset that can be checksummed, compared against neighbors, restored from backup, or protected through redundancy), ultimately aiming to achieve negligible genomic senescence by ensuring that the probability of catastrophic repair pathway failure remains below the threshold required for indefinite organismal maintenance.

Note on your HSC mutation rate: The figure of ~40 mutations/year is approximately correct but reflects total somatic mutations across the genome; landmark studies (Welch et al., Cell 2012; Osorio et al., Cell Stem Cell 2018) measured ~10-17 mutations/year in human HSC exomes, extrapolating to ~1-2 × 10³ genome-wide when including non-coding regions, though the commonly cited "~40/year" likely derives from specific whole-genome sequencing studies of aged HSCs showing accumulation rates of 10-20 coding mutations plus several hundred non-coding mutations annually.

See also DNA damage repair.

Biological DNA repair (BER, NER, homologous recombination) is fundamentally reactive, patching structural damage without a reliable way to detect information-theoretic drift (mutations) in the absence of a verified template. To achieve negligible senescence, we must transition from "repairing damage" to "guaranteeing integrity".

Simple Enhancements to Existing Repair Pathways

Before pursuing radical architectural changes, conventional repair machinery can be augmented:

• Improve mismatch repair fidelity and processivity
• Improve homologous recombination accuracy
• Upregulate DNA repair enzymes (PARP, ATM, ATR, DNA-PKcs)
• Improve DNA damage radiation resistance via enhanced nucleotide excision repair
• Enhanced proofreading in polymerases

These interventions are incremental and do not address the fundamental problem that repair machinery has no reference to a "known-good" template, other than the other side of the double-strand.

Architectural Topologies for Error Correction

(A) Mesh/Consensus: Somatic cells (execution nodes) exchange sequence samples via exosomes to establish a local truth consensus; outliers trigger self-apoptosis logic based on majority vote.

(B) Star/Hierarchical: A protected stem cell niche (storage node) retains the master copy, exporting verified read-only genome packets to disposable somatic cells, rigorously enforcing a localized Weismann barrier.

(C) Local/Intrinsic: DNA structure includes redundant parity bits or ECC, enabling autonomous enzymatic correction of read/write errors.

(D) External/Restoration: Corrected sequence data is pushed from an exogenous trusted source (via viral vector/nanomachine) to reset genomic fidelity.

Local/Intrinsic Integrity Mechanisms

These approaches encode error-detection or error-correction information directly into the genome, enabling autonomous repair without external reference.

Methylation as Parity Bits

Epigenetic marks already encode regulatory information; they could be repurposed for integrity checking. A simple scheme: methylation state of specific CpG sites encodes a parity bit for nearby nucleotide windows. Maintenance methyltransferases already propagate methylation patterns through replication; engineered variants could compute and verify parity during replication. Mismatch between computed and observed parity triggers repair or apoptosis. This is low-overhead but limited to single-bit error detection per window.

Forward Error Correction in Coding Regions

Re-engineer protein-coding sequences to include mathematical error-correcting codes (e.g., Hamming codes, Reed-Solomon). Several sub-approaches:

• Expanded codon alphabet: Move beyond 3-bp codons to 4-bp or 6-bp "magic codons" with sufficient Hamming distance between valid states. Polymerases can deterministically "snap" single-nucleotide errors to the nearest valid codon rather than incorporating a mutation. Requires re-engineering the entire translation machinery (tRNAs, aminoacyl-tRNA synthetases, ribosomes).

• Synonymous codon constraints: Within the existing 64-codon space, constrain which synonymous codons are valid at each position based on neighboring sequence context. This creates implicit checksums without expanding the alphabet, though with weaker error correction capability.

• Interspersed parity nucleotides: Insert dedicated parity nucleotides at regular intervals within coding sequences (spliced out before translation). Repair enzymes verify parity and correct errors. Increases genome size but preserves existing translation machinery.

Checksum Enzymes

Engineer polymerases, tRNA synthetases, or dedicated repair enzymes to validate cryptographic checksums embedded in non-coding regions flanking genes. If compute(sequence) != checksum, the cell triggers deterministic repair or apoptosis. This requires substantial protein engineering but could provide block-level integrity verification.

Ribosome Re-engineering

If ribosomes already translate 3-bp codons to amino acids (information decoding), then perhaps a repurposed and re-engineered ribosome could translate encoded mRNA commands directly into error correction activity. This is a speculative path toward enzymatic "compilers" that transform genetic information into molecular outputs.

Mesh/Consensus Approaches (Peer-to-Peer Validation)

The Distributed Systems Approach: Tissue as a Byzantine Fault Tolerant (BFT) network.

Cell Network Consensus Protocol

Cells establish high-bandwidth communication (gap junctions, exosomes, large natural competence pores, quorum sensing molecules) to randomly sample genomic segments ("heartbeats"). They query neighbors: "Do you see sequence 0xA3F... at locus Chr1:4000?" Synthetic G-protein coupled receptor signaling pathways respond Ack/Nack.

This approach exploits the statistical improbability that identical mutations occur independently across multiple adjacent cells. Byzantine fault-tolerant algorithms implemented through genetic circuits distinguish between:

• Inherited damage: Present across lineages, tolerated as germline variation

• Spontaneous mutations: Isolated to individual cells, flagged for repair or elimination

Divergent sequences trigger apoptosis or repair based on local majority voting.

DNA Fragment Querying

Cells export random genomic fragments (via exosomes or through large transmembrane pores similar to natural competence systems) and compare against fragments received from neighbors. Sequence divergence beyond a threshold triggers consensus-based decisions about which cell carries the error.

Expanded MHC Surveillance

The immune system already performs rudimentary genomic surveillance through MHC presentation and elimination of cells displaying aberrant peptide signatures. This could be extended:

• MHC Class I expanded to present random mRNA transcript fragments alongside peptides
• NK cells and T cells trained to recognize sequence-level aberrations, not just protein misfolding
• Essentially gives the immune system a "checksum" view of transcriptional state

Polyploidy and Chromosome Elimination

Leverage high-ploidy states (multiple copies of each chromosome) as an internal consistency buffer. Similar to "uniparental genome elimination" observed in interspecific hybrids, cells could detect diverging chromosome copies and selectively degrade the outlier, regenerating it from the consensus of the remaining sisters. This provides intra-cellular redundancy without requiring inter-cellular communication.

Star Topology (Hardened Weismann Barrier)

The "Streamed Genome" Approach: Hardware separation of Storage vs. Execution.

Architecture

A protected stem-cell niche ("The Server") acts as the read-only Golden Master, shielded from metabolic stress and replication errors. This niche would have:

• Reduced metabolic activity (lower ROS production)
• Enhanced local repair machinery
• Physical shielding from environmental mutagens
• Minimal replication (quiescent state)

Deployment

Somatic cells ("Clients") are stateless execution nodes. They receive verified instruction sets (mini-chromosomes or stabilized mRNA) but never serve as templates for future generations. Somatic cells are periodically flushed and replaced by fresh exports from the trusted root, rendering somatic mutations irrelevant for long-term organismal integrity.

This breaks the "game of telephone" in somatic mitosis where errors accumulate through successive divisions.

External/Restoration Approaches

The Exogenous Approach: Systemic delivery of verified state.

Chromosome Delivery and Replacement

Design mechanisms for delivering and replacing entire chromosomes to cells throughout the body:

• Very large natural competence pores engineered for eukaryotic chromosome import
• Exosome-based delivery of mini-chromosomes or chromosome arms
• Direct replacement of damaged chromosomes with known-good copies delivered through the bloodstream

This could apply also to mtDNA (or mtDNA could be internalized into the nuclear genome for unified maintenance).

Synthetic Horizontal Gene Transfer

Cells communicate and decide which cell has superior genomic integrity, then copies are transferred to damaged cells. Alternatively (and probably easier): damaged cells undergo apoptosis and are replaced via cellular division from verified neighbors.

Viral Vector Restoration

Periodic delivery of corrected genetic material via AAV, lipid nanoparticles, or synthetic shuttle agents overwrites accumulated errors. This effectively treats the organism as a client syncing with a cloud-based "golden image." Requires high-fidelity genome copying at scale (kicking the can down the road).

Bootstrapping High-Fidelity Genomes

Build an initial high-fidelity genome using imperfect tools.

Iterative In Vitro Enzyme Decoding

A scheme to bootstrap high-fidelity DNA from cheap, error-prone synthesis (e.g., high-throughput synthesis with 10% error rates).

Treat DNA as a "memory tape" for a biological Turing machine to compile redundant "source code" DNA into clean "binary" DNA. Trades chemical precision (which is hard/expensive to scale) for enzymatic computation (which allows logic-based verification of the product).

Use a library of zinc-finger recombinases (or Cas9/TALENs) engineered to recognize "encoded" DNA segments containing data + error-correction redundancy.

Process: (needs work)

1. Synthesize a "compressed" or "encoded" strand with redundancy.
2. Apply Enzyme A: It binds to an encoded block, verifies the logic/checksum, and catalytically converts it to a "decoded" sequence (potentially excising itself or "NOP" spacer nucleotides used to handle frameshifts).
3. Iterate: Repeated rounds of enzymatic processing progressively "clean" the dirty input tape into a perfect output sequence.

Radiation Detection and Quorum-Based Apoptosis

Simple interventions for acute damage scenarios:

• Radiation counter: Intracellular sensor that detects elevated incidence of DNA lesions (strand breaks, oxidized bases)
• Mutation load monitor: Track ratio of repair events to replication events
• Quorum sensing trigger: A single DNA base flip is tolerable; multiple mutations in short succession triggers communication with neighbors
• Collective decision: Localized high mutational load detected across multiple cells triggers coordinated apoptosis or senescence, treating the region as potentially compromised by an ongoing mutagenic insult (radiation exposure, chemical exposure, viral attack)

This distinguishes between background mutation rates (normal) and acute mutational storms (pathological).

Intra-cellular Self-Consensus (S/G2 Phase)

The 8-way "Super-Majority" Vote.

During the S and G2 phases of the cell cycle, genomic information exists in a transient state of hyper-redundancy. Each locus is physically instantiated across eight nucleotide strands: two homologous chromosomes × two sister chromatids per homolog × two complementarity strands per duplex. This offers an intra-cellular redundancy pool sufficient for rigorous error correction without requiring inter-cellular communication.

A localized repair orchestrator can perform a "deep read" of a specific locus across all eight strands. By normalizing base calls (mapping A/T duplexes to "A" and G/C to "G"), the system executes a majority-vote logic. Since random, independent damage events (oxidation, hydrolysis) are statistically unlikely to align across a supermajority of strands at the exact same coordinate, the consensus sequence is overwhelming likely to be correct.

Decision Logic:

• 0–2 Divergent Strands: Overwrite outliers using the 6–8 strand consensus.
• Near-Ties (4–4 Split): Invoke tie-breaking protocols weighting older template strands over nascent strands, or prioritizing strands lacking chemical lesion signatures.
• Fail-Closed: If consensus cannot be reached, the cell triggers a checkpoint or apoptosis rather than guessing. Or falls back to byzantine consensus with nearby neighboring cells. Or deletes that part of the genome and increases a genomic marker of cellular damage.

Intra-cellular Self-Consensus from Diploidy

The 4-way "Diploid" Vote.

Even outside of replication (G1 phase), diploid organisms possess an inherent 4-strand redundancy at every autosomal locus (Paternal Homolog strands $P_1/P_2$ and Maternal Homolog strands $M_1/M_2$). Current repair mechanisms generally fail to exploit this, treating each double-strand break or mismatch as an isolated event on a single duplex.

This architecture treats the locus as a 4-channel readout. Upon detecting a mismatch or lesion, a repair controller queries the complementary strands of the homologous chromosome. This effectively creates a RAID-1 style mirroring array within the nucleus. To preserve necessary heterozygosity, the system must distinguish between inherited allelic variation (consistent Paternal vs. Maternal differences) and de novo somatic mutations (outliers against the remaining three strands). This reframes DNA repair from a local chemical patch to a confidence-based decision system.

Transcriptional Backfilling (RNA "Read Cache")

Using mRNA as a temporal buffer.

Current molecular biology central dogma views information flow as unidirectional (Central Dogma: DNA → RNA). However, for high-fidelity maintenance, recent mRNA transcripts can serve as a transient "L1 cache" or authoritative backup of the genomic state.

If a DNA locus suffers acute, "lumpy" damage (e.g., a clustered lesion from ionizing radiation) that obscures the template on both strands, the cell can query the pool of existing mRNA or pre-mRNA transcripts produced prior to the damage event. Using an engineered reverse-transcriptase-mediated repair pathway or prime-editing mechanism, the cell creates a repair template from the transcript to restore the DNA.

• Advantages: Provides a template even when both DNA strands are compromised.
• Limitations: Only effective for actively expressed genes; relies on the transcript preceding the damage event; vulnerable to transcriptional noise unless validated by UMI-like molecular barcoding.

Reference-Only "Genomic Library" Arrays

The "Cold Storage" Approach.

A significant driver of mutagenesis is the act of transcription itself (replication-transcription collisions and R-loop formation). To counter this, cells could maintain "genomic libraries"—vast arrays of non-functional, non-expressed gene copies used strictly for reference.

Unlike active genes, these copies would reside in deep heterochromatic "cold storage," shielded from the metabolic wear-and-tear of expression. They serve as read-only lookup tables for repair machinery. When an active, high-traffic gene accumulates damage, the repair complex retrieves the sequence from the quiescent library copy rather than guessing or relying on a potentially damaged homolog.

Architectural Variants:

• Intrachromosomal Vaults: Tandem backup copies locked in heterochromatin.
• Episomal Archives: High-fidelity mini-chromosomes maintained purely for archival parity.
• Distributed Pseudogene Ledgers: Dispersed copies to prevent correlated loss from local chromosomal deletion events.

Redundant Specification of Critical Residues

A complementary approach: change the human genome so that no single point mutation can significantly disrupt any particular vital protein residue function. Methods:

• Re-encode critical proteins so that important residues have redundant specification (multiple codons in tandem, only one needs to be correct)
• Systematic mutagenesis testing to identify fragile positions
• Extra backup copies of especially fragile genes at risk from single mutations
• Focus initially on known genetic diseases where single mutations (even heterozygous) are fatal
• Note: Fatal mutations are often filtered out before week 10 of pregnancy, making them harder to catalog

ref: Enzymatic elimination of errors from DNA using error correction codes which also mentions an idea for "ECDSA encryption enzymes" (yeah good luck with that buddy).

IRC logs: https://gnusha.org/logs/2017-05-12.log and https://gnusha.org/logs/2017-05-16.log and https://gnusha.org/logs/2025-09-29.log and https://gnusha.org/logs/2025-12-17.log and https://gnusha.org/logs/2026-01-04.log

Cellular changes and molecular biology

https://twitter.com/AdamMarblestone/status/792803428774866944

From "GWAS catalog"

https://www.ebi.ac.uk/gwas

• self-employment: rs10776614-T, rs17166082-A
• skin youthfulness
• amphetamine response
• response to metformin: rs11212617-A, rs11212617-C, etc.
• verbal-numerical reasoning
• puberty onset
• high number of children: rs13161115-C, rs10908474-A, rs2415984-A, rs10009124
• human facial variation: nose, lip morphology
• eyebrow thickness: rs112458845 (FOXL2), etc.
• reading ability: ABCC13 rs2192161-A, rs7187223-A, or rs349045-T and rs133885 in dyslexia
• narcolepsy: rs1154155-G, rs1154155-C, rs10995245-A, etc.
• musical aptitude
• monobrow
• manic episodes
• loneliness
• longevity and lifespan such as rs12949468 (TLK2), rs4639950 (C1QTNF5), rs7894051 (ECHS1), rs4904670 (NRED2), rs2292664 (RIMBP2)
• insomnia
• length of menstrual cycle: rs564036233-GA (FSHB), rs3124592-G (NOTCH1)
• hoarding: rs3747767-A (LCA5), rs1844437-C, rs2388436-G
• handedness: rs7182874-T (VIMP, PCSK6, CHSY1, SNRPA1), rs11855415-A (PCSK6)
• age-related hearing impairment: rs4932196-T (ISG20, ACAN)
• freckles: rs1805007-T (MC1R), rs12203592-T (IRF4), rs12931267-G (FANCA), rs1015362-G (ASIP), rs4911414-T (ASIP)
• extraversion (personality): rs644148-G (ZNF180)

Really just download the GWAS catalog and build a software pipeline to analyze the data all at once. This should all be automated with a pipeline to ingest the data, analyze SNPs and genes/proteins by LLMs, read the original articles and supplementary data files, search and review the literature, and then generate theories or hypotheses for transgenic modifications to recapitulate the positive traits through germline genetic engineering.

(insert rant here about how GWAS has rotted everyone's brain and everyone hyperfocuses on GWAS to the detriment of human life...)

there's also OMIM "Online mendelian inheritance in man".

there's also "GWAS atlas"

there's also genebass which provides some information from UK Biobank. At some point during this project it may be worthwhile to simply pay for UK Biobank data access.

Authorship

This document is old and still updated as of 2025. It is the largest document on the Internet pertaining to human germline genetic engineeirng enhancements. Originally authored by yashgaroth on 2012-06-28. See http://gnusha.org/logs/2012-06-28.log for more context about the original authorship. It has since been updated by multiple different authors and editors.

There are some other modification items remaining in genetic-modifications.csv.