# Synthetic morphogenesis

This page pertains to synthetic morphogenesis, synthetic-patterning circuits, morphogenetic engineering, programmable tissue patterning, programmable tissue morphology, genetic morphogenesis, and synthetic developmental biology.

Synthetic morphogenesis treats the shape, size, organization and fate of multicellular tissues as a programmable trait. By combining synthetic gene circuits, cell-cell signaling, mechanical cues and self-organization rules, engineering can be used to direct populations of living cells (from bacteria to mammalian stem cells) to autonomously build predetermined 3d structures and patterns thereby mimicking or surpassing normal embryonic or other development.

[Harnessing synthetic biology to engineer organoids and tissues](https://pmc.ncbi.nlm.nih.gov/articles/PMC11684341/) this has a good overview of prospective techniques for programmable developmental biology, cell-cell adhesion, multi-state genetic circuits to control morphology, optogenetic chimeric receptors, synNotch receptor system, synthetic diffusive morphogen system using a synthetic receptor "such as MESA", synthetic cell-cell adhesion molecules, multi-fate synthetic circuits, juxtacrine signaling, diffusible morphogens, differential cell adhesion, etc.

Still, we are not yet to the point of encoding large-scale multi-tyoe network topology even in a probabilistic encoding kinda way. In the future we ought to be able to encode entire 3d anatomies into a genome and have it reliably expressed as a volumetric phenotype.

[Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues](https://www.nature.com/articles/s41467-022-33115-0) shows cell sheet folding, thickening, flattening, etc.

[Patterning of brain organoids derived from human pluripotent stem cells](https://pmc.ncbi.nlm.nih.gov/articles/PMC9167774/)

See also [[optogenetics]].

For capturing information from embryological development consider [[lineage tracing]].

# Cell–cell sensing & programmable logic

* **synNotch receptors** – modular receptors that turn custom cell–cell contacts into gene programs. [PubMed](https://pubmed.ncbi.nlm.nih.gov/20418862/?utm_source=chatgpt.com)
* **Native/rewired Notch–Delta lateral inhibition for patterning** – foundations for boundary sharpening & stripe/spot formation. [American Chemical Society Publications](https://pubs.acs.org/doi/10.1021/sb400128g?utm_source=chatgpt.com)
* **MESA & other synthetic extracellular sensors** – ligand → transcription with defined wiring in mammalian cells. [PubMed](https://pubmed.ncbi.nlm.nih.gov/19266339/?utm_source=chatgpt.com)

# Chemically gated & recombinase-based fate control

* **Cre-ERT2 (tamoxifen-inducible Cre)** – time-controlled recombination for fate switches. [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867416000520?utm_source=chatgpt.com)
* **Split-Cre via rapalog (FKBP/FRB)** – dimerizer-gated recombination. [PubMed](https://pubmed.ncbi.nlm.nih.gov/14576331/?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC275488/?utm_source=chatgpt.com)
* **Serine integrases (Bxb1/ΦC31/Dre/Vika) for logic & memory** – irreversible “DNA writing” in mammalian cells. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC11195097/?utm_source=chatgpt.com)
* **Orthogonal inducible split recombinases (drug/light/temp)** – large toolset for multi-input control. [Nature](https://www.nature.com/articles/s41467-019-12800-7?utm_source=chatgpt.com)

# Small-molecule dimerizers & degraders

* **Rapamycin FKBP–FRB heterodimerization** – classic fast, tight control. [PubMed](https://pubmed.ncbi.nlm.nih.gov/26777239/?utm_source=chatgpt.com)
* **ABA PYL–ABI heterodimerization** – plant hormone system ported to mammalian cells. [PNAS](https://www.pnas.org/doi/10.1073/pnas.1112838108?utm_source=chatgpt.com)
* **GA GID1–GAI heterodimerization** – gibberellin-gated control. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC3368803/?utm_source=chatgpt.com)
* **Auxin-inducible degron (AID)** – rapid, reversible protein knockdown. [Nature](https://www.nature.com/articles/nmeth.1401?utm_source=chatgpt.com)
* **dTAG targeted degradation** – selective FKBP12F36V degron with clinical-grade ligands. [Nature](https://www.nature.com/articles/s41589-018-0021-8.pdf?utm_source=chatgpt.com)
* **SMASh/self-removing tags & hydrophobic-tag (Halo/HyT) degraders** – degradation on demand. [Addgene Blog](https://blog.addgene.org/dtag-youre-it?utm_source=chatgpt.com), [tsienlab.ucsd.edu](https://tsienlab.ucsd.edu/Publications/Lin%202015%20Nature%20Chem%20Bio%20-%20Tunable%20and%20reversible%20drug%20control.pdf?utm_source=chatgpt.com)

# Optogenetic switches (spatiotemporal control)

* **CRY2–CIB blue-light dimerization** – many variants; also used for PA-Cre2.0. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4871718/?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/27065233/?utm_source=chatgpt.com)
* **iLID/SspB (LOV-based)** – compact, reversible blue-light dimerizer. [PNAS](https://www.pnas.org/doi/10.1073/pnas.1417910112?utm_source=chatgpt.com)
* **PhyB–PIF (red/far-red)** – deep-tissue friendly on/off control. [ResearchGate](https://www.researchgate.net/publication/26807830_Spatiotemporal_Control_of_Cell_Signalling_Using_A_Light-Switchable_Protein_Interaction?utm_source=chatgpt.com)
* **BphP1–QPAS1 (near-infrared)** – NIR activation in cells and animals. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6239862/?utm_source=chatgpt.com)
* **Photoactivatable Cre (PA-Cre)** – light-gated recombination (CRY2/CIB or Magnets). [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4871718/?utm_source=chatgpt.com), [Laboratory Investigation](https://laboratoryinvestigation.org/article/S0023-6837%2822%2900325-7/fulltext?utm_source=chatgpt.com), [ResearchGate](https://www.researchgate.net/publication/308993104_A_photoactivatable_Cre-loxP_recombination_system_for_optogenetic_genome_engineering?utm_source=chatgpt.com)
* **Split-Cas9** – conditional genome editing by reconstitution. [Nature](https://www.nature.com/articles/nbt.3149?utm_source=chatgpt.com)


# Morphogen shaping & reaction–diffusion

* **Synthetic activator–inhibitor circuits (e.g., Nodal/Lefty)** – self-organized Turing-like patterns in mammalian cells. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6303393/?utm_source=chatgpt.com), [Science](https://www.science.org/doi/10.1126/science.abc0033?utm_source=chatgpt.com)
* **Microfluidic gradient generators** – stable, user-defined morphogen fields. [American Chemical Society Publications](https://pubs.acs.org/doi/10.1021/la000600b?utm_source=chatgpt.com), [Harvard Projects](https://projects.iq.harvard.edu/files/gmwgroup/files/733.pdf?utm_source=chatgpt.com)
* **Tethered/immobilized growth factors & heparin-hydrogels** – localized, sustained morphogen presentation. [Royal Society Publishing](https://royalsocietypublishing.org/doi/10.1098/rsif.2010.0223?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/32515102/?utm_source=chatgpt.com)

# Engineered synaptic cell adhesion molecules

[Engineered adhesion molecules drive synapse organization](https://www.pnas.org/doi/10.1073/pnas.2215905120)

# Adhesion code & synthetic cell–cell “glues”

* **Cadherin-level/type tuning for sorting & patterning** – “adhesion code” design principle. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC8164589/?utm_source=chatgpt.com)
* **DNA-programmed assembly of cells (DPAC)** – sequence-addressable adhesion for 2D/3D patterning. [PubMed](https://pubmed.ncbi.nlm.nih.gov/26322836/?utm_source=chatgpt.com)
* **Orthogonal synthetic CAMs (coiled-coil ‘helixCAM’, SynCAM toolkit)** – large libraries for selective pairing & multicellular architecture. [PubMed](https://pubmed.ncbi.nlm.nih.gov/36055250/?utm_source=chatgpt.com), [Nature](https://www.nature.com/articles/s41586-022-05622-z?utm_source=chatgpt.com)
* **Opto-E-cadherin** – reversible light control of adherens junctions. [Nature](https://www.nature.com/articles/s41467-023-41932-0?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC11116891/?utm_source=chatgpt.com)

# Contractility & tissue mechanics actuators

* **OptoRhoA/ROCK (force up/down)** – acute control of traction & tissue compaction. [Nature](https://www.nature.com/articles/ncomms14396?utm_source=chatgpt.com)
* **OptoShroom3 (apical constriction)** – light-induced epithelial folding & organoid shape changes. [Nature](https://www.nature.com/articles/s41467-022-33115-0?utm_source=chatgpt.com)
* **OptoSOS/ERK, OptoFGFR/EGFR** – map and drive mechano-morphogenetic programs via RTK→ERK dynamics. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC3925772/?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/24981772/?utm_source=chatgpt.com)

# MultiFate via zinc finger transcription factors

"MultiFate uses engineered zinc finger transcription factors that self-activate their own transcription as homodimers and mutually inhibit one another when they form heterodimers. Their homo- or heterodimerization can be controlled by small molecules. Thus, by expressing only three types of such synthetic transcription factors, the cell lines can generate seven distinct cell states. Of note, this MultiFate system can, in principle, be combined with other synthetic circuits mentioned above, which enables cells to make a series of fate choices in multicellular systems as in normal tissue formation. When applying these tools to organoids, it is important to consider their tunability. How much signal is required to induce a response, and what will be the intensity or duration of the response?"

# Organoid & “synthetic development” platforms

* **Micropatterned gastruloids (2D)** – reproducible germ-layer rings from BMP→WNT→NODAL cascades. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4341966/?utm_source=chatgpt.com)
* **3D gastruloids & embryo models** – axis formation and early morphogenesis in vitro. [Hubrecht Institute](https://www.hubrecht.eu/app/uploads/2020/07/VanOudenaarden_2020_Nature_Moris.pdf?utm_source=chatgpt.com), [Cell](https://www.cell.com/trends/cell-biology/fulltext/S0962-8924%2821%2900123-9?utm_source=chatgpt.com)
* **Optogenetic Wnt in hESCs (‘optoWnt’)** – dose/timing-controlled self-organization. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10399980/?utm_source=chatgpt.com)

# Photopatterned & 4D biomaterials to sculpt tissues

* **Photodegradable/photoadaptable PEG hydrogels** – in-gel channels & cue release for guided folding/invasion. [Science](https://www.science.org/doi/abs/10.1126/science.1169494?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2756032/?utm_source=chatgpt.com)
* **Two-photon protein patterning inside gels** – 3D maps of instructive ligands. [coledeforest.com](https://coledeforest.com/pdfs/papers/2015_DeForest_NatMater.pdf?utm_source=chatgpt.com)
* **Geometry/curvature templates to deterministically pattern organoids**. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC9131435/?utm_source=chatgpt.com)

# Live readouts for closed-loop control

* **ERK-KTR & other KTRs** – multiplexable, kinetic reporters for signaling dynamics. [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867414006552?utm_source=chatgpt.com)
* **SMAD pathway dynamics in human gastruloids** – live tracking of morphogen responses. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6398983/?utm_source=chatgpt.com)
* **Wnt/TCF reporters (TOPFlash family) & YAP/TAZ (TEADlight/YRE)** – pathway-specific activity reporters during patterning. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC3536346/?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/40482695/?utm_source=chatgpt.com)
* **Molecular tension sensors (TSMod/VinTS; junction sensors)** – quantify forces across adhesion proteins in living tissues. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2901888/?utm_source=chatgpt.com)

# CRISPR toolkits for cell fate & patterning

* **CRISPRi (dCas9-KRAB) & CRISPRa (SAM/VPR)** – programmable repression/activation. [PubMed](https://pubmed.ncbi.nlm.nih.gov/23849981/?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4927356/?utm_source=chatgpt.com)
* **Cas9/Cas12a editing (HDR/indels)** – general genome editing frameworks. (See CRISPRi/a above for platform intros; add Jinek/Mali as needed.)
* **Base editors** – precise C→T or A→G edits without DSB. [Nature](https://www.nature.com/articles/nature17946?utm_source=chatgpt.com)
* **Prime editing** – templated small insertions/point edits without DSB. [Nature](https://www.nature.com/articles/s41586-019-1711-4?utm_source=chatgpt.com)
* **Epigenetic editors (CRISPRoff/on)** – heritable silencing/rewiring without changing DNA sequence. [Cell](https://www.cell.com/cell/fulltext/S0092-8674%2821%2900353-6?utm_source=chatgpt.com)
* **Lineage/event recorders (GESTALT, LINNAEUS)** – CRISPR barcoding of histories in tissues/organoids. [Science](https://www.science.org/doi/10.1126/science.aaf7907?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC5942543/?utm_source=chatgpt.com)
* **Light-gated CRISPR (PA-Cas9/CRISPRa; caged gRNAs)** – photo-tunable editing/TF control. [PubMed](https://pubmed.ncbi.nlm.nih.gov/26076431/?utm_source=chatgpt.com), [Europe PMC](https://europepmc.org/article/med/28892089?utm_source=chatgpt.com)

See also "synthetic transcription factors".