# The Synthetic Extracellular Matrix as a Maestro of the In Vitro Stem Cell Niche: Orchestrating Fate and Function

**Authors:** Subhajit Giri, Pratyush Rajesh

PMC · DOI: 10.3390/biomedicines14020485 · Biomedicines · 2026-02-23

## TL;DR

This paper discusses how synthetic extracellular matrices can better control stem cell behavior compared to traditional methods like Matrigel.

## Contribution

The paper introduces synthetic extracellular matrices as a defined and tunable alternative to Matrigel for hiPSC culture and differentiation.

## Key findings

- Synthetic ECM matrices offer fully defined and tunable properties for hiPSC culture.
- They can be functionalized with signaling peptides and growth factors for directed differentiation.
- Synthetic matrices are suitable for clinical-grade tissue engineering and regenerative medicine.

## Abstract

Human-induced pluripotent stem cells (hiPSCs) have an innate ability to differentiate into the three germ layers: the ectoderm, endoderm, and mesoderm. By using targeted differentiation methods and carefully controlling growth factors, morphogens, and signaling modulators, hiPSCs can be guided to develop into specific lineage cell types. For clinical applications of hiPSCs and their derivatives, it is crucial to use xenogen-free, chemically defined culture media, reagents, recombinant growth factors, morphogens, and extracellular matrix (ECM) scaffolds. One major obstacle is the widespread use of Matrigel as an hiPSC culture matrix. Matrigel, derived from Engelbreth–Holm–Swarm (EHS) mouse sarcoma, is an extract of basement membrane material with a complex, poorly defined, and variable composition. It also exhibits batch-to-batch variability in mechanical and biochemical properties and is difficult to modify, which limits its rational use in the production of therapeutic cells and organoids. Synthetic ECM matrices and scaffolds offer a promising alternative because they can have a fully defined composition, highly tunable physical properties, surface modifications, and functionalization with recombinant signaling peptides and growth factors. This provides a suitable microenvironment for hiPSC culture and the directed differentiation towards lineage-specific cells and organoid development, and can be used in clinical-grade tissue transplantation and regenerative medicine.

## Full-text entities

- **Genes:** PTK2 (protein tyrosine kinase 2) [NCBI Gene 5747] {aka FADK, FADK 1, FAK, FAK1, FRNK, PPP1R71}, FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, ADAM17 (ADAM metallopeptidase domain 17) [NCBI Gene 6868] {aka ADAM18, CD156B, CSVP, HYPT16, NISBD, NISBD1}, TP63 (tumor protein p63) [NCBI Gene 8626] {aka AIS, B(p51A), B(p51B), EEC3, KET, LMS}, CDH2 (cadherin 2) [NCBI Gene 1000] {aka ACOGS, ADHD8, ARVD14, CD325, CDHN, CDw325}, FGF2 (fibroblast growth factor 2) [NCBI Gene 2247] {aka BFGF, FGF-2, FGFB, HBGF-2}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, LPA (lipoprotein(a)) [NCBI Gene 4018] {aka AK38, APOA, LP}, RHO (rhodopsin) [NCBI Gene 6010] {aka CSNBAD1, OPN2, RP4}, ELN (elastin) [NCBI Gene 2006] {aka ADCL1, SVAS, WBS, WS}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, LGR5 (leucine rich repeat containing G protein-coupled receptor 5) [NCBI Gene 8549] {aka FEX, GPR49, GPR67, GRP49, HG38}, Nkx6-1 (NK6 homeobox 1) [NCBI Gene 18096] {aka NKX6A, Nkx6.1}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}, CDKN1B (cyclin dependent kinase inhibitor 1B) [NCBI Gene 1027] {aka CDKN4, KIP1, MEN1B, MEN4, P27KIP1}, RAPGEF5 (Rap guanine nucleotide exchange factor 5) [NCBI Gene 9771] {aka GFR, MR-GEF, MRGEF, REPAC}, Bmp4 (bone morphogenetic protein 4) [NCBI Gene 12159] {aka Bmp-4, Bmp2b, Bmp2b-1, Bmp2b1}, NKX2-1 (NK2 homeobox 1) [NCBI Gene 7080] {aka BCH, BHC, NK-2, NKX2.1, NKX2A, NMTC1}, MAPK14 (mitogen-activated protein kinase 14) [NCBI Gene 1432] {aka CSBP, CSBP1, CSBP2, CSPB1, EXIP, Mxi2}, CYP4F3 (cytochrome P450 family 4 subfamily F member 3) [NCBI Gene 4051] {aka CPF3, CYP4F, CYPIVF3, LTB4H}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, GATA3 (GATA binding protein 3) [NCBI Gene 2625] {aka HDR, HDRS}, SRC (SRC proto-oncogene, non-receptor tyrosine kinase) [NCBI Gene 6714] {aka ASV, SRC1, THC6, c-SRC, p60-Src}, Pdx1 (pancreatic and duodenal homeobox 1) [NCBI Gene 18609] {aka IDX-1, IPF-1, Ipf1, Mody4, STF-1, pdx-1}, DNM1L (dynamin 1 like) [NCBI Gene 10059] {aka DLP1, DRP1, DVLP, DYMPLE, EMPF, EMPF1}, NCAM1 (neural cell adhesion molecule 1) [NCBI Gene 4684] {aka CD56, MSK39, NCAM}, TAFAZZIN (tafazzin, phospholipid-lysophospholipid transacylase) [NCBI Gene 6901] {aka BTHS, CMD3A, EFE, EFE2, G4.5, LVNCX}, OLIG2 (oligodendrocyte transcription factor 2) [NCBI Gene 10215] {aka BHLHB1, OLIGO2, PRKCBP2, RACK17, bHLHe19}, VTN (vitronectin) [NCBI Gene 7448] {aka V75, VN, VNT}, RELN (reelin) [NCBI Gene 5649] {aka ETL7, LIS2, PRO1598, RL}, IGF1 (insulin like growth factor 1) [NCBI Gene 3479] {aka IGF, IGF-I, IGFI, MGF}, LMNA (lamin A/C) [NCBI Gene 4000] {aka CDCD1, CDDC, CMD1A, CMT2B1, EMD2, FPL}, LAMB2 (laminin subunit beta 2) [NCBI Gene 3913] {aka LAMS, NPHS5, PIERS}, TRPV4 (transient receptor potential cation channel subfamily V member 4) [NCBI Gene 59341] {aka BCYM3, CMT2C, HMSN2C, OTRPC4, SMAL, SPSMA}, YAP1 (Yes1 associated transcriptional regulator) [NCBI Gene 10413] {aka COB1, YAP, YAP-1, YAP2, YAP65, YKI}, ALPP (alkaline phosphatase, placental) [NCBI Gene 250] {aka ALP, PALP, PLAP, PLAP-1}, RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860] {aka AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD}, RHOA (ras homolog family member A) [NCBI Gene 387] {aka ARH12, ARHA, EDFAOB, RHO12, RHOH12}, GCM1 (GCM transcription factor 1) [NCBI Gene 8521] {aka GCMA, hGCMa}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, FOXJ1 (forkhead box J1) [NCBI Gene 2302] {aka CILD43, FKHL13, HFH-4, HFH4}
- **Diseases:** myocardial infarction (MESH:D009203), retinal degeneration (MESH:D012162), bone-injured (MESH:D001847), cytotoxicity (MESH:D064420), kidney cysts (MESH:D007674), hepatic disease (MESH:D056486), fibrosis (MESH:D005355), hyperglycemia (MESH:D006943), injury to (MESH:D014947), degenerative eye diseases (MESH:D019636), inflammation (MESH:D007249), diabetic (MESH:D003920), tumor (MESH:D009369), chronic kidney disease (MESH:D051436), EHS (MESH:D012513), AMD (MESH:D008268), hypoxia (MESH:D000860)
- **Chemicals:** Y27632 (MESH:C108830), Gelatin-Dextran (-), Arginylglycylaspartic acid (MESH:C047981), bisacrylamide (MESH:C021221), GAG (MESH:D006025), RA (MESH:D014212), Pluronic F127 (MESH:D020442), carbon nanotubes (MESH:D037742), polyester (MESH:D011091), HEMA (MESH:C005044), PVA (MESH:D011142), thiol (MESH:D013438), Ti6Al4V (MESH:C031462), -poly(epsilon-caprolactone) (MESH:C016240), guggulsterone (MESH:C023617), Polystyrene (MESH:D011137), PDMS (MESH:C013830), maleimide (MESH:C043592), PMEDSAH (MESH:C568649), PLLA (MESH:C033616), lipid (MESH:D008055), cellulose (MESH:D002482), heparin (MESH:D006493), PLGA (MESH:D000077182), Poly(N-isopropylacrylamide (MESH:C052970), Gellan Gum (MESH:C048288), PEGDE (MESH:C035364), DBS (MESH:C001114), calcium (MESH:D002118), EDC (MESH:C024565), alkyne (MESH:D000480), ROS (MESH:D017382), poly(ethylene glycol) methacrylate (MESH:C524499), polyethersulfone (MESH:C022840), glucose (MESH:D005947), poly (OEGMA (MESH:C528061), PSS (MESH:C077114), PEG-diacrylate (MESH:C437167), Alginate (MESH:D000464), poly(N, N-dimethylacrylamide) (MESH:C429790), Chitosan (MESH:D048271), poly(styrene sulfonic acid) (MESH:C003321), PEG (MESH:D011092), azide (MESH:D001386), polysaccharide (MESH:D011134), PEG-dithiol (MESH:C535242), polypyrrole (MESH:C067635), vinyl sulfone (MESH:C009873), PAM (MESH:C016679), polymer (MESH:D011108), methylcellulose (MESH:D008747), polyglycolic acid (MESH:D011100), PHEMA (MESH:D011102), cytosine (MESH:D003596), water (MESH:D014867), PuraMatrix (MESH:C546681), retinoids (MESH:D012176), PA (MESH:C006903), VS (MESH:D014639), peptides (MESH:D010455)
- **Species:** Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Canis lupus familiaris (dog, subspecies) [taxon 9615]
- **Cell lines:** RPE — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_4388), ARPE-19 — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0145), hESCs — Homo sapiens (Human), Embryonic stem cell (CVCL_UI95), MEFs — Mus musculus (Mouse), Finite cell line (CVCL_9115), ESCs — Mus musculus (Mouse), Embryonic stem cell (CVCL_9108), EHS — Mus musculus (Mouse), Mouse chondrosarcoma, Cancer cell line (CVCL_3506)

## Full text

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## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12937747/full.md

## References

302 references — full list in the complete paper: https://tomesphere.com/paper/PMC12937747/full.md

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Source: https://tomesphere.com/paper/PMC12937747