# The Crucial Role of Epigenetic Modifications in Wharton’s Jelly Stem Cells

**Authors:** Mao Yang, Juan Wang, Wensheng Deng, Qiang Wu

PMC · DOI: 10.3390/ijms26157169 · International Journal of Molecular Sciences · 2025-07-24

## TL;DR

This paper reviews how epigenetic changes control the function of Wharton’s jelly stem cells, which are important for regenerative medicine.

## Contribution

The paper provides a comprehensive review of epigenetic mechanisms regulating Wharton’s jelly stem cells for regenerative applications.

## Key findings

- Epigenetic modifications like DNA methylation and histone changes regulate stem cell behavior.
- Non-coding RNAs play a role in modulating gene expression in Wharton’s jelly stem cells.
- Understanding these mechanisms could improve stem cell therapies for tissue repair.

## Abstract

Wharton’s jelly mesenchymal stem cells (WJ-SCs) are a promising source for regenerative medicine due to their multipotency, low immunogenicity, and ethical acceptability. Epigenetic regulation plays a crucial role in modulating their proliferation, differentiation, and therapeutic potential. Key mechanisms, including DNA methylation, histone modifications, and non-coding RNAs (e.g., miRNAs and lncRNAs), influence WJ-SC behavior by dynamically altering gene expression without changing the DNA sequence. DNA methylation often silences genes involved in differentiation, while histone acetylation/methylation can activate or repress lineage-specific pathways. Non-coding RNAs further fine-tune these processes by post-transcriptional regulation. Understanding these mechanisms could optimize WJ-SC-based therapies for tissue repair and immune modulation. This review summarizes current insights into epigenetic regulation in WJ-SCs and its implications for regenerative applications.

## Full-text entities

- **Genes:** MKRN2 (makorin ring finger protein 2) [NCBI Gene 23609] {aka HSPC070, RNF62}, EIF3A (eukaryotic translation initiation factor 3 subunit A) [NCBI Gene 8661] {aka EIF3, EIF3S10, P167, TIF32, eIF3-p170, eIF3-theta}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, GATA2 (GATA binding protein 2) [NCBI Gene 2624] {aka DCML, IMD21, MONOMAC, NFE1B}, MITF (melanocyte inducing transcription factor) [NCBI Gene 4286] {aka CMM8, COMMAD, MI, MITF-A, WS2, WS2A}, TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790] {aka IMD75, KIAA1546, MDS}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, NT5E (5'-nucleotidase ecto) [NCBI Gene 4907] {aka CALJA, CD73, E5NT, NT, NT5, NTE}, PROM1 (prominin 1) [NCBI Gene 8842] {aka AC133, CD133, CORD12, MCDR2, MSTP061, PROML1}, BMI1 (BMI1 proto-oncogene, polycomb ring finger) [NCBI Gene 648] {aka FLVI2/BMI1, PCGF4, RNF51, flvi-2/bmi-1}, KDM3A (lysine demethylase 3A) [NCBI Gene 55818] {aka JHDM2A, JHMD2A, JMJD1, JMJD1A, TSGA}, TGFBR2 (transforming growth factor beta receptor 2) [NCBI Gene 7048] {aka AAT3, FAA3, LDS1B, LDS2, LDS2B, MFS2}, EID3 (EP300 interacting inhibitor of differentiation 3) [NCBI Gene 493861] {aka NS4EB, NSE4B, NSMCE4B}, H19 (H19 imprinted maternally expressed transcript) [NCBI Gene 283120] {aka ASM, ASM1, BWS, D11S813E, GMRSP, LINC00008}, MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, CDKN1C (cyclin dependent kinase inhibitor 1C) [NCBI Gene 1028] {aka BWCR, BWS, KIP2, WBS, p57, p57Kip2}, COX2 (cytochrome c oxidase subunit II) [NCBI Gene 4513] {aka COII, MTCO2}, EP300 (EP300 lysine acetyltransferase) [NCBI Gene 2033] {aka KAT3B, MKHK2, RSTS2, p300}, NCAPD2 (non-SMC condensin I complex subunit D2) [NCBI Gene 9918] {aka CAP-D2, CNAP1, MCPH21, hCAP-D2}, CXCR2 (C-X-C motif chemokine receptor 2) [NCBI Gene 3579] {aka CD182, CDw128b, CMKAR2, IL8R2, IL8RA, IL8RB}, NOP2 (NOP2 nucleolar protein) [NCBI Gene 4839] {aka NOL1, NOP120, NSUN1, p120}, KRT8 (keratin 8) [NCBI Gene 3856] {aka CARD2, CK-8, CK8, CYK8, K2C8, K8}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, PTGES (prostaglandin E synthase) [NCBI Gene 9536] {aka MGST-IV, MGST1-L1, MGST1L1, MPGES, PGES, PIG12}, TBX5 (T-box transcription factor 5) [NCBI Gene 6910] {aka HOS}, MMP2 (matrix metallopeptidase 2) [NCBI Gene 4313] {aka CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1}, PPARGC1A (PPARG coactivator 1 alpha) [NCBI Gene 10891] {aka LEM6, PGC-1(alpha), PGC-1alpha, PGC-1v, PGC1, PGC1A}, MIR543 (microRNA 543) [NCBI Gene 100126335] {aka MIRN543, hsa-mir-543, mir-543}, SP7 (Sp7 transcription factor) [NCBI Gene 121340] {aka OI11, OI12, OSX, osterix}, H3C3 (H3 clustered histone 3) [NCBI Gene 8352] {aka H3.1, H3/c, H3FC, HIST1H3C}, MIR935 (microRNA 935) [NCBI Gene 100126325] {aka MIRN935, hsa-mir-935, mir-935}, KDM5B (lysine demethylase 5B) [NCBI Gene 10765] {aka CT31, JARID1B, MRT65, PLU-1, PLU1, PPP1R98}, BNIP3 (BCL2 interacting protein 3) [NCBI Gene 664] {aka HABON, NIP3}, MIR26B (microRNA 26b) [NCBI Gene 407017] {aka MIRN26B, hsa-mir-26b, miR-26b}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, LMNA (lamin A/C) [NCBI Gene 4000] {aka CDCD1, CDDC, CMD1A, CMT2B1, EMD2, FPL}, MIR1290 (microRNA 1290) [NCBI Gene 100302276] {aka MIRN1290, hsa-mir-1290}, MIR4521 (microRNA 4521) [NCBI Gene 100616406] {aka mir-4521}, POU5F1 (POU class 5 homeobox 1) [NCBI Gene 5460] {aka OCT3, OCT4, OCT4Borf1, OTF-3, OTF3, OTF4}, HOTTIP (HOXA distal transcript antisense RNA) [NCBI Gene 100316868] {aka HOXA-AS6, HOXA13-AS1, NCRNA00213}, ATOH8 (atonal bHLH transcription factor 8) [NCBI Gene 84913] {aka HATH6, bHLHa21}, HMGA2 (high mobility group AT-hook 2) [NCBI Gene 8091] {aka BABL, HMGI-C, HMGIC, LIPO, SRS5, STQTL9}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, TET1 (tet methylcytosine dioxygenase 1) [NCBI Gene 80312] {aka CXXC6, LCX, bA119F7.1}, CD34 (CD34 molecule) [NCBI Gene 947], VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, SIRT1 (sirtuin 1) [NCBI Gene 23411] {aka SIR2, SIR2L1, SIR2alpha}, YTHDF2 (YTH N6-methyladenosine RNA binding protein F2) [NCBI Gene 51441] {aka CAHL, DF2, HGRG8, NY-REN-2}, MIR145 (microRNA 145) [NCBI Gene 406937] {aka MIRN145, miR-145, miRNA145}, HDAC1 (histone deacetylase 1) [NCBI Gene 3065] {aka GON-10, HD1, KDAC1, RPD3, RPD3L1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, THY1 (Thy-1 cell surface antigen) [NCBI Gene 7070] {aka CD90, CDw90}, IFNG-AS1 (IFNG regulatory antisense RNA 1) [NCBI Gene 100885789] {aka GS1-410F4.2, NEST, Tmevpg1}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, ITIH5 (inter-alpha-trypsin inhibitor heavy chain 5) [NCBI Gene 80760] {aka ITI-HC5, PP14776}, RUNX2 (RUNX family transcription factor 2) [NCBI Gene 860] {aka AML3, CBF-alpha-1, CBFA1, CCD, CCD1, CLCD}, GAS5 (growth arrest specific 5) [NCBI Gene 60674] {aka NCRNA00030, SNHG2}, ALPP (alkaline phosphatase, placental) [NCBI Gene 250] {aka ALP, PALP, PLAP, PLAP-1}, ACKR3 (atypical chemokine receptor 3) [NCBI Gene 57007] {aka CMKOR1, CXC-R7, CXCR-7, CXCR7, GPR159, RDC-1}, MIR1275 (microRNA 1275) [NCBI Gene 100302123] {aka MIRN1275, hsa-mir-1275, mir-1275}
- **Diseases:** fibrosis (MESH:D005355), inflammatory (MESH:D007249), periodontitis (MESH:D010518), injury to (MESH:D014947), GVHD (MESH:D006086), liver fibrosis (MESH:D008103), cancer (MESH:D009369), chromosomal abnormalities (MESH:D002869), tumorigenesis (MESH:D063646), hypoxic (MESH:D002534), autoimmune and inflammatory diseases (MESH:D001327), WJ-SCs (MESH:D000092423), osteoarthritis (MESH:D010003), tumorigenicity (MESH:D002471), RA (MESH:D001172), embryonic lethality (MESH:D020964), teratomas (MESH:D013724), IBD (MESH:D015212), neurodevelopmental disorders (MESH:D002658), liver cancer (MESH:D006528)
- **Chemicals:** uridine (MESH:D014529), oxygen (MESH:D010100), N6-methyladenosine (MESH:C010223), S-adenosylmethionine (MESH:D012436), TSA (MESH:C012589), 5-mC (MESH:D044503), 5-methylcytidine (MESH:C016568), alpha-KG (MESH:D007656), 5-hmC (MESH:C011865), DM6B (-), arginine (MESH:D001120), FAD (MESH:D005182), VPA (MESH:D014635), Pseudouridine (MESH:D011560), N1-methyladenosine (MESH:C002230), lipid (MESH:D008055), sodium butyrate (MESH:D020148), ATP (MESH:D000255), 5-azacytidine (MESH:D001374), glucose (MESH:D005947), lysine (MESH:D008239)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** LNC12 — Mus musculus (Mouse), Mouse lymphoma, Cancer cell line (CVCL_9578), WJ — Homo sapiens (Human), Glioblastoma, Cancer cell line (CVCL_W352)

## Full text

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## Figures

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## References

135 references — full list in the complete paper: https://tomesphere.com/paper/PMC12345706/full.md

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Source: https://tomesphere.com/paper/PMC12345706