# The extracellular matrix: structure, composition, biological functions, diseases, and therapeutic targets

**Authors:** Khairunnisa Mohd Kamal, Ahmad Rohi Ghazali, Gayathri Thevi Selvarajah, Nurul Syakima Ab Mutalib, Nadiah Abu, Eng Wee Chua, Siti Fathiah Masre

PMC · DOI: 10.1186/s43556-026-00436-1 · Molecular Biomedicine · 2026-03-26

## TL;DR

This review explores how the extracellular matrix interacts with epigenetic mechanisms to influence tissue health and disease, such as fibrosis and cancer.

## Contribution

The paper provides an integrated framework of bidirectional interactions between the extracellular matrix and epigenetic regulation in disease contexts.

## Key findings

- Epigenetic mechanisms like DNA methylation and histone modifications regulate extracellular matrix composition and signaling pathways.
- Matrix stiffness and epigenetic changes work together to drive pathological tissue remodeling and tumor progression.
- Therapeutic strategies targeting the ECM-epigenetic axis are emerging, though challenges remain in restoring matrix homeostasis.

## Abstract

The extracellular matrix (ECM) is a highly organised and dynamic regulator of tissue structural integrity and biochemical signalling, and its dysregulation is a hallmark of fibrosis and cancer. Recent evidence highlights the critical role of epigenetic mechanisms in controlling ECM-related gene expression and remodelling activity. This review integrates recent advances in understanding how epigenetic mechanisms govern ECM composition, remodelling, and mechanotransduction, and how reciprocal ECM-derived signals reshape the epigenetic landscape. Growing evidence links DNA methylation, histone modifications, and non-coding RNAs to the regulation of key ECM components, matrix-modifying enzymes, and stiffness-associated signalling pathways, including TGF-β, Wnt, and PI3K/Akt are summarised in this review. The bidirectional feedback between altered ECM mechanics and epigenetic enzyme activity is emphasised, showing how matrix stiffening and aberrant epigenetic programming cooperatively drive pathological tissue remodelling and tumour progression. This review summarises findings from in vitro systems, animal models, and human disease studies that illustrate the functional consequences of ECM-epigenetic crosstalk. The emerging therapeutic approaches targeting the ECM-epigenetic axis, including epigenetic modulators and ECM-directed interventions, outline current challenges and future directions for restoring matrix homeostasis in disease. Together, this review provides an integrated framework for understanding the bidirectional ECM-epigenetic interactions and their translational relevance in molecular biomedicine.

## Linked entities

- **Proteins:** TGFB1 (transforming growth factor beta 1), Wnt (protein Wnt-2)
- **Diseases:** cancer (MONDO:0004992)

## Full-text entities

- **Genes:** TIMP1 (TIMP metallopeptidase inhibitor 1) [NCBI Gene 7076] {aka CLGI, EPA, EPO, HCI, TIMP, TIMP-1}, HDAC6 (histone deacetylase 6) [NCBI Gene 10013] {aka CPBHM, HD6, JM21, KDAC6, PPP1R90}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, VTCN1 (V-set domain containing T cell activation inhibitor 1) [NCBI Gene 79679] {aka B7-H4, B7H4, B7S1, B7X, B7h.5, PRO1291}, H2AC18 (H2A clustered histone 18) [NCBI Gene 8337] {aka H2A, H2A.2, H2A/O, H2A/q, H2AFO, H2a-615}, LAMB2 (laminin subunit beta 2) [NCBI Gene 3913] {aka LAMS, NPHS5, PIERS}, LOXL3 (lysyl oxidase like 3) [NCBI Gene 84695] {aka LOXL, MYP28}, Dnmt3l (DNA methyltransferase 3-like) [NCBI Gene 54427] {aka D6Ertd14e, ecat7}, LOXL2 (lysyl oxidase like 2) [NCBI Gene 4017] {aka LOR, LOR2, WS9-14}, HGF (hepatocyte growth factor) [NCBI Gene 3082] {aka DFNB39, F-TCF, HGFB, HPTA, SF}, COL7A1 (collagen type VII alpha 1 chain) [NCBI Gene 1294] {aka EBD1, EBDCT, EBR1, NDNC8}, FBN2 (fibrillin 2) [NCBI Gene 2201] {aka CCA, DA9, EOMD}, HOTAIR (HOX transcript antisense RNA) [NCBI Gene 100124700] {aka HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072}, Ptk2 (PTK2 protein tyrosine kinase 2) [NCBI Gene 14083] {aka FADK 1, FAK, FRNK, Fadk, p125FAK}, FBLN2 (fibulin 2) [NCBI Gene 2199], ACOT12 (acyl-CoA thioesterase 12) [NCBI Gene 134526] {aka CACH-1, Cach, STARD15, THEAL}, MALAT1 (metastasis associated lung adenocarcinoma transcript 1) [NCBI Gene 378938] {aka HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, miPEP-52}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, JAG1 (jagged canonical Notch ligand 1) [NCBI Gene 182] {aka AGS, AGS1, AHD, AWS, CD339, CMT2HH}, TAFAZZIN (tafazzin, phospholipid-lysophospholipid transacylase) [NCBI Gene 6901] {aka BTHS, CMD3A, EFE, EFE2, G4.5, LVNCX}, ELN (elastin) [NCBI Gene 2006] {aka ADCL1, SVAS, WBS, WS}, ACTA1 (actin alpha 1, skeletal muscle) [NCBI Gene 58] {aka ACTA, ASMA, CFTD, CFTD1, CFTDM, CMYO2A}, FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, H19 (H19 imprinted maternally expressed transcript) [NCBI Gene 283120] {aka ASM, ASM1, BWS, D11S813E, GMRSP, LINC00008}, MRTFA (myocardin related transcription factor A) [NCBI Gene 57591] {aka BSAC, MAL, MKL, MKL1, MRTF-A}, Col11a1 (collagen, type XI, alpha 1) [NCBI Gene 12814] {aka C530001D20Rik, cho}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, HNMT (histamine N-methyltransferase) [NCBI Gene 3176] {aka HMT, HNMT-S1, HNMT-S2, MRT51}, TNC (tenascin C) [NCBI Gene 3371] {aka 150-225, DFNA56, GMEM, GP, HXB, JI}, PRDM9 (PR/SET domain 9) [NCBI Gene 56979] {aka KMT8B, MEISETZ, MSBP3, PFM6, ZNF899}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, Src (src proto-oncogene, non-receptor tyrosine kinase) [NCBI Gene 20779] {aka pp60c-src}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, Prkca (protein kinase C, alpha) [NCBI Gene 18750] {aka Pkca}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, ACAN (aggrecan) [NCBI Gene 176] {aka AGC1, AGCAN, CSPG1, CSPGCP, MSK16, SEDK}, TIMP3 (TIMP metallopeptidase inhibitor 3) [NCBI Gene 7078] {aka HSMRK222, K222, K222TA2, SFD}, RHOA (ras homolog family member A) [NCBI Gene 387] {aka ARH12, ARHA, EDFAOB, RHO12, RHOH12}, SETD7 (SET domain containing 7, histone lysine methyltransferase) [NCBI Gene 80854] {aka KMT7, SET7, SET7/9, SET9}, LOX (lysyl oxidase) [NCBI Gene 4015] {aka AAT10}, Cthrc1 (collagen triple helix repeat containing 1) [NCBI Gene 68588] {aka 1110014B07Rik}, TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790] {aka IMD75, KIAA1546, MDS}, SNCA (synuclein alpha) [NCBI Gene 6622] {aka NACP, PARK1, PARK4, PD1}, ITGA4 (integrin subunit alpha 4) [NCBI Gene 3676] {aka CD49D, IA4}, Col10a1 (collagen, type X, alpha 1) [NCBI Gene 12813] {aka Col10, Col10a-1}, MIR21 (microRNA 21) [NCBI Gene 406991] {aka MIRN21, hsa-mir-21, miR-21, miRNA21}, AP1S2 (adaptor related protein complex 1 subunit sigma 2) [NCBI Gene 8905] {aka DC22, MRX59, MRXS21, MRXS5, MRXSF, PGS}, MET (MET proto-oncogene, receptor tyrosine kinase) [NCBI Gene 4233] {aka AUTS9, DA11, DFNB97, HGFR, RCCP2, c-Met}, KMT2A (lysine methyltransferase 2A) [NCBI Gene 4297] {aka ALL-1, ALL1, CXXC7, GAS7, HRX, HTRX}, MMRN1 (multimerin 1) [NCBI Gene 22915] {aka ECM, EMILIN4, GPIa*, MMRN}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, YAP1 (Yes1 associated transcriptional regulator) [NCBI Gene 10413] {aka COB1, YAP, YAP-1, YAP2, YAP65, YKI}, H2BC21 (H2B clustered histone 21) [NCBI Gene 8349] {aka GL105, H2B, H2B-GL105, H2B.1, H2BE, H2BFQ}, KDM6B (lysine demethylase 6B) [NCBI Gene 23135] {aka JMJD3, NEDCFSA, NEDSST}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, Dnmt1 (DNA methyltransferase 1) [NCBI Gene 13433] {aka Cxxc9, Dnmt, Dnmt1o, MCMT, MTase, Met-1}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, BGLAP (bone gamma-carboxyglutamate protein) [NCBI Gene 632] {aka BGP, OC, OCN}
- **Diseases:** lung cancer (MESH:D008175), Fibrosis (MESH:D005355), tissue injury (MESH:D017695), tumorigenesis (MESH:D063646), kidney, and lung diseases (MESH:D007674), multiple sclerosis (MESH:D009103), ECM dysregulation (MESH:C535509), Cancer (MESH:D009369), oncogenes (MESH:D000074723), NAFLD (MESH:D065626), obesity (MESH:D009765), cardiovascular, metabolic, neurological, and autoimmune diseases (MESH:D020274), T2DM (MESH:D003924), fibrodegenerative diseases (MESH:D004194), hypoxia (MESH:D000860), pathologic remodelling (MESH:D066253), atopic dermatitis (MESH:D003876), metastasis (MESH:D009362), mammary and prostate cancers (MESH:D011471), cardiac damage (MESH:D006331), metabolic disease (MESH:D008659), melanoma (MESH:D008545), joint destruction (MESH:D008105), autoimmune conditions (MESH:D001327), neuroblastoma (MESH:D009447), insulin resistance (MESH:D007333), organ dysfunction (MESH:D009102), cartilage breakdown (MESH:D002357), fibrotic disorders (MESH:D009358), cardiovascular, and musculoskeletal diseases (MESH:D009140), thyroid carcinoma (MESH:D013964), idiopathic pulmonary fibrosis (MESH:D054990), vascular dysfunction (MESH:D002561), inflammatory bowel disease (MESH:D015212), rheumatoid arthritis (MESH:D001172), oral cancer (MESH:D009062), hematologic malignancies (MESH:D019337), systemic sclerosis (MESH:D012595), Cardiovascular and musculoskeletal disorders (MESH:D009139), neurodegeneration (MESH:D019636), inflammatory cytokines (MESH:D000080424), steatohepatitis (MESH:D005234), chronic inflammation (MESH:D007249), osteoarthritis (MESH:D010003), cardiac remodelling (MESH:D020257), chronic obstructive pulmonary disease (MESH:D029424), oral SCC (MESH:D000077195), neurological diseases (MESH:D020271), SCC (MESH:D002294), lung (MESH:D008171), ovarian cancer (MESH:D010051), liver and lung fibrosis (MESH:D008103), colon cancer (MESH:D015179), Parkinson's disease (MESH:D010300), gastric cancer (MESH:D013274), neuropsychiatric disorders (MESH:D001523), Alzheimer's disease (MESH:D000544), cardiovascular, and metabolic disorders (MESH:D024821), neuroinflammation (MESH:D000090862), HCC (MESH:D006528)
- **Chemicals:** panobinostat (MESH:D000077767), defactinib (MESH:C584510), GAGs (MESH:D006025), azacitidine (MESH:D001374), H2O2 (MESH:D006861), 5-aza (-), 5-aza-dC (MESH:D000077209), trichostatin A (MESH:C012589), lysine (MESH:D008239), Tazemetostat (MESH:C000593333), cisplatin (MESH:D002945), pirfenidone (MESH:C093844), S-adenosylmethionine (MESH:D012436), polysaccharides (MESH:D011134), water (MESH:D014867), hyaluronan (MESH:D006820), sugars (MESH:D000073893), nintedanib (MESH:C530716), cytosine (MESH:D003596), simtuzumab (MESH:C000613471), ammonia (MESH:D000641), vorinostat (MESH:D000077337), 5-methylcytosine (MESH:D044503), acetyl-CoA (MESH:D000105)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** H19X

## Full text

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## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13022127/full.md

## References

14 references — full list in the complete paper: https://tomesphere.com/paper/PMC13022127/full.md

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Source: https://tomesphere.com/paper/PMC13022127