# Implication of Epigenetic Alterations of ZEB1 in Colorectal Cancer (CRC) Pathogenesis and Therapy Development

**Authors:** Tasnima Kamal, Asma Ul Husna Biswas, Azadur Rahman Bhuiyan, Al-Amin Hossain, Chandan Barai, Yearul Kabir, Farhadul Islam

PMC · DOI: 10.3390/cimb48030276 · Current Issues in Molecular Biology · 2026-03-04

## TL;DR

This paper reviews how ZEB1, a key protein in colorectal cancer, influences cancer progression through epigenetic changes and signaling pathways, offering insights for new therapies.

## Contribution

The paper provides a comprehensive review of ZEB1's role in CRC by integrating epigenetic, ncRNA, and signaling pathway interactions.

## Key findings

- ZEB1 promotes CRC metastasis by silencing epithelial markers and inducing mesenchymal properties.
- ZEB1 coordinates epigenetic reprogramming through histone and DNA modifications.
- Oncogenic signaling pathways regulate ZEB1 activity, making it a central node in CRC progression.

## Abstract

Colorectal cancer (CRC) is a significant cause of cancer mortality in the world, and its etiology is complicated by genetic and epigenetic changes. As one of the most important tumor progression regulators, Zinc Finger E-box Binding Homeobox 1 (ZEB1) is a transcription factor that has a key role in epithelial–mesenchymal transition (EMT), which is essential in the metastasis, drug resistance, and plasticity of cancer cells in CRC. ZEB1 silences the expression of epithelial markers, including E-cadherin, and it induces the development of mesenchymal properties, such as invasion and metastasis, i.e., tumor aggressiveness. ZEB1 drives epigenetic reprogramming in CRC by coordinating histone deacetylation, histone methylation, and DNA methylation of epithelial tumor suppressor gene promoters and by engaging in reciprocal regulatory interactions with non-coding RNAs, including the miR-200 family. Furthermore, multiple oncogenic signaling cascades, including Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α, converge on ZEB1 to amplify its transcriptional and epigenetic activity, positioning ZEB1 as a nodal integrator of extracellular cues and epigenetic reprogramming in CRC metastasis. This review integrates three interconnected regulatory layers, i.e., (1) ZEB1’s direct epigenetic control of target gene expression via histone modification and DNA methylation, (2) post-transcriptional regulation of ZEB1 itself by ncRNAs (miRNAs, circRNAs, and lncRNAs) that create feedback circuits modulating layer 1, and (3) upstream modulation of ZEB1 transcriptional activity by oncogenic signaling pathways (Wnt/β-catenin, TGF-β, NF-κB, MEK-ERK, JAK/STAT3, and HIF-1α) to provide a comprehensive picture of ZEB1 in CRC metastasis and its therapeutic implications.

## Linked entities

- **Genes:** ZEB1 (zinc finger E-box binding homeobox 1) [NCBI Gene 6935], shg (shotgun) [NCBI Gene 37386]
- **Proteins:** ZEB1 (zinc finger E-box binding homeobox 1), ctnnb1.S (catenin beta 1 S homeolog), TGFB1 (transforming growth factor beta 1), NFKB1 (nuclear factor kappa B subunit 1), HIF1A (hypoxia inducible factor 1 subunit alpha)
- **Diseases:** Colorectal cancer (MONDO:0005575), CRC (MONDO:0005575)

## Full-text entities

- **Genes:** TFRC (transferrin receptor) [NCBI Gene 7037] {aka CD71, IMD46, T9, TFR, TFR1, TR}, ZEB1 (zinc finger E-box binding homeobox 1) [NCBI Gene 6935] {aka AREB6, BZP, DELTAEF1, FECD6, NIL2A, PPCD3}, SMAD7 (SMAD family member 7) [NCBI Gene 4092] {aka CRCS3, MADH7, MADH8}, E2F3 (E2F transcription factor 3) [NCBI Gene 1871] {aka E2F-3}, PSMD4 (proteasome 26S subunit ubiquitin receptor, non-ATPase 4) [NCBI Gene 5710] {aka AF, AF-1, ASF, MCB1, Rpn10, S5A}, MIR205 (microRNA 205) [NCBI Gene 406988] {aka MIRN205, mir-205}, PHLPP1 (PH domain and leucine rich repeat protein phosphatase 1) [NCBI Gene 23239] {aka PHLPP, PLEKHE1, PPM3A, SCOP}, PRDM9 (PR/SET domain 9) [NCBI Gene 56979] {aka KMT8B, MEISETZ, MSBP3, PFM6, ZNF899}, DAPK1 (death associated protein kinase 1) [NCBI Gene 1612] {aka DAPK, ROCO3}, PROM1 (prominin 1) [NCBI Gene 8842] {aka AC133, CD133, CORD12, MCDR2, MSTP061, PROML1}, PURPL (p53 upregulated regulator of p53 levels) [NCBI Gene 643401] {aka LINC01021}, CCND1 (cyclin D1) [NCBI Gene 595] {aka BCL1, D11S287E, PRAD1, U21B31}, FBXO45 (F-box protein 45) [NCBI Gene 200933] {aka Fbx45}, CDKN2B (cyclin dependent kinase inhibitor 2B) [NCBI Gene 1030] {aka CDK4I, INK4B, MTS2, P15, TP15, p15INK4b}, HIF3A (hypoxia inducible factor 3 subunit alpha) [NCBI Gene 64344] {aka HIF-3A, HIF3-alpha-1, IPAS, MOP7, PASD7, bHLHe17}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, MECP2 (methyl-CpG binding protein 2) [NCBI Gene 4204] {aka AUTSX3, MRX16, MRX79, MRXS13, MRXSL, PPMX}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, HDAC2 (histone deacetylase 2) [NCBI Gene 3066] {aka HD2, KDAC2, RPD3, YAF1}, YAP1 (Yes1 associated transcriptional regulator) [NCBI Gene 10413] {aka COB1, YAP, YAP-1, YAP2, YAP65, YKI}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, TJP3 (tight junction protein 3) [NCBI Gene 27134] {aka ZO-3, ZO3}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, MIR200C (microRNA 200c) [NCBI Gene 406985] {aka MIRN200C, mir-200c}, SPI1 (Spi-1 proto-oncogene) [NCBI Gene 6688] {aka AGM10, OF, PU.1, SFPI1, SPI-1, SPI-A}, GSK3B (glycogen synthase kinase 3 beta) [NCBI Gene 2932], NLRP2 (NLR family pyrin domain containing 2) [NCBI Gene 55655] {aka CLR19.9, NALP2, NBS1, OZEMA18, PAN1, PYPAF2}, CDH1 (cadherin 1) [NCBI Gene 999] {aka Arc-1, BCDS1, CD324, CDHE, ECAD, LCAM}, MIR34A (microRNA 34a) [NCBI Gene 407040] {aka MIRN34A, miRNA34A, mir-34, mir-34a}, PTK2 (protein tyrosine kinase 2) [NCBI Gene 5747] {aka FADK, FADK 1, FAK, FAK1, FRNK, PPP1R71}, HTR2B (5-hydroxytryptamine receptor 2B) [NCBI Gene 3357] {aka 5-HT(2B), 5-HT-2B, 5-HT2B}, DDX3X (DEAD-box helicase 3 X-linked) [NCBI Gene 1654] {aka CAP-Rf, DBX, DDX14, DDX3, HLP2, MRX102}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, KAT2B (lysine acetyltransferase 2B) [NCBI Gene 8850] {aka CAF, P/CAF, PCAF}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, MIR708 (microRNA 708) [NCBI Gene 100126333] {aka MIRN708, hsa-mir-708}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, RAF1 (Raf-1 proto-oncogene, serine/threonine kinase) [NCBI Gene 5894] {aka CMD1NN, CRAF, NS5, Raf-1, c-Raf}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, MIR200B (microRNA 200b) [NCBI Gene 406984] {aka MIRN200B, mir-200b}, CREBBP (CREB binding lysine acetyltransferase) [NCBI Gene 1387] {aka CBP, KAT3A, MKHK1, RSTS, RSTS1}, e2f1.L (E2F transcription factor 1 L homeolog) [NCBI Gene 100036852] {aka e2f1, xE2F}, EPCAM (epithelial cell adhesion molecule) [NCBI Gene 4072] {aka Ber-Ep4, BerEp4, DIAR5, EGP-2, EGP314, EGP40}, SMAD3 (SMAD family member 3) [NCBI Gene 4088] {aka HSPC193, HsT17436, JV15-2, LDS1C, LDS3, MADH3}, zeb1.L (zinc finger E-box binding homeobox 1 L homeolog) [NCBI Gene 444391] {aka areb6, bzp, deltaef1, fecd6, nil-2a, nil2a}, CHD1L (chromodomain helicase DNA binding protein 1 like) [NCBI Gene 9557] {aka ALC1, CHDL}, TWIST1 (twist family bHLH transcription factor 1) [NCBI Gene 7291] {aka ACS3, BPES2, BPES3, CRS, CRS1, CSO}, PHF20 (PHD finger protein 20) [NCBI Gene 51230] {aka C20orf104, GLEA2, HCA58, NZF, TDRD20A, TZP}, CXCL8 (C-X-C motif chemokine ligand 8) [NCBI Gene 3576] {aka GCP-1, GCP1, IL8, LECT, LUCT, LYNAP}, SLCO4A1-AS1 (SLCO4A1 antisense RNA 1) [NCBI Gene 100127888] {aka DAMER}, GRHL2 (grainyhead like transcription factor 2) [NCBI Gene 79977] {aka BOM, DFNA28, ECTDS, PPCD4, TFCP2L3}, stat6.L (signal transducer and activator of transcription 6 L homeolog) [NCBI Gene 495683] {aka stat6}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, AREG (amphiregulin) [NCBI Gene 374] {aka AR, AREGB, CRDGF, SDGF}, NFE2L2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 4780] {aka IMDDHH, NRF2, Nrf-2}, PLK1 (polo like kinase 1) [NCBI Gene 5347] {aka PLK, STPK13}, HNRNPK (heterogeneous nuclear ribonucleoprotein K) [NCBI Gene 3190] {aka AUKS, CSBP, HNRPK, TUNP}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, NADSYN1 (NAD synthetase 1) [NCBI Gene 55191] {aka VCRL3}, CD47 (CD47 molecule) [NCBI Gene 961] {aka IAP, MER6, OA3}
- **Diseases:** inflammation (MESH:D007249), fatigue (MESH:D005221), hypoxic (MESH:D002534), lymph node metastasis (MESH:D008207), aggressive (MESH:D010554), Tumor (MESH:D009369), mesenchymal (MESH:C535700), Hypoxia (MESH:D000860), chromosome abnormalities (MESH:D002869), DR (MESH:D004370), CRC (MESH:D015179), toxicity (MESH:D064420), tumorigenesis (MESH:D063646), deaths (MESH:D003643), liver metastasis (MESH:D009362), injury to (MESH:D014947)
- **Chemicals:** butyrate (MESH:D002087), etoposide (MESH:D005047), GTP (MESH:D006160), RS127445 (MESH:C121466), doxorubicin (MESH:D004317), cisplatin (MESH:D002945), 5-FU (MESH:D005472), UA (MESH:C005466), m6A (MESH:C005955), OXA (MESH:D000077150), iron (MESH:D007501), vorinostat (MESH:D000077337), LBH589 (MESH:D000077767), oxygen (MESH:D010100), H3K4 (-)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** BRAFV600E, G12D, Q22K
- **Cell lines:** LoVo — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0399), RKO — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_0504), HCT-116 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_0291), SW480 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0546), RP11-138J23.1 — Cricetulus griseus (Chinese hamster), Hybrid cell line (CVCL_1Q55), DLD1 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0248), HT-29 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0320), HCT-R — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_RB18), HCT-8 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_2478), SW480KD — Mus musculus (Mouse), Mouse lymphoma, Cancer cell line (CVCL_IU35), LS174T — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_1384)

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13026001/full.md

## References

177 references — full list in the complete paper: https://tomesphere.com/paper/PMC13026001/full.md

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Source: https://tomesphere.com/paper/PMC13026001