# Diet-Driven Epigenetic Alterations in Colorectal Cancer: From DNA Methylation and microRNA Expression to Liquid Biopsy Readouts

**Authors:** Theodora Chindea, Alina-Teodora Nicu, Gheorghe Dănuț Cimponeriu, Bianca Galateanu, Ariana Hudita, Mirela Violeta Șerban, Remus Iulian Nica, Liliana Burlibasa

PMC · DOI: 10.3390/biomedicines14020267 · Biomedicines · 2026-01-24

## TL;DR

This review explores how diet influences colorectal cancer through epigenetic changes and how liquid biopsy can detect these changes for early detection and prevention.

## Contribution

The paper introduces a novel framework for using diet-sensitive epigenetic signatures in liquid biopsy for personalized CRC risk assessment and prevention.

## Key findings

- Western diets cause global DNA hypomethylation and hypermethylation of tumor suppressor genes.
- Mediterranean diet compounds like resveratrol and curcumin can restore epigenetic balance.
- Circulating methylated DNA and microRNAs in liquid biopsy reflect diet-induced epigenetic changes.

## Abstract

The escalating incidence of colorectal cancer (CRC), particularly the alarming rise in early-onset cases, necessitates a paradigm shift from a purely genetic perspective to a broader investigation of promising pathways. This review explores the “nutri-epigenetic” interface, positioning liquid biopsy as a critical technology for translating dietary impacts into actionable clinical biomarkers. We contrast the molecular consequences of the Western dietary pattern, characterized by methyl-donor deficiency and pro-inflammatory metabolites, with the protective mechanisms of the Mediterranean diet. Mechanistically, we detail how Western-style diets drive a specific “epigenetic double-hit”: promoting global DNA hypomethylation (destabilizing LINE-1) while paradoxically inducing promoter hypermethylation of critical tumour suppressors (MLH1, APC, MGMT) and silencing tumour-suppressive microRNAs (miR-34b/c, miR-137) via methylation of their encoding genes. Conversely, we highlight the capacity of Mediterranean bioactive compounds (e.g., resveratrol, curcumin, butyrate) to inhibit DNA methyltransferases and restore epigenetic homeostasis. Bridging molecular biology and clinical utility, we demonstrate how these diet-sensitive signatures, specifically circulating methylated DNA and dysregulated microRNAs, can be captured via liquid biopsy. We propose that these circulating analytes serve as dynamic, accessible biomarkers for monitoring the molecular progression toward a carcinogenic state, thereby establishing a novel framework for personalized risk stratification and validating the efficacy of preventive nutritional strategies.

## Linked entities

- **Genes:** MLH1 (mutL homolog 1) [NCBI Gene 4292], APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324], MGMT (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 4255]
- **Chemicals:** resveratrol (PubChem CID 5056), curcumin (PubChem CID 969516), butyrate (PubChem CID 104775)
- **Diseases:** colorectal cancer (MONDO:0005575)

## Full-text entities

- **Genes:** MIR17HG (miR-17-92a-1 cluster host gene) [NCBI Gene 407975] {aka C13orf25, LINC00048, MIHG1, MIRH1, MIRHG1, NCRNA00048}, MIR9-3 (microRNA 9-3) [NCBI Gene 407051] {aka MIRN9-3, hsa-mir-9-3, miRNA9-3, mir-9-3}, MLH1 (mutL homolog 1) [NCBI Gene 4292] {aka COCA2, FCC2, HNPCC, HNPCC2, LYNCH2, MLH-1}, MIR27B (microRNA 27b) [NCBI Gene 407019] {aka MIR-27b, MIRN27B, miRNA27B}, TENM1 (teneurin transmembrane protein 1) [NCBI Gene 10178] {aka ODZ1, ODZ3, TEN-M1, TEN1, TNM, TNM1}, MSH6 (mutS homolog 6) [NCBI Gene 2956] {aka GTBP, GTMBP, HNPCC5, HSAP, LYNCH5, MMRCS3}, MIR135B (microRNA 135b) [NCBI Gene 442891] {aka MIRN135B, mir-135b}, MSH2 (mutS homolog 2) [NCBI Gene 4436] {aka COCA1, FCC1, HNPCC, HNPCC1, LCFS2, LYNCH1}, CXCL12 (C-X-C motif chemokine ligand 12) [NCBI Gene 6387] {aka IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, DROSHA (drosha ribonuclease III) [NCBI Gene 29102] {aka ETOHI2, HSA242976, RANSE3L, RN3, RNASE3L, RNASEN}, GDE1 (glycerophosphodiester phosphodiesterase 1) [NCBI Gene 51573] {aka 363E6.2, MIR16}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, MIR145 (microRNA 145) [NCBI Gene 406937] {aka MIRN145, miR-145, miRNA145}, MIR126 (microRNA 126) [NCBI Gene 406913] {aka MIRN126, miRNA126, mir-126}, MIR18A (microRNA 18a) [NCBI Gene 406953] {aka C13orf25, MIR18, MIRH1, MIRHG1, MIRN18, MIRN18A}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, MIR17 (microRNA 17) [NCBI Gene 406952] {aka MIR17-5p, MIR91, MIRN17, MIRN91, hsa-mir-17, miR-17}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, Mir146 (microRNA 146) [NCBI Gene 387164] {aka Mirn146, miR-146a, mmu-mir-146}, SFRP2 (secreted frizzled related protein 2) [NCBI Gene 6423] {aka FRP-2, SARP1, SDF-5}, EPCAM (epithelial cell adhesion molecule) [NCBI Gene 4072] {aka Ber-Ep4, BerEp4, DIAR5, EGP-2, EGP314, EGP40}, BRAF (B-Raf proto-oncogene, serine/threonine kinase) [NCBI Gene 673] {aka B-RAF1, B-raf, BRAF-1, BRAF1, NS7, RAFB1}, MIR27A (microRNA 27a) [NCBI Gene 407018] {aka MIR27, MIRN27A, mir-27a}, PMS2 (PMS1 homolog 2, mismatch repair system component) [NCBI Gene 5395] {aka HNPCC4, LYNCH4, MLH4, MMRCS4, PMS-2, PMSL2}, MIR139 (microRNA 139) [NCBI Gene 406931] {aka MIR139-3p, MIRN139, mir-139}, RENBP (renin binding protein) [NCBI Gene 5973] {aka RBP, RNBP}, MIR155 (microRNA 155) [NCBI Gene 406947] {aka MIRN155, miRNA155, mir-155}, MIR21 (microRNA 21) [NCBI Gene 406991] {aka MIRN21, hsa-mir-21, miR-21, miRNA21}, Mir494 (microRNA 494) [NCBI Gene 723878] {aka Mirn494, mir-494, mmu-mir-494}, MIR26B (microRNA 26b) [NCBI Gene 407017] {aka MIRN26B, hsa-mir-26b, miR-26b}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, SFRP1 (secreted frizzled related protein 1) [NCBI Gene 6422] {aka FRP, FRP-1, FRP1, FrzA, SARP2}, JUNB (JunB proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 3726] {aka AP-1}, MIR150 (microRNA 150) [NCBI Gene 406942] {aka MIRN150, miRNA150, mir-150}, Ppargc1a (peroxisome proliferative activated receptor, gamma, coactivator 1 alpha) [NCBI Gene 19017] {aka A830037N07Rik, Gm11133, PGC-1, PPARGC-1-alpha, Pgc-1alpha, Pgc1}, MIR19B1 (microRNA 19b-1) [NCBI Gene 406980] {aka C13orf25, MIR19B, MIRH1, MIRHG1, MIRN19B1, miR-19b-1}, MGMT (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 4255], Mgmt (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 17314] {aka AGT, Agat}, MIR542 (microRNA 542) [NCBI Gene 664617] {aka MIRN542, hsa-mir-542, mir-542}, IGF2 (insulin like growth factor 2) [NCBI Gene 3481] {aka C11orf43, GRDF, IGF-II, PP9974, SRS3}, PDCD4 (programmed cell death 4) [NCBI Gene 27250] {aka H731}, NRAS (NRAS proto-oncogene, GTPase) [NCBI Gene 4893] {aka ALPS4, CMNS, N-ras, NCMS, NRAS1, NS6}, MIR425 (microRNA 425) [NCBI Gene 494337] {aka MIRN425, hsa-mir-425, mir-425}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, MIR137 (microRNA 137) [NCBI Gene 406928] {aka MIRN137, miR-137}, TMEM54 (transmembrane protein 54) [NCBI Gene 113452] {aka BCLP, CAC-1, CAC1}, MIR143 (microRNA 143) [NCBI Gene 406935] {aka MIRN143, mir-143}, SEPTIN9 (septin 9) [NCBI Gene 10801] {aka AF17q25, MSF, MSF1, PNUTL4, SEPT9, SINT1}, IGF1 (insulin like growth factor 1) [NCBI Gene 3479] {aka IGF, IGF-I, IGFI, MGF}, DICER1 (dicer 1, ribonuclease III) [NCBI Gene 23405] {aka DCR1, Dicer, Dicer1e, GLOW, HERNA, K12H4.8-LIKE}, MIR22 (microRNA 22) [NCBI Gene 407004] {aka MIRN22, hsa-mir-22, miR-22}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A}, VDR (vitamin D receptor) [NCBI Gene 7421] {aka NR1I1, PPP1R163}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, Apc (APC, WNT signaling pathway regulator) [NCBI Gene 11789] {aka CC1, Min, mAPC}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, AGER (advanced glycosylation end-product specific receptor) [NCBI Gene 177] {aka RAGE, SCARJ1, sRAGE}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, MIR34A (microRNA 34a) [NCBI Gene 407040] {aka MIRN34A, miRNA34A, mir-34, mir-34a}
- **Diseases:** LS (MESH:D003123), Chronic hyperglycaemia (MESH:D002908), adenosquamous carcinoma (MESH:D018196), aneuploidy (MESH:D000782), adenosquamous, squamous cell, or undifferentiated carcinomas (MESH:D002294), CIN (MESH:D043171), autosomal dominant syndrome (MESH:D030342), H (MESH:D000848), metabolic dysregulation (MESH:D021081), Colorectal Carcinogenesis (MESH:D063646), serrated pathway lesions (MESH:D058606), adenomas (MESH:D000236), CIMP (MESH:D007516), Obesity (MESH:D009765), Type 2 diabetes mellitus (MESH:D003924), gestational diseases (MESH:D031901), spindle cell carcinoma (MESH:D002277), insulin resistance (MESH:D007333), autosomal dominant condition (MESH:C566739), MMR-deficient tumours (MESH:C536928), MSI (MESH:D053842), Adenomatous Polyposis Coli ( (MESH:D011125), adenocarcinoma (MESH:D000230), Tumour (MESH:D009369), diabetic (MESH:D003920), dysbiosis (MESH:D064806), CRC (MESH:D015179), Inherited syndromes (MESH:D009386), deaths (MESH:D003643), MD (MESH:D007161), carcinogenic (MESH:D011230), tumorigenic (MESH:D002471), liver metastases (MESH:D009362), metabolic disturbances (MESH:D024821), inflammation (MESH:D007249), injury to (MESH:D014947), early (MESH:C580055)
- **Chemicals:** polycyclic aromatic hydrocarbons (MESH:D011084), B (MESH:D001895), calcium (MESH:D002118), Folate (MESH:D005492), SCFAs (MESH:D005232), flavonoid (MESH:D005419), glucose (MESH:D005947), alcohol (MESH:D000438), calcitriol (MESH:D002117), oleic acid (MESH:D019301), Resveratrol (MESH:D000077185), S-adenosylmethionine (MESH:D012436), catechin (MESH:D002392), cobalamin (MESH:D014805), lipid (MESH:D008055), sucrose (MESH:D013395), DHA (MESH:D004281), luminal (MESH:D010634), Polyphenols (MESH:D059808), AGEs (MESH:D017127), cytosine (MESH:D003596), selenium (MESH:D012643), Carbohydrates (MESH:D002241), fatty acids (MESH:D005227), oil (MESH:D009821), riboflavin (MESH:D012256), Quercetin (MESH:D011794), choline (MESH:D002794), Omega-3 PUFAs (MESH:D015525), Butyrate (MESH:D002087), sulphate (MESH:D013431), pyridoxine (MESH:D011736), sugars (MESH:D000073893), PUFAs (MESH:D005231), Vitamin D (MESH:D014807), Deoxycholic acid (MESH:D003840), H2S (MESH:D006862), LA (MESH:D019787), Curcumin (MESH:D003474), sulphur (MESH:D013455), Olive oil (MESH:D000069463), EGCG (MESH:C045651), 25(OH)D (-), methionine (MESH:D008715)
- **Species:** Meleagris gallopavo (common turkey, species) [taxon 9103], Curcuma longa (turmeric, species) [taxon 136217], Homo sapiens (human, species) [taxon 9606], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116]
- **Mutations:** V600E, p.V677Sfs*3, G to A
- **Cell lines:** CT26 — Mus musculus (Mouse), Mouse colon adenocarcinoma, Cancer cell line (CVCL_7254)

## Full text

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## Figures

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## References

177 references — full list in the complete paper: https://tomesphere.com/paper/PMC12938801/full.md

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Source: https://tomesphere.com/paper/PMC12938801