{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T11:02:19Z","timestamp":1785495739502,"version":"3.56.0"},"reference-count":51,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:00:00Z","timestamp":1767916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PNRR-HPC","award":["F13C22000710007"],"award-info":[{"award-number":["F13C22000710007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Background\/Objectives: DNA methylation is a key epigenetic process that regulates gene expression and is often disrupted in colorectal cancer (CRC). Aberrant methylation of promoter CpG islands can silence tumor suppressor genes and drive tumorigenesis. A subset of CRCs exhibits the CpG Island Methylator Phenotype (CIMP), characterized by widespread hypermethylation and distinct clinical outcomes. Identifying genes whose expression is epigenetically regulated by methylation is important for prioritizing candidate biomarkers and therapeutic targets in CRC. Methods: We developed and compared a series of computational approaches to identify genes whose expression is regulated by DNA methylation in The Cancer Genome Atlas (TCGA) cohort of Colon Adenocarcinoma (COAD) patients. Samples were stratified according to their CpG Island Methylator Phenotype (CIMP) level to capture distinct epigenetic subgroups. The proposed framework integrates methylation and transcriptomic data to systematically detect methylation\u2013expression associations indicative of epigenetic regulation. Results: The best-performing method identified gene sets strongly associated with promoter methylation\u2013expression relationships and enriched for pathways relevant to colorectal cancer progression and patient stratification. To evaluate the robustness and transferability of the approach, it was further validated on independent datasets, including Stomach Adenocarcinoma (STAD), Glioblastoma Multiforme (GBM), and Mesothelioma (MESO), supporting its robustness and potential generalizability across multiple tumor types. Conclusions: Our study highlights the potential of computational pipelines to uncover epigenetically regulated genes in colorectal cancer. The identified candidate genes provide a hypothesis-generating foundation for refining molecular stratification and guiding future studies aimed at epigenetic biomarker discovery and therapeutic hypothesis development.<\/jats:p>","DOI":"10.3390\/cancers18020211","type":"journal-article","created":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T09:25:02Z","timestamp":1767950702000},"page":"211","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Exploring the Impact of DNA Methylation on Gene Expression in CRC: A Computational Approach for Identifying Epigenetically Regulated Genes in Multi-Omic Datasets"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-4974-3101","authenticated-orcid":false,"given":"Andrei Stefan","family":"Blindu","sequence":"first","affiliation":[{"name":"Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata, 5, 27100 Pavia, Italy"},{"name":"enGenome s.r.l., Via Ferrata, 5, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5468-1466","authenticated-orcid":false,"given":"Silvia","family":"Berardelli","sequence":"additional","affiliation":[{"name":"Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata, 5, 27100 Pavia, Italy"},{"name":"enGenome s.r.l., Via Ferrata, 5, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8027-5666","authenticated-orcid":false,"given":"Federica","family":"De Paoli","sequence":"additional","affiliation":[{"name":"enGenome s.r.l., Via Ferrata, 5, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7288-9414","authenticated-orcid":false,"given":"Federico","family":"Manai","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnology \u201cL. Spallanzani\u201d, University of Pavia, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7055-7208","authenticated-orcid":false,"given":"Rossella","family":"Tricarico","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnology \u201cL. Spallanzani\u201d, University of Pavia, 27100 Pavia, Italy"},{"name":"Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8465-632X","authenticated-orcid":false,"given":"Susanna","family":"Zucca","sequence":"additional","affiliation":[{"name":"enGenome s.r.l., Via Ferrata, 5, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8931-4676","authenticated-orcid":false,"given":"Paolo","family":"Magni","sequence":"additional","affiliation":[{"name":"Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata, 5, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nrg816","article-title":"The Fundamental Role of Epigenetic Events in Cancer","volume":"3","author":"Jones","year":"2002","journal-title":"Nat. Rev. Genet."},{"key":"ref_2","first-page":"376","article-title":"Cancer Epigenetics in Clinical Practice","volume":"73","author":"Davalos","year":"2023","journal-title":"CA Cancer J. Clin."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/s41392-023-01528-y","article-title":"Methylation across the Central Dogma in Health and Diseases: New Therapeutic Strategies","volume":"8","author":"Liu","year":"2023","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1056\/NEJMra023075","article-title":"Gene Silencing in Cancer in Association with Promoter Hypermethylation","volume":"349","author":"Herman","year":"2003","journal-title":"N. Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1038\/nrc1507","article-title":"CpG Island Methylator Phenotype in Cancer","volume":"4","author":"Issa","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"ref_6","first-page":"120","article-title":"The CpG Island Methylator Phenotype (CIMP) in Colorectal Cancer","volume":"6","author":"Kuppen","year":"2013","journal-title":"Gastroenterol. Hepatol. Bed Bench"},{"key":"ref_7","first-page":"5438","article-title":"Aberrant Methylation in Gastric Cancer Associated with the CpG Island Methylator Phenotype","volume":"59","author":"Toyota","year":"1999","journal-title":"Cancer Res."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/neuonc\/nox183","article-title":"Glioma CpG Island Methylator Phenotype (G-CIMP): Biological and Clinical Implications","volume":"20","author":"Malta","year":"2018","journal-title":"Neuro-Oncology"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"902674","DOI":"10.4061\/2011\/902674","article-title":"CpG Island Methylation in Colorectal Cancer: Past, Present and Future","volume":"2011","author":"Curtin","year":"2011","journal-title":"Pathol. Res. Int."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/s40001-024-01805-8","article-title":"Multi-Omics Cluster Defines the Subtypes of CRC with Distinct Prognosis and Tumor Microenvironment","volume":"29","author":"Ma","year":"2024","journal-title":"Eur. J. Med. Res."},{"key":"ref_11","first-page":"188722","article-title":"DNA Methylation-Based Diagnostic, Prognostic, and Predictive Biomarkers in Colorectal Cancer","volume":"1877","year":"2022","journal-title":"Biochim. Biophys. Acta BBA\u2014Rev. Cancer"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1002\/ijc.34186","article-title":"DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine","volume":"151","author":"Fatemi","year":"2022","journal-title":"Int. J. Cancer"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"bbaf355","DOI":"10.1093\/bib\/bbaf355","article-title":"A Technical Review of Multi-Omics Data Integration Methods: From Classical Statistical to Deep Generative Approaches","volume":"26","author":"Cai","year":"2025","journal-title":"Brief. Bioinform."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e00938","DOI":"10.1016\/j.btre.2025.e00938","article-title":"Integrating Multi-Omics Data: Methods and Applications in Human Complex Diseases","volume":"48","author":"Sibilio","year":"2025","journal-title":"Biotechnol. Rep."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Majumdar, K., Jaffr\u00e9zic, F., Rau, A., Gormley, I.C., and Murphy, T.B. (2024). Integrated Differential Analysis of Multi-Omics Data Using a Joint Mixture Model: Idiffomix. arXiv.","DOI":"10.32614\/CRAN.package.idiffomix"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3055","DOI":"10.1093\/bioinformatics\/bty1054","article-title":"DIABLO: An Integrative Approach for Identifying Key Molecular Drivers from Multi-Omics Assays","volume":"35","author":"Singh","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3044","DOI":"10.1093\/bioinformatics\/bty156","article-title":"MethylMix 2.0: An R Package for Identifying DNA Methylation Genes","volume":"34","author":"Cedoz","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Huang, H., Fu, J., Zhang, L., Xu, J., Li, D., Onwuka, J.U., Zhang, D., Zhao, L., Sun, S., and Zhu, L. (2021). Integrative Analysis of Identifying Methylation-Driven Genes Signature Predicts Prognosis in Colorectal Carcinoma. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.629860"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/bty902","article-title":"ELMER v.2: An R\/Bioconductor Package to Reconstruct Gene Regulatory Networks from DNA Methylation and Transcriptome Profiles","volume":"35","author":"Silva","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Ruiz-Arenas, C., and Gonz\u00e1lez, J.R. (2017). Redundancy Analysis Allows Improved Detection of Methylation Changes in Large Genomic Regions. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1986-0"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The Cancer Genome Atlas Pan-Cancer Analysis Project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1093\/nar\/gkv1507","article-title":"TCGAbiolinks: An R\/Bioconductor Package for Integrative Analysis of TCGA Data","volume":"44","author":"Colaprico","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.ygeno.2011.07.007","article-title":"High Density DNA Methylation Array with Single CpG Site Resolution","volume":"98","author":"Bibikova","year":"2011","journal-title":"Genomics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.ccell.2018.03.010","article-title":"Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas","volume":"33","author":"Liu","year":"2018","journal-title":"Cancer Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.cell.2013.09.034","article-title":"The Somatic Genomic Landscape of Glioblastoma","volume":"155","author":"Brennan","year":"2013","journal-title":"Cell"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/s41588-023-01321-1","article-title":"Multiomic Analysis of Malignant Pleural Mesothelioma Identifies Molecular Axes and Specialized Tumor Profiles Driving Intertumor Heterogeneity","volume":"55","author":"Mangiante","year":"2023","journal-title":"Nat. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1053\/j.gastro.2023.01.039","article-title":"TET1 and TDG Suppress Inflammatory Response in Intestinal Tumorigenesis: Implications for Colorectal Tumors with the CpG Island Methylator Phenotype","volume":"164","author":"Tricarico","year":"2023","journal-title":"Gastroenterology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1186\/s12967-022-03664-5","article-title":"Identification of DNA Methylation-Regulated Differentially Expressed Genes in RA by Integrated Analysis of DNA Methylation and RNA-Seq Data","volume":"20","author":"Zhang","year":"2022","journal-title":"J. Transl. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41392-019-0081-6","article-title":"Integrative Analysis of DNA Methylation and Gene Expression Identified Cervical Cancer-Specific Diagnostic Biomarkers","volume":"4","author":"Xu","year":"2019","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"14200","DOI":"10.1038\/s41598-017-14314-y","article-title":"Promoter DNA Methylation Analysis Reveals a Novel Diagnostic CpG-Based Biomarker and RAB25 Hypermethylation in Clear Cell Renel Cell Carcinoma","volume":"7","author":"Gu","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s42003-020-01469-0","article-title":"DNA Methylation Patterns Identify Subgroups of Pancreatic Neuroendocrine Tumors with Clinical Association","volume":"4","author":"Lakis","year":"2021","journal-title":"Commun. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1158\/1055-9965.EPI-15-0935","article-title":"Clinicopathological Risk Factor Distributions for MLH1 Promoter Region Methylation in CIMP Positive Tumors","volume":"25","author":"Levine","year":"2016","journal-title":"Cancer Epidemiol. Biomark. Prev."},{"key":"ref_35","first-page":"221","article-title":"Chapter 6\u2014Dnmt1: Structure and Function","volume":"Volume 101","author":"Cheng","year":"2011","journal-title":"Progress in Molecular Biology and Translational Science"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41392-021-00762-6","article-title":"Wnt\/\u03b2-Catenin Signalling: Function, Biological Mechanisms, and Therapeutic Opportunities","volume":"7","author":"Liu","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1002\/ijc.25432","article-title":"Prognostic Significance of CDKN2A (P16) Promoter Methylation and Loss of Expression in 902 Colorectal Cancers: Cohort Study and Literature Review","volume":"128","author":"Shima","year":"2011","journal-title":"Int. J. Cancer"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"102824","DOI":"10.1016\/j.isci.2021.102824","article-title":"Integrative Omics Analysis Reveals Effective Stratification and Potential Prognosis Markers of Pan-Gastrointestinal Cancers","volume":"24","author":"Jiangzhou","year":"2021","journal-title":"iScience"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"7259","DOI":"10.18632\/aging.202582","article-title":"Pan-Cancer Investigation Reveals Mechanistic Insights of Planar Cell Polarity Gene Fuz in Carcinogenesis","volume":"13","author":"Chen","year":"2021","journal-title":"Aging"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1002\/path.6291","article-title":"PCDHGC3 Hypermethylation as a Potential Biomarker of Intestinal Neuroendocrine Carcinomas","volume":"263","author":"Cubiella","year":"2024","journal-title":"J. Pathol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s13148-019-0695-0","article-title":"Clustered Protocadherins Methylation Alterations in Cancer","volume":"11","author":"Loi","year":"2019","journal-title":"Clin. Epigenet."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Liu, S., Liu, X., Lin, X., and Chen, H. (2023). Zinc Finger Proteins in the War on Gastric Cancer: Molecular Mechanism and Clinical Potential. Cells, 12.","DOI":"10.3390\/cells12091314"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"4112","DOI":"10.1158\/0008-5472.CAN-09-0028","article-title":"A Multicenter, Double-Blinded Validation Study of Methylation Biomarkers for Progression Prediction in Barrett\u2019s Esophagus","volume":"69","author":"Jin","year":"2009","journal-title":"Cancer Res."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Wang, Z., Gao, L., Guo, X., Lian, W., Deng, K., and Xing, B. (2020). Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients with Glioblastoma: A Multiomic Analysis. Front. Cell Dev. Biol., 8.","DOI":"10.3389\/fcell.2020.576996"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"9636897211007395","DOI":"10.1177\/09636897211007395","article-title":"Overexpression of FBXO17 Promotes the Proliferation, Migration and Invasion of Glioma Cells Through the Akt\/GSK-3\u03b2\/Snail Pathway","volume":"30","author":"Wang","year":"2021","journal-title":"Cell Transplant."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Du, D., Yuan, J., Ma, W., Ning, J., Weinstein, J.N., Yuan, X., Fuller, G.N., and Liu, Y. (2018). Clinical Significance of FBXO17 Gene Expression in High-Grade Glioma. BMC Cancer, 18.","DOI":"10.1186\/s12885-018-4680-3"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Li, L., Xia, S., Zhao, Z., Deng, L., Wang, H., Yang, D., Hu, Y., Ji, J., Huang, D., and Xin, T. (2024). EMP3 as a Prognostic Biomarker Correlates with EMT in GBM. BMC Cancer, 24.","DOI":"10.1186\/s12885-023-11796-0"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Zhu, H., Hu, X., Gu, L., Jian, Z., Li, L., Hu, S., Qiu, S., and Xiong, X. (2021). TUBA1C Is a Prognostic Marker in Low-Grade Glioma and Correlates with Immune Cell Infiltration in the Tumor Microenvironment. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.759953"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Xu, S., Wang, Z., Ye, J., Mei, S., and Zhang, J. (2021). Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.729103"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"334","DOI":"10.21037\/atm-22-520","article-title":"Hypomethylation-Induced Prognostic Marker Zinc Finger DHHC-Type Palmitoyltransferase 12 Contributes to Glioblastoma Progression","volume":"10","author":"Lu","year":"2022","journal-title":"Ann. Transl. Med."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Ansar, M., Thu, L.T.A., Hung, C.-S., Su, C.-M., Huang, M.-H., Liao, L.-M., Chung, Y.-M., and Lin, R.-K. (2022). Promoter Hypomethylation and Overexpression of TSTD1 Mediate Poor Treatment Response in Breast Cancer. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.1004261"}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/18\/2\/211\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T09:29:28Z","timestamp":1767950968000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/18\/2\/211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,9]]},"references-count":51,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["cancers18020211"],"URL":"https:\/\/doi.org\/10.3390\/cancers18020211","relation":{},"ISSN":["2072-6694"],"issn-type":[{"value":"2072-6694","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,9]]}}}