Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers

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dc.authoridHossein Lanjanian / 0000-0003-4284-6592en_US
dc.authorscopusidHossein Lanjanian / 57193408899
dc.authorwosidHossein Lanjanian / AAT-7873-2021en_US
dc.contributor.authorMoravveji, Sayyed Sajjad
dc.contributor.authorKhoshbakht, Samane
dc.contributor.authorMokhtari, Majid
dc.contributor.authorSalimi, Mahdieh
dc.contributor.authorLanjanian, Hossein
dc.contributor.authorNematzadeh, Sajjad
dc.contributor.authorTorkamanian-Afshar, Mahsa
dc.contributor.authorMasoudi-Nejad, Ali
dc.date.accessioned2022-07-05T14:07:41Z
dc.date.available2022-07-05T14:07:41Z
dc.date.issued2022en_US
dc.departmentİstinye Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Moleküler Biyoloji ve Genetik Bölümüen_US
dc.description.abstractBackground: Aberrant levels of 5-hydroxymethylcytosine (5-hmC) can lead to cancer progression. Identifcation of 5-hmC-related biological pathways in cancer studies can produce better understanding of gastrointestinal (GI) cancers. We conducted a network-based analysis on 5-hmC levels extracted from circulating free DNAs (cfDNA) in GI cancers including colon, gastric, and pancreatic cancers, and from healthy donors. The co-5-hmC network was reconstructed using the weighted-gene co-expression network method. The cancer-related modules/subnetworks were detected. Preservation of three detected 5-hmC-related modules was assessed in an external dataset. The 5-hmC-related modules were functionally enriched, and biological pathways were identifed. The relationship between modules was assessed using the Pearson correlation coefcient (p-value<0.05). An elastic network classifer was used to assess the potential of the 5-hmC modules in distinguishing cancer patients from healthy individuals. To assess the efciency of the model, the Area Under the Curve (AUC) was computed using fve-fold cross-validation in an external dataset. Results: The main biological pathways were the cell cycle, apoptosis, and extracellular matrix (ECM) organization. Direct association between the cell cycle and apoptosis, inverse association between apoptosis and ECM organiza? tion, and inverse association between the cell cycle and ECM organization were detected for the 5-hmC modules in GI cancers. An AUC of 92% (0.73–1.00) was observed for the predictive model including 11 genes. Conclusion: The intricate association between biological pathways of identifed modules may reveal the hidden signifcance of 5-hmC in GI cancers. The identifed predictive model and new biomarkers may be benefcial in cancer detection and precision medicine using liquid biopsy in the early stages.en_US
dc.identifier.citationMoravveji SS, Khoshbakht S, Mokhtari M, Salimi M, Lanjanian H, Nematzadeh S, Torkamanian-Afshar M, Masoudi-Nejad A. Impact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancers. BMC Genom Data. 2022 Jun 29;23(1):49. doi: 10.1186/s12863-022-01061-x. PMID: 35768769.en_US
dc.identifier.doi10.1186/s12863-022-01061-xen_US
dc.identifier.issue49en_US
dc.identifier.pmid35768769en_US
dc.identifier.scopus2-s2.0-85133140863en_US
dc.identifier.scopusqualityN/Aen_US
dc.identifier.urihttp://doi.org/10.1186/s12863-022-01061-x
dc.identifier.urihttps://hdl.handle.net/20.500.12713/2963
dc.identifier.volume23en_US
dc.identifier.wosWOS:000818760500001en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorLanjanian, Hossein
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.ispartofBMC Genomic Dataen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectcfDNAen_US
dc.subject5-Hydroxymethylcytosineen_US
dc.subjectNetworken_US
dc.subjectPredictive Modelen_US
dc.subjectGastrointestinal Cancersen_US
dc.titleImpact of 5HydroxyMethylCytosine (5hmC) on reverse/direct association of cell-cycle, apoptosis, and extracellular matrix pathways in gastrointestinal cancersen_US
dc.typeArticleen_US

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