Comprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer

Yin F, Yi S, Wei L, Zhao B, Li J, Cai X, Liu X. Microarray-based identification of genes associated with prognosis and drug resistance in ovarian cancer. J Cell Biochem. 2019;120(4):6057–70.

Article  CAS  PubMed  Google Scholar 

Reyes HD, Devor EJ, Warrier A, Newtson AM, Mattson J, Wagner V, Gonzalez-Bosquet J. Differential DNA methylation in high-grade serous ovarian cancer (HGSOC) is associated with tumor behavior. Sci Rep. 2019;9(1):1–13.

Article  CAS  Google Scholar 

Hatina J, Boesch M, Sopper S, Kripnerova M, Wolf D, Reimer D, Zeimet AG. Ovarian cancer stem cell heterogeneity. Stem cells heterogeneity in Cancer. Cham: Springer; 2019. pp. 201–21.

Chapter  Google Scholar 

National Cancer Institute, Cancer Stat Facts. Ovarian Cancer. https://seer.cancer.gov/statfacts/html/ovary.html, 2023 (accessed May 17, 2023).

Simmons AR, Fourkala EO, Gentry-Maharaj A, Ryan A, Sutton MN, Baggerly K, Menon U. Complementary longitudinal serum biomarkers to CA125 for early detection of ovarian cancer. Cancer Prev Res. 2019;12(6):391–400.

Article  CAS  Google Scholar 

Montagnana M, Benati M, Danese E. (2017). Circulating biomarkers in epithelial ovarian cancer diagnosis: from present to future perspective. Annals Translational Med, 5(13).

Sarojini, S., Tamir, A., Lim, H., Li, S., Zhang, S., Goy, A., … Suh, K. S. (2012).Early detection biomarkers for ovarian cancer. Journal of oncology, 2012.

Takeshima H, Yamada H, Ushijima T. Cancer epigenetics: aberrant DNA methylation in cancer diagnosis and treatment. Oncogenomics. Academic; 2019. pp. 65–76.

Hentze JL, Høgdall CK, Høgdall EV. Methylation and ovarian cancer: can DNA methylation be of diagnostic use? Mol Clin Oncol. 2019;10(3):323–30.

CAS  PubMed  PubMed Central  Google Scholar 

Li Y, Liu H, Chen H, Shao J, Su F, Zhang S, He X. DERL3 functions as a tumor suppressor in gastric cancer. Comput Biol Chem. 2020;84:107172.

Article  CAS  PubMed  Google Scholar 

Cai C, Xie X, Zhou J, Fang X, Wang F, Wang M. Identification of TAF1, SAT1, and ARHGEF9 as DNA methylation biomarkers for hepatocellular carcinoma. J Cell Physiol. 2020;235(1):611–8.

Article  CAS  PubMed  Google Scholar 

Swamy SN, Premalatha CS, Pallavi VR, Gawari R. Aberrant promoter hypermethylation of RASSF1a and BRCA1 in circulating cell-free tumor DNA serves as a biomarker of ovarian carcinoma. Asian Pac J Cancer Prev. 2019;20(10):3001–5.

Article  PubMed  PubMed Central  Google Scholar 

Barekati Z, Radpour R, Lu Q, Bitzer J, Zheng H, Toniolo P, Zhong XY. Methylation signature of lymph node metastases in breast cancer patients. BMC Cancer. 2012;12(1):244.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ashour, N., Angulo, J. C., Andrés, G., Alelú, R., González-Corpas, A., Toledo, M.V., … Ropero, S. (2014). A DNA hypermethylation profile reveals new potential biomarkers for prostate cancer diagnosis and prognosis. The Prostate, 74(12), 1171–1182.

Liu K, Dong F, Gao H, Guo Y, Li H, Yang F, Zou C. Promoter hypermethylation of the CFTR gene as a novel diagnostic and prognostic marker of breast cancer. Cell Biol Int. 2020;44(2):603–9.

Article  CAS  PubMed  Google Scholar 

Down T. A., Rakyan V. K., Turner D. J., Flicek P., Li H., Kulesha E., Thorne N. P. A bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008;26(7):779–85.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Taiwo, O., Wilson, G. A., Morris, T., Seisenberger, S., Reik, W., Pearce, D., … Butcher,L. M. (2012). Methylome analysis using MeDIP-seq with low DNA concentrations. Nature protocols, 7(4), 617.

Shi Y, Gong W, Gong X, Wang P, Zhao X. Genome-wide DNA methylation analysis of breast cancer MCF-7/Taxol cells with MeDIP-Seq. PLoS ONE. 2020;15(12):e0241515. https://doi.org/10.1371/journal.pone.0241515

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lu, H., Liu, Y., Wang, J., Fu, S., Wang, L., Huang, C., … Rao, Q. (2022). Detection of ovarian cancer using plasma cell-free DNA methylomes. Clinical Epigenetics, 14(1),74.https://doi.org/10.1186/s13148-022-01285-9

Li, S., Wang, L., Zhao, Q., Wang, Z., Lu, S., Kang, Y., … Tian, J. (2020). Genome-wide analysis of cell-free DNA methylation profiling for the early diagnosis of pancreatic cancer. Frontiers in genetics, 11, 596078. https://doi.org/10.3389/fgene.2020.596078

Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44.

Article  PubMed  Google Scholar 

Yang X, Zhu S, Li L, Zhang L, Xian S, Wang Y, Cheng Y. Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis. OncoTargets Therapy. 2018;11:1457.

Article  PubMed  PubMed Central  Google Scholar 

Rezaei-Tavirani M, Rezaei-Tavirani S, Mansouri V, Rostami-Nejad M, Rezaei-Tavirani M. Protein-protein interaction network analysis for a biomarker panel related to human esophageal adenocarcinoma. Asian Pac J cancer Prevention: APJCP. 2017;18(12):3357.

Google Scholar 

Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21(16):3448–9.

Article  CAS  PubMed  Google Scholar 

Mercier PL, Bachvarova M, Plante M, Gregoire J, Renaud MC, Ghani K, Bachvarov D. Characterization of DOK1, a candidate tumor suppressor gene, in epithelial ovarian cancer. Mol Oncol. 2011;5(5):438–53.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Häfner N, Steinbach D, Jansen L, Diebolder H, Dürst M, Runnebaum IB. RUNX3 and CAMK2N1 hypermethylation as prognostic marker for epithelial ovarian cancer. Int J Cancer. 2016;138(1):217–28.

Article  PubMed  Google Scholar 

Kang S, Dong SM, Park NH. Frequent promoter hypermethylation of TGFBI in epithelial ovarian cancer. Gynecol Oncol. 2010;118(1):58–63.

Article  CAS  PubMed  Google Scholar 

Ozdemir F, Altinisik J, Karateke A, Coksuer H, Buyru N. Methylation of tumor suppressor genes in ovarian cancer. Experimental Therapeutic Med. 2012;4(6):1092–6.

Article  CAS  Google Scholar 

Kim M, Costello J. DNA methylation: an epigenetic mark of cellular memory. Exp Mol Med. 2017;49(4):e322–322. https://doi.org/10.1038/emm.2017.10

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barton CA, Hacker NF, Clark SJ, O’Brien PM. DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment. Gynecol Oncol. 2008;109(1):129–39.

Article  CAS  PubMed  Google Scholar 

Gloss, B. S., Patterson, K. I., Barton, C. A., Gonzalez, M., Scurry, J. P., Hacker,N. F., … Clark, S. J. (2012). Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers. Cancer letters, 318(1), 76–85.

Tilghman RW, Parsons JT. (2008, February). Focal adhesion kinase as a regulator of cell tension in the progression of cancer. In Seminars in cancer biology (Vol. 18, No. 1, pp. 45–52). Academic Press. https://doi.org/10.1016/j.semcancer.2007.08.002

Hendrikse CSE, Theelen PMM, van der Ploeg P, Westgeest HM, Boere IA, Thijs AMJ… Piek, J. M. J. The potential of RAS/RAF/MEK/ERK(MAPK) signaling pathway inhibitors in ovarian cancer: a systematic review and meta-analysis. Gynecol Oncol. 2023;171:83–94. https://doi.org/10.1016/j.ygyno.2023.01.038

Article  CAS  PubMed  Google Scholar 

Moufarrij, S., Dandapani, M., Arthofer, E., Gomez, S., Srivastava, A., Lopez-Acevedo,M., … Chiappinelli, K. B. (2019). Epigenetic therapy for ovarian cancer: promise and progress. Clinical epigenetics, 11(1), 1–11.https://doi.org/10.1186/s13148-018-0602-0

Therachiyil L, Anand A, Azmi A, Bhat A, Korashy HM, Uddin S. Role of RAS signaling in ovarian cancer. F1000Research. 2022;11. https://doi.org/10.12688/f1000research.126337.1

Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Meissner A. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011;7(12):e1002389.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ramasamy D, Magendhra Rao D, Rajkumar AK, T., Mani S. Non-CpG methylation—a key epigenetic modification in cancer. Brief Funct Genomics. 2021;20(5):304–11.

Article  CAS  PubMed  Google Scholar 

Xiao W, Liu X, Niu X, Li C, Guo Y, Tan J, Li Y. The frequency of CpG and non-CpG methylation of Notch3 gene promoter determines its expression levels in breast cancer cells. Exp Cell Res. 2020;386(2):111743.

Article  CAS  PubMed  Google Scholar 

Ishii T, Fujishiro M, Masuda M, Teramoto S, Matsuse T. A methylated oligonucleotide induced methylation of GSTP1 promoter and suppressed its expression in A549 lung adenocarcinoma cells. Cancer Lett. 2004;212(2):211–23.

Article  CAS  PubMed  Google Scholar 

Kouidou, S., Agidou, T., Kyrkou, A., Andreou, A., Katopodi, T., Georgiou, E., … Tzimagiorgis,G. (2005). Non-CpG cytosine methylation of p53 exon 5 in non-small cell lung carcinoma.Lung Cancer, 50(3), 299–307.

Patil V, Ward RL, Hesson LB. The evidence for functional non-CpG methylation in mammalian cells. Epigenetics. 2014;9(6):823–8. https://doi.org/10.4161/epi.28741

Article  PubMed  PubMed Central  Google Scholar 

Ramasamy D, Magendhra Rao D, Rajkumar AK, T., Mani S. Non-CpG methylation—a key epigenetic modification in cancer. Brief Funct Genomics. 2021;20(5):304–11. https://doi.org/10.1093/bfgp/elab035

Article  CAS  PubMed  Google Scholar 

Luo WM, Wang ZY, Zhang X. Identification of four differentially methylated genes as prognostic signatures for stage I lung adenocarcinoma. Cancer Cell Int. 2018;18(1):1–8. https://doi.org/10.1186/s12935-018-0547-6

Article  CAS  Google Scholar 

Han Y, Zheng Q, Tian Y, Ji Z, Ye H. Identification of a nine-gene panel as a prognostic indicator for recurrence with muscle‐invasive bladder cancer. J Surg Oncol. 2019;119(8):1145–54.https://doi.org/10.1002/jso.25446

Article  CAS  PubMed  Google Scholar 

Zhu, L., Yao, Z., Luo, Q., Liu, Y., Zhao, W., Shao, C., … Cui, F. (2023). Low Expression of GIGYF1 Inhibits Metastasis, Proliferation, and Promotes Apoptosis and Autophagy of Gastric Cancer Cells. International Journal of Medical Sciences, 20(8), 1038–1045.https://doi.org/10.7150/ijms.82719

Yang, W., Yuan, Q., Zhang, S., Zuo, M., Li, T., Li, J., … Liu, Y. (2022). Elevated GIGYF2 expression suppresses tumor migration and enhances sensitivity to temozolomide in malignant glioma. Cancer Gene Therapy, 29(6), 750–757.https://doi.org/10.1038/s41417-021-00353-1

Vivekanadhan S, Mukhopadhyay D. (2019). Divergent roles of Plexin D1 in cancer. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 1872(1), 103–10. https://doi.org/10.1016/j.bbcan.2019.05.004

Li J, Hu K, He D, Zhou L, Wang Z, Tao Y. Prognostic value of PLXND1 and TGF-β1 coexpression and its correlation with immune infiltrates in hepatocellular carcinoma. Front Oncol. 2021;10:604131. https://doi.org/10.3389/fo

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