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Journal of Ovarian Research (2024) 17:83 Journal of Ovarian Research  \n[https://doi.org/10.1186/s13048-024-01395-3](https://doi.org/10.1186/s13048-024-01395-3)  \nRESEARCH Open Access  \nComprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer  \nPriyanka Gautam 1, Sameer Gupta2 and Manisha Sachan 1*  \nAbstract  \nOvarian cancer, among all gynecologic malignancies, exhibits the highest incidence and mortality rate, primarily because it is often presents with non-specific or no symptoms during its early stages. For the advancement of Ovarian Cancer Diagnosis, it is crucial to identify the potential molecular signatures that could significantly differentiate between healthy and ovarian cancerous tissues and can be used further as a diagnostic biomarker for detecting ovarian cancer. In this study, we investigated the genome-wide methylation patterns in ovarian cancer patients using Methylated DNA Immunoprecipitation (MeDIP-Seq) followed by NGS. Identified differential lymethylated regions (DMRs) were further validated by targeted bisulfite sequencing for CpG site-specific methylation profiles. Furthermore, expression validation of six genes by Quantitative Reverse Transcriptase-PCR was also performed. Out of total 120 differential ly methylated genes (DMGs), 68 genes were hypermethylated, and 52 were hypomethylated in their promoter region. After analysis, we identified the top 6 hub genes, namely POLR3B, PLXND1, GIGYF2, STK4, BMP2 and CRKL. Interestingly we observed Non-CpG site methylation in the case of POLR3B and CRKL which was statistically significant in discriminating ovarian cancer samples from normal controls. The most significant pathways identified were focal adhesion, the MAPK signaling pathway, and the Ras signaling pathway. Expression analysis of hypermethylated genes was correlated with the downregulation of the genes. POLR3B and GIGYF2 turned out to be the novel genes associated with the carcinogenesis of EOC. Our study demonstrated that methylation profiling through MeDIP-sequencing has effectively identified six potential hub genes and pathways that might exacerbate our understanding of underlying molecular mechanisms of ovarian carcinogenesis.  \nKeywords Ovarian cancer, MeDIP-seq, Bioinformatics analysis, Differential ly methylated regions (DMRs), DNA methylation, QRT-PCR, Biomarker  \n*Correspondence: Manisha Sachan [manishas@mnnit.ac.in](manishas@mnnit.ac.in)  \n1Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj 211004, India  \n2Department of Surgical Oncology, King George Medical University, Lucknow, India  \n© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit [http://creativecommons.org/l](http://creativecommons.org/l)icenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ([http://creativecommons.org/publicdomain/zero/1.0/](http://creativecommons.org/publicdomain/zero/1.0/)) applies to the data made available in this article, unless otherwise stated in a credit line to the data.  \nGautam et al. Journal of Ovarian Research (2024) 17:83  \nIntroduction  \nOvarian cancer is the fifth most lethal gynecologic malignancy ","cbCaii0sIIlFvyNW","https://ap.wps.com/l/cbCaii0sIIlFvyNW","pdf",3740227,16,"English","# Abstract\n# Introduction\n## Ovarian cancer burden and diagnostic challenges\n## Current detection strategies and biomarkers\n## Rationale for DNA methylation profiling","[{\"question\":\"Why is early diagnosis of epithelial ovarian cancer difficult?\",\"answer\":\"Early stages often present with non-specific or no symptoms, leading to advanced-stage diagnosis. Imaging and current serum biomarkers have limited sensitivity and specificity for early detection.\"},{\"question\":\"How were DNA methylation changes measured in the study?\",\"answer\":\"Genome-wide methylation patterns were analyzed using MeDIP-Seq followed by NGS. Differential methylated regions were then validated with targeted bisulfite sequencing for CpG site-specific methylation profiles.\"},{\"question\":\"Which genes and pathways were highlighted by the results?\",\"answer\":\"Six hub genes were identified: POLR3B, PLXND1, GIGYF2, STK4, BMP2, and CRKL. The most significant pathways included focal adhesion, MAPK signaling, and Ras signaling.\"}]","Comprehensive DNA methylation profiling by MeDIP-NGS identifies potential genes and pathways for epithelial ovarian cancer | PDF",1789988994]