Screening and identification of key biomarkers associated with endometriosis using bioinformatics and next-generation sequencing data analysis

Basavaraj Vastrad, Chanabasayya Vastrad
In: Egyptian Journal of Medical Human Genetics · 2024 · vol. 25(1) · doi:10.1186/s43042-024-00572-9 · W4403356926
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⚙ AI-generated summary by claude@2026-06, 2026-06-08 ⓘ

This study identified 10 hub genes, including vcam1 and snca, and predicted regulatory miRNAs and TFs from next-generation sequencing data to find potential endometriosis biomarkers.

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⚙ AI-generated deep summary by claude@2026-06, 2026-06-09 ⓘ

This study used the publicly available RNA-seq dataset GSE243039 (20 endometriosis samples and 20 normal controls) to identify differentially expressed genes with limma, then performed GO and Reactome pathway enrichment, built protein–protein interaction networks, and used Cytoscape module detection to identify 10 hub genes; it further constructed miRNA–hub gene and TF–hub gene regulatory networks using miRNet and NetworkAnalyst and predicted key miRNAs (e.g., hsa-mir-3143, hsa-mir-2110) and TFs (e.g., tcf3, clock). The authors found 958 DEGs (479 upregulated, 479 downregulated), with enriched processes including GPCR signaling and pathways such as multicellular organismal processes, and reported hub genes including vcam1, snca, prkcb, adrb2, foxq1, mdfi, actbl2, prkd1, dapk1, and actc1. Hub genes were assessed using receiver operating characteristic analysis, with the paper presenting them as potential diagnostic biomarkers, while its main limitation is reliance on in silico bioinformatics analyses without experimental validation in this write-up. This paper is centrally about endometriosis — it identifies and validates candidate gene, miRNA, and TF biomarkers for endometriosis using bioinformatics and next-generation sequencing analysis.

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Abstract

Abstract Background Endometriosis is a common cause of endometrial-type mucosa outside the uterine cavity with symptoms such as painful periods, chronic pelvic pain, pain with intercourse and infertility. However, the early diagnosis of endometriosis is still restricted. The purpose of this investigation is to identify and validate the key biomarkers of endometriosis. Methods Next-generation sequencing dataset GSE243039 was obtained from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) between endometriosis and normal control samples were identified. After screening of DEGs, gene ontology (GO) and REACTOME pathway enrichment analyses were performed. Furthermore, a protein–protein interaction (PPI) network was constructed and modules were analyzed using the Human Integrated Protein–Protein Interaction rEference database and Cytoscape software, and hub genes were identified. Subsequently, a network between miRNAs and hub genes, and network between TFs and hub genes were constructed using the miRNet and NetworkAnalyst tool, and possible key miRNAs and TFs were predicted. Finally, receiver operating characteristic curve analysis was used to validate the hub genes. Results A total of 958 DEGs, including 479 upregulated genes and 479 downregulated genes, were screened between endometriosis and normal control samples. GO and REACTOME pathway enrichment analyses of the 958 DEGs showed that they were mainly involved in multicellular organismal process, developmental process, signaling by GPCR and muscle contraction. Further analysis of the PPI network and modules identified 10 hub genes, including vcam1, snca, prkcb, adrb2, foxq1, mdfi, actbl2, prkd1, dapk1 and actc1. Possible target miRNAs, including hsa-mir-3143 and hsa-mir-2110, and target TFs, including tcf3 (transcription factor 3) and clock (clock circadian regulator), were predicted by constructing a miRNA-hub gene regulatory network and TF-hub gene regulatory network. Conclusions This investigation used bioinformatics techniques to explore the potential and novel biomarkers. These biomarkers might provide new ideas and methods for the early diagnosis, treatment and monitoring of endometriosis.

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Condition tags

endometriosischronic_pelvic_paininfertility

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