DEGs and Biological Process Profiling to screen the novel biomarkers associated with both Uterine Leiomyomas and Uterine leiomyosarcomas

Abstract

Background Uterine Leiomyomas (ULM) or Uterine fibroid are benign lesion of unspecified aetiology and still there is dearth of prognostic biomarkers for diagnosis. The aim of this present study is to explore the novel biomarkers to be associated with Uterine Leiomyomas (ULM) and Uterine leiomyosarcomas (ULMS) that were responsible for their pathogenicity. Methods The microarray dataset (GSEID:GSE64763) was retrieved from the Gene Expression Omnibus database. Data preprocessing and differential gene expression analysis was performed. Principal Component Analysis (PCA) plot and heat map for ULM and ULMS were constructed for respective differentially expressed genes. The DEGs were further intersected to find the common DEGs in ULM and ULMS. Based upon STRING v 10.5, protein- protein interaction network was constructed. Further, Gene Ontology (GO) and KEGG pathway enrichment analysis were also performed to dissect out possible function and pathways. Results A total of 50 significant DEGs for ULM while 321 DEGs for ULMS have been identified with their official gene symbol. Between ULM and ULMS, total 14 common DEGs were identified of which 8 were up-regulated while 6 were down-regulated. Comparison of DEGs list with annotated gene list obtained from OMIM and Gene Cards, lead to identification of only 3 known disease genes (RAD51B, ESR1 and PDGFRA) while SHOX2, TNN and COL11A1 genes were found to be novel biomarkers in ULM and ULMS both. Gene ontology and KEGG pathway enrichment analysis of common novel and known candidate genes led to the identification of several important processes and pathways like ECM receptor interactions and Focal adhesion. Conclusions SHOX2, TNN and COL11A1 are the novel biomarkers related to both ULM and ULMS disease and have been found to be associated with ECM receptor interactions and Focal adhesion like pathways and hence can serve as novel diagnostic as well as therapeutic targets.