Identification of LPIN۱ and MTCO۱P۱۲ genes as gastric cancer-related potential biomarkers based on a ceRNA network

Gastric cancer (GC) is one of the most common causes of cancer-related death in the world . Finding new biomarkers in the detection of tumor in early stages is crucial as GC patients are mostly diagnosed at advanced stages . Di↵erent kind of RNA molecules can compete and interact with each other as competing endogenous RNAs (ceRNAs) through their microRNA (miRNA) response elements (MREs) which influence tumorigenesis in di↵erent cancers such as GC . Purpose:In the present study, we constructed and analyzed a three-component ceRNA network in GC for finding potential diagnostic biomarkers.Methods:Gene expression data of The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset including ۳۷۵ tumoral and ۳۲ normal samples were retrieved using TCGABiolinks R package. Then differentiallyexpressed mRNAs (DEMs), pseudogenes (DEPs) and miRNAs (DEMis) between tumoral and normal samples with adjusted p<۰.۰۵ were extracted utilizing DESeq۲ R package. Different databases like RNAInter (RNA Interactome Database), miRDB, miRTarBase and TargetScan were utilized for finding and predicting interaction between miRNAs and pseudogenes/mRNAs. Subsequently, Cytoscape software (version ۳.۸.۱) was utilized to construct a three-component ceRNA network including mRNAs, pseudogenes and miRNAs.Results:۱۰,۱۴۵ DEMs, ۳,۵۷۶ DEPs, and ۶۰ DEMis were identified in TCGA-STAD tumoral vs. normal samples with the defined p-value cut o↵. A ceRNA network including ۲۷۷ nodes (۲۶۳ DEMs, ۱۰ DEPs and ۴ DEMis) and ۲۸۴ edges was then constructed. A four-component axis including hsamiR-۱۰۵-۵p, hsa-miR-۱۲۲-۵p, LPIN۱ and MTCO۱P۱۲ was selected for further experimental validation.Conclusion:Current study gives an outline of DEMs, DEPs and DEMis in GC that communicate with each other by a sophisticated mechanism which is ceRNA network having a potential to introduce ceRNAs as e↵ective diagnostic biomarkers and therapeutic tools.

کلیدواژه ها:

Competing endogenous RNAs ، Gastric cancer ، microRNAs ، Pseudogenes