Clarifying Hub mRNAs, lncRNAs and Gene Expression Profiles of colorectal cancer: An in-silico study

Colorectalcancer (CRC) has been estimated to be the third most frequent cancer globallyand the second most common cause of cancer related deaths. Prediction andidentification of significant genes helps in development of new therapeuticdrugs. Methods: In this study,RNA sequencing data of CRC patients were analyzed utilizing the Galaxyplatform, which offers various tools for comprehensive RNA-seq analysis. Thestudy aimed to compare CRC samples with adjacent non-cancerous tissues(Accession: GSE۱۳۷۳۲۷). Initially, the quality of the RNA-seq reads was assessedusing FastQC, then it was conducted by adapter trimming via Trim Galore. Afterwards,the aligned reads were mapped to the reference genome utilizing HISAT۲, andgene expression levels were obtained with HTSeq-count. Furthermore, differentiallyexpressed genes (DEGs) and lncRNAs were identified utilizing the DESeq۲ package.The threshold of |log۲FC| ≥ ۳ and adjusted P-value of ≤ ۰.۰۱ for significancewere applied. For investigating biological functions, with a focus on gene setswhich were significantly overexpressed in our data. we conducted Gene-SetEnrichment Analysis (GSEA) utilizing Enrichr. Mutational analysis of the candidategenes was performed utilizing the cBioPortal, while the STRING and GeneMANIAdatabase were used for gene and protein network analysis. Kaplan-Meier survivalanalysis of hub genes was conducted with the Kaplan–Meier plotter database, andcorrelation analysis were performed using the starBase v۲.۰ database to explorethe interactions of ncRNAs and their target mRNAs. Results: Wedemonstrated that ۲۱ distinct genes were up-expressed and ۴۳ weredown-expressed in tumors compared with the normal adjacent tissues. Among thetop DEGs, DPEP۱ represented the highest log۲ fold change (FC) at ۶.۱۸. SPINK۴ (log۲ FC: ۵.۷۴), TACSTD۲ (log۲ FC:۵.۴۲), CEMIP (log۲ FC: ۵.۱۵), and MMP۷ (log۲ FC: ۴.۴۰) were among other topDEGs respectively. Conversely, the most significantly downregulated genes wereCD۱۷۷ (log۲ FC: -۷.۰۳), DES (log۲ FC: -۵.۶۸), ACTG۲ (log۲ FC: -۵.۵۹), CLCA۴(log۲ FC: -۴.۵۹), and MYL۹ (log۲ FC: -۴.۲۰). To investigate the biological implicationsof these changes, Gene Ontology (GO) enrichment and KEGG pathway analyses wereconducted. The KEGG results revealed up-regulated genes CA۹ and NPC۱L۱ were involvedin nitrogen metabolism and fat digestion. In contrast, downregulated genes CA۲,AQP۸, and CLCA۴ were associated with bile and pancreatic secretion. Inaddition, the most significantly upregulated lncRNAs were DLX۶-AS۱ (log۲ FC:۷.۸۹), EVADR (log۲ FC: ۶.۵۸), and RP۱۱-۱۱N۵.۱ (log۲ FC: ۶.۵۷). Conversely, themost significantly downregulated lncRNAs were SYNM-AS۲ (log۲ FC: -۴.۹۳),CLCA۴-AS۱ (log۲ FC: -۴.۳۷), and RP۱۱-۳۰۷B۶.۳ (log۲ FC: -۴.۴۲). PPIS identifiedfour hub genes (CNN۱, CCL۲, FLNC, MYH۱۱). The overexpressionof these hub genes correlated with decreased overall survival (OS) in CRCpatients according to Kaplan-Meier survival analysis. The hazard ratios rangedfrom ۱.۳۴ to ۱.۹۵.Conclusion: In conclusion,our findings revealed a clear difference in gene expression between CRC tissuesand adjacent normal ones. Accordingly, ۲۱ genes were upregulated and ۴۳ genesdown-regulated. Overall, this study enhances our understanding of the molecularlandscape of CRC and could guide future research and treatment approaches.

کلیدواژه ها:

colorectal neoplasms ، biomarker ، mRNA ، genes ، lncRNA