Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort

Abstract

Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.

In silicoapproaches to identify the role of lncRNAs in Prostate cancer and Androgen receptor-targeted proteins

“…From our recently published RNA-Seq analyses ( Shukla et al 2023), 11 lncRNAs identified (SCARNA10, LINC01973, LINC00940, NPBWR1, FLJ16779, ANKRD20A9P, LINC00298, SNHG19, LOC341056, TLX1NB, LINC00662:60) were screened in the form of FASTA files which were then retrieved as discussed previously (using NCBI, NONCODE, LINCipedia and RNA central public portals). We considered the HDOCK web server for the molecular docking studies to identify the interactions of receptor-ligands.…”

“…Few limitations such as rearrangement were not considered in aneuploidy. In our lab, RNA-seq data from a small cohort of PCa patients was analyzed and some critical lncRNAs were identified as deterministic markers (Shukla et al, 2023). In present study, docking analysis of prostate specific proteins and AR with lncRNAs was performed to explore binding potential towards identifying interacting residues and putative RNA-binding motifs.…”

“…Similarly, the RNA-sequencing (RNA-seq) approach is used to measure the expression across a transcriptome and identify gene fusions, single nucleotide variants etc. In a parallel study in our lab, using the RNA-seq approach we have identified many differentially expressed genes (DEGs) and long non-coding RNAs (lncRNAs) (Shukla et al, 2023) in PCa samples specific to India. LncRNAs have been implicated as a diagnostic and prognostic biomarkers in different cancers (Qian et al, 2020) with well-known lncRNAs such as MALAT, HOTAIR, XIST have been reported in genitourinary cancers but their role as biomarkers is warranted (Tortora et al, 2023).…”