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Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian
Nidhi Shukla1,2, Bhumandeep Kour3, Devendra Sharma4
1Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India.
Diseases (Basel, Switzerland)
|May 23, 2023
Summary
This study used RNA sequencing to identify novel genes and long non-coding RNAs in Indian prostate cancer (PCa) patients. Findings may lead to new biomarkers and therapies for PCa.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Prostate cancer (PCa) is a prevalent cancer in India, with limited Next-Generation Sequencing (NGS) studies.
- Previous research identified PCa-specific genes and mutations in Indian populations using Whole Exome Sequencing (WES).
- Novel non-coding RNAs are emerging as potential biomarkers in various cancers, identified through large-scale genomic initiatives.
Purpose of the Study:
- To identify differentially expressed genes (DEGs), including long non-coding RNAs (lncRNAs), associated with signature pathways in an Indian PCa cohort.
- To utilize RNA-sequencing (RNA-seq) for comprehensive transcriptome analysis of PCa tissues.
- To discover novel PCa-specific molecular markers for potential therapeutic development.
Main Methods:
- RNA-sequencing (whole transcriptome shotgun sequencing) was performed on six Indian PCa patients who underwent prostatectomy.
- Read counts were normalized using fragments per kilobase of transcript per million mapped reads (FPKM).
- Differentially expressed genes (DEGs) were analyzed using bioinformatics tools (GeneMANIA, Stringdb, Cytoscape-Cytohubba, cbioportal) and an in-house cuffdiff pipeline.
Main Results:
- Identified key PCa-specific genes (e.g., STEAP2, APP, PMEPA1) and genes involved in cancer pathways (e.g., COL6A1, BACE1).
- Discovered several novel long non-coding RNAs (lncRNAs) such as LINC01440 and SOX2OT requiring further characterization.
- Compared findings with public datasets, highlighting characteristic DEGs and lncRNAs in Indian PCa not previously reported.
Conclusions:
- RNA-seq analysis revealed characteristic DEGs and novel lncRNAs in an Indian PCa cohort.
- These findings implicate specific molecular signatures in PCa pathways within this population.
- The study provides a foundation for experimental validation, potentially leading to new PCa biomarkers and therapies.
