RNA-Seq reveals skipping of exon 3 in a breast cancer patient carrying G118D PIK3CA mutation

Abstract

Breast cancer is the most commonly diagnostic cancer and the leading cause of cancer death in females. An important gene PIK3CA is known for playing the important role in breast cancer pathogenesis. In this study, we carried out RNA sequencing of cancer and normal samples of a breast cancer patient positive for PIK3CA G118D somatic mutation to identify the potential targets through differential gene expression and alternative splicing of genes. RNA sequencing of cancer and normal samples was carried out using Illumina Hiseq 2500. Sequencing reads were mapped with the human reference genome hg19 using algorithm implemented in STAR. Cuffdiff of Cufflinks was used to identify differentially expressed genes (DEGs) and rMATS was used to identify differentially alternative splicing (DASs) events. Functional enrichment and pathway analysis was carried out using DAVID database. Overall, the cancer sample resulted in the identification of a total of 322 DEGs; 64% of them were down regulated and 36% were up-regulated. Skipping Exon (SE) was found to be most common alternative splicing (AS) event and accounted for 73% of all the AS events. The important cancer genes showing AS include PIK3CA, MUTYH, PALB2, NTRK1, DNMT3A. The GO annotation revealed very important biological processes associated with DAS including cell death, apoptosis, response to stress, cell differentiation. We also obtained very interesting pathways using the KEGG pathway database including TNF signaling pathway, estrogen signaling pathway, ErbB signaling pathway and cAMP signaling pathway. We conclude that splicing alterations would be a great source to elucidate the potential biomarkers for breast cancer treatment.