Whole exome sequencing for identification of specific gene mutations in an Indian cohort of triple- negative breast cancer patients

Abstract Background: Triple-negative breast cancers (TNBCs) are pathologically the most aggressive and heterogenous subtype of carcinoma breast displaying increased chemo-resistance and a high rate of relapse. A compelling need exists to discover specific gene mutation(s) and exomic mutational landscape associated with Indian TNBC patients in identifying potential therapeutic target(s) for effective treatment. Methods: The status of the hormone receptors and human epidermal growth factor receptor 2 was confirmed. Genomic DNA was extracted from TNBC tissues and adjacent non-cancerous breast tissues. Quantification and quality of gDNA samples were checked. Whole exome sequencing (WES) was performed on 15 TNBC patients along with 5 random adjacent non-cancerous tissue specimens. WES data alignment and mapping to reference human genome hg19 was done using BWA, SAMtools, and Picard tools. The data analysis and mutation calling were performed using the Genome Analysis Toolkit (GATK). The signal and PANTHER pathways tools were used for mutational significance and pathway analysis, respectively. Results: Our data reveals that the TNBC genomes carried an average of ~106 mutations per sample. MutSig2CV analysis showed the most significant recurrent mutations in CTNNB1 (47%; 7/15), TP53 (33%; 5/15), SLC7A8 (27%; 4/15), AMOT (20%; 3/15), CLEC11A (20%; 3/15), and ECHDC1 (13%; 2/15) with a q value of ≤ 0.1. We also observed recurrent mutations in other important cancer-associated genes such as ABCC3 , BRCA1 , BRCA2 , BIRC6 , CDH7 , CSMD3 , MUC12 , MUC16 , NT5C1B , PIK3CA , POLE , STK31 , TTN , and ZFHX4 . Interestingly, the TNBC genomes exhibited a predominance of signature 1 associated with spontaneous deamination of 5-methylcytosine, signature 3 represented the failure of DNA double-strand break repair by homologous recombination, while signature 5 correlated with transcriptional strand bias. Furthermore, these mutations were involved in several major signaling pathways such as the Wnt, p53, PDGF, cadherin, DNA replication, integrin, and apoptosis signaling. Conclusions: Together, the findings of this study indicated that a crucial role played by these key exonic mutations in Indian TNBC patients which could be utilized in screening and TNBC risk predictions in clinical settings, and developing potential targeted therapeutics for TNBC. Furthermore, studies may focus on identifying genetic variability among TNBC patients for developing effective treatment.