ArticleDiscover oncology2025
Whole-exome sequencing for identification of specific gene mutations in an Indian cohort of triple-negative breast cancer patients.
Article in Discover oncology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
BACKGROUND/
objectivesTriple-negative breast cancers (TNBCs) are the most aggressive, heterogeneous subtype of breast carcinoma with increased chemoradioresistance and a high rate of relapse. A compelling need exists to discover specific gene mutation(s) and the exomic mutational landscape associated with Indian TNBC patients to identify potential therapeutic target(s) for effective treatment of TNBC.
methodsWhole-exome sequencing (WES) was performed on 15 TNBC patients along with 5 random adjacent normal control tissue (ANCT) specimens. WES data alignment and mapping to the reference human genome (hg19) were done using BWA, SAMtools, and Picard tools. The data analysis and mutation calling were performed using the Genome Analysis Toolkit. The Signal Analyze and PANTHER pathways tools were utilized for mutational signature(s) and pathway(s) analysis, respectively.
resultsOur data revealed that the TNBC genomes carried an average of ~ 106 mutations per sample. MutSig2CV analysis showed the most significant recurrent somatic 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 somatic 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. Moreover, we have noticed germline mutations in TP53, BIN1, MLH1, PIK3CA, and GPSM2. Interestingly, the TNBC genomes exhibited a predominance of signature 1, which is associated with spontaneous deamination of 5-methylcytosine; signature 3 represented the failure of DNA double-strand break repair by homologous recombination; and signature 5 correlated with transcriptional strand bias. Interestingly, the high tumor mutational burden was observed specifically in TNBC patients with signature 3. Furthermore, these mutations were involved in several major signaling pathways, including the Wnt, p53, PDGF, cadherin, DNA replication, integrin, and apoptosis signaling pathways.
conclusionsTogether, the findings indicated that the crucial role played by these key genetic mutations could be utilized in screening and developing potential targeted therapeutics for TNBC patients.
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