Mutational signature differences in paired tissues of triple-negative breast cancer receiving neoadjuvant therapy: Preliminary analysis.
Authors: Hemavathi Baskarane, Mohit Kumar Divakar, Atul Batra, Akash Kumar, Biswajit Dubashi, Amit Sehrawat, Parmod Kumar, Ashutosh Mishra, Pranay Tanwar, Suhani Suhani, Brijesh Kumar, Sandeep Mathur, Vishakha Hooda
Journal: Journal of Clinical Oncology (2025)

e12555 Background: Triple-negative breast cancer (TNBC), accounting for 15%–20% of breast cancers, is aggressive, with higher relapse rates and worse outcomes than hormone receptor-positive tumors. Despite higher pathologic complete response (pCR) rates (30%–40%) after neoadjuvant chemotherapy, residual disease predicts poor prognosis, with no targeted therapies currently available. Molecular studies, using either pre- or post-treatment sequencing, have identified mutations such as TP53, PIK3CA, PTEN , and MYC affecting chemosensitivity.Asian cohorts have demonstrated unique molecular signatures, particularly with alterations in TP53, PIK3CA, and AR . However, such insights remain unexplored in the Indian TNBC population. Methods: In this multi-center study, we enrolled newly diagnosed TNBC patients receiving neoadjuvant chemotherapy (anthracycline and taxane) after informed consent. Pre-treatment biopsies were collected, and targeted next generation sequencing was performed on both pre-treatment and residual tumor samples from patients who did not achieve path CR after treatment to evaluate mutational signature differences. Results: A total of 108 confirmed TNBC cases were enrolled for the study. Preliminary analysis was done on the sequencing data available for 44 patients (21 path CR and 23 with residual disease). Tumor mutational burden (TMB) analysis revealed an average TMB of 18.15 in the primary tumors of pathCR samples, in contrast with TMB of 26.52 in primary tumors, and TMB of 19.69 in residual tumors of patients, who did not achieve the pathCR after treatment. Mutation spectra showed distinct patterns, with C &gt; A transversions dominating in path CR tumors (65.25%) and C &gt; T transitions progressively increasing in non-path CR primary tumors (71.91%) and residual tumors (84.27%), suggesting genomic instability. The most frequently mutated genes varied across cohorts. Cohort-wise analysis of all the variants revealed BRCA2, TP53 and EP300 being highly mutated in pathCR primary tumors, while BRCA2, KMT2A and ROS1 as highly mutated genes in the nonpathCR primary tumors. In the residual tumor sample of the nonpathCR group, KMT2A, TP53 and APC were the most mutated genes. Extended evaluation of unique variants among each cohort showed the top mutated genes as BRCA2 in pathCR samples, while MTOR in primary tumor and KMT2A in residual tumor of nonpathCR samples. Conclusions: This study highlights distinct mutational signatures between the path CR and non-path CR samples, suggesting a potential gene expression differences that influence treatment outcomes but also the acquisition of genetic mechanisms through clonal evolution and changes in the tumor microenvironment during treatment. Larger studies are needed to unravel resistance mechanisms and develop novel therapies for residual disease to improve patient outcomes.