Abstract PS4-03-22: High throughput analysis in locally advanced triple negative breast cancer TNBC: pathological complete response pCR and mutational status

Abstract Background Pathologic complete response after neoadjuvant treatment is a strong prognostic biomarker associated with improved survival in breast cancer patients, especially in triple negative breast cancer and HER2 positive subtypes. Despite high response rates to neoadjuvant chemotherapy, triple negative breast cancer has been linked to higher rates of recurrence and poorer outcome. The aim of this study is to evaluate the genomic landscape of tissue samples from locally advanced breast cancer patients treated in a neoadjuvant setting and to correlate the genomic analysis to response and clinical outcome. Methods We retrospectively evaluated 48 core needle biopsies before chemotherapy from a cohort of 136 patients with locally advanced triple negative breast cancer. Pathological chemotherapy response and not responders was assessed by surgery. DNA extracted from archival formalin-fixed paraffin-embedded samples was subjected to sequencing using the TruSight Oncology 500 panel (Illumina, San Diego, USA; 523 genes, size: 1. 94 Mb), following the manufacturer’s protocol, which assesses microsatellite instability status, tumor mutation burden, recurrent somatic copy number variations, somatic sequence variants as single nucleotide variants and Insertion/Deletion. Libraries were sequenced on NovaSeq 6000 Illumina platform to reach a minimum of 500× read depth. 67 (51. 3%) out of 136 patients received a standard anthracycline and taxane regimen and 69 (50. 7%) patients received a platinum-containing chemotherapy regimen. Somatic mutations classified as Oncogenic or Likely Oncogenic according to OncoKB with a variant allele frequency ≥0. 03 were included. Differences of mutational profile were assessed using Chi-squared test. Statistical analysis was performed with R Studio (version 4. 2. 2). Results In total we analyzed samples from 48 patients. The median age was 46 years. 22 of 48 (46%) were HER2 low, 42 (87%) with G3, 27 (56%) with stage II and 16 (33%) with stage III. 28 out of 48 patients (58. 3%) not obtained pCR. We showed statistically significant correlations between PIK3CA mutations and PI3K pathway mutations with the absence of pathological complete response with p-values of 0. 013 and 0. 024 respectively. Genomic analysis of the entire cohort revealed the most frequently altered genes to be TP53 (94%), PIK3CA (21%), BRCA1 (15%), along with amplifications of MYC (23%) and GATA3 (17%) and MCL1 (15%). The most aberrant pathways in not pCR population are PI3K and RTK-RAS signaling. Alterations in PIK3CA was observed in 39% of not responders and absent in responder patients (p-value 0. 05, reflecting its key role in PI3K-AKT-mTOR signaling pathway. The lollipop plots show how missense (H1047R, E542K, R88Q, V344G) and inframe deletion (G106E109del, E110del) mutations are presents in not responder patients after neoadjuvant chemotherapy. Interestingly, median TMB in not responder’s cohort is 5. 5 while in chemo sensitive patients is 4. 8 (p-value 0. 93). Conclusions In this preliminary report, PIK3CA mutations and related pathways may impact the effectiveness of neoadjuvant chemotherapy in achieving pCR. A larger sample size is needed to further evaluate the significance of mutations and co-alterations in different subgroups. We would like to acknowledge the contribution of the Multispecialistic Biobank Research Core Facility of Fondazione Policlinico Universitario A. Gemelli Biobank, for providing the bioresources. Citation Format: I. Paris, G. Mantini, T. D'Angelo, A. Minucci, G. Luciano, C. Parrillo, M. De Bonis, D. Generali, G. Raspaglio, M. De Donato, F. Pavese, C. Nero, A. Fabi, A. Piermattei, P. Fuso, V. Ricozzi, L. Carbognin, S. Rotondaro, T. Pasciuto, M. Marrazzo, A. Mulè, G. Garganese, A. Di Leone, M. Sanchez, A. Migliore, D. Giannarelli, G. Franceschini, A. Fagotti. High throughput analysis in locally advanced triple negative breast cancer TNBC: pathological complete response pCR and mutational status abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32 (4 Suppl): Abstract nr PS4-03-22.