Abstract 1886: Proteogenomic insights into chemotherapy resistance and therapeutic strategies in triple-negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive subtype associated with high mortality and frequent chemotherapy resistance, necessitating the identification of biomarkers to predict treatment outcomes and elucidate resistance mechanisms. To address this challenge, we conducted a comprehensive proteogenomic analysis to uncover molecular determinants of chemotherapy response in TNBC. Methods: Pretreatment tumor samples from stage II or III TNBC patients (n=50) treated with adriamycin, cyclophosphamide, and taxane-based neoadjuvant chemotherapy, along with post-treatment samples from patients (n=31) who did not achieve a pathologic complete response (pCR), were analyzed. Multiomics integration of exome sequencing, RNA-seq, and TMT-based proteomics and phosphoproteomics identified key pathways and molecular subtypes. Results: Non-negative matrix factorization (NMF) clustering identified five molecular subtypes: “immune-enriched” (n=9), “xenobiotic metabolism” (n=2), “epithelial-mesenchymal transition (EMT)” (n=7), “Myc target” (n=12), and “myogenesis” (n=11). The “immune-enriched” subtype exhibited the highest pCR rate (5/9, 55.6%), whereas no pCRs were observed in the “xenobiotic metabolism” or “EMT” subtypes. Gene set enrichment analysis (GSEA) revealed immune-related pathways enriched in the pCR group across RNA and protein data, while EMT pathways were predominant in the non-pCR group. Notably, the estrogen response pathway was enriched in the non-pCR group exclusively in the protein GSEA data, emphasizing the greater clinical relevance of proteomics over transcriptomics in this context. Differentially expressed genes in the immunomodulatory subtype, based on the Lehmann classification, demonstrated upregulation of doxorubicin metabolism (ARK1C2) and efflux (ABCA13) genes in non-pCR patients, contributing to chemotherapy resistance. Cytoband GSEA identified ITGB8, a membrane protein on chromosome 7p21, whose loss correlated with a significantly higher pCR rate (48.3% vs. 14.3%, p = 0.031). Phosphoproteomics-based PTM-SEA highlighted the GRK2 pathway as enriched in non-pCR tumors and tumors without ITGB8 loss, suggesting its role as a resistance mechanism. In vitro experiments confirmed that GRK2 silencing enhanced the efficacy of taxane-based chemotherapy. Comparison of pre-treatment and post-treatment tumor phosphoproteomes unveiled enrichment of the AURKB pathway in post-treatment samples, with functional validation demonstrating a synergistic effect of AURKB inhibition with paclitaxel, suggesting a promising combination therapy. Conclusion: This integrative proteogenomic analysis identifies proteomic estrogen signature, ITGB8, GRK2, and AURKB as promising biomarkers and therapeutic targets, providing new insights into chemotherapy resistance and response in TNBC. Citation Format: Dong Ki Lee, 1 Min Hwan Kim, 1 Yumi Hwang, 2 Seul-Gi Kim, 1 Gun Min Kim, 1 Kyung-Hee Kim, 3 Jong Bae Park, 3 Min Jung Kim, 1 Jee Ye Kim, 1 Hyung Seok Park, 1 Seho Park, 1 Seung Il Kim, 1 Heon Yung Gee, 1 Joohyuk Sohn1. Proteogenomic insights into chemotherapy resistance and therapeutic strategies in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1886.