Abstract 2967: Evolution of TOP1 variants under selective pressure from topoisomerase-based therapeutics.

Abstract Background: Antibody-drug conjugates (ADCs) that incorporate topoisomerase I inhibitor payloads, including sacituzumab govitecan (SG) and trastuzumab deruxtecan (T-DXd), have demonstrated activity across multiple solid tumors. SG is approved for previously treated triple-negative and hormone receptor-positive breast cancers, while T-DXd is approved for HER2-expressing malignancies. Despite broad clinical use, the mechanisms underlying resistance to topoisomerase-based ADCs remain insufficiently defined. Recent reports indicate that acquired TOP1 mutations may contribute to therapeutic failure. We evaluated the frequency and characteristics of TOP1 alterations in patients who progressed on ADCs carrying topoisomerase payloads or on camptothecin-based chemotherapy. Methods: We reviewed 17,092 solid tumor samples profiled by tumor and/or liquid biopsy next-generation sequencing (NGS) through the MDA MAPP platform at The University of Texas MD Anderson Cancer Center from January 2019 to January 2025. Patients exposed to topoisomerase inhibitor-based ADCs (SG, T-DXd, or datopotamab deruxtecan [Dato-DXd]) or irinotecan/topotecan-containing chemotherapy were identified (n = 1,807). Those with available paired pre- and post-treatment NGS formed the analytic cohort (n = 343). We assessed the emergence of TOP1 variants at progression, changes in variant allele frequency (VAF), and annotated mutations using ClinVar, InterVar, and literature review. Results: TOP1 mutations were detected in 160 of 17,092 patients (0.94%). This included 14 of 2,040 patients (0.68%) with liquid-biopsy NGS only, 18 of 1,324 (1.35%) with both liquid biopsy and tumor NGS, and 128 of 13,728 (0.93%) with tumor-only NGS. Nine unique TOP1 variants, G363S, G365V, G365S, R364C, K333fs, R434Q, R84K, A670G, and R364H, arose at progression. Emergent alterations occurred in 3.4% (5/145) of patients treated with topoisomerase-payload ADCs and 2.1% (4/193) of those receiving irinotecan-based chemotherapy. G365S and R364H were previously described as pathogenic variants associated with camptothecin resistance, with R364H also linked to ADC resistance. One SG-treated breast cancer patient developed three concurrent alterations, G365V (VAF 23%), G365S (12%), and R364C (8%), at progression. Four colorectal cancer patients receiving FOLFIRI plus bevacizumab or panitumumab exhibited distinct emergent TOP1 mutations at disease progression. Conclusions: TOP1 alterations can appear after exposure to topoisomerase-payload ADCs or irinotecan-containing regimens, suggesting a potential resistance mechanism in a subset of patients. The functional impact of these variants and their relevance to therapeutic response remain undefined, warranting further mechanistic and clinical investigation. Citation Format: Tejaswini Reddy, Lei Kang, Hung Le, Senthil Damodaran, Kanwal Pratap Singh Raghav, Scott Kopetz, Jordi Rodon Ahnert, Ecaterina Elena Dumbrava, Timothy A. Yap, Stephen Williams, Mark J. Routbort, Keyur P. Patel, Funda Meric-Bernstam. Evolution of TOP1 variants under selective pressure from topoisomerase-based therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2967.