Abstract A041: Emergence of TOP1 mutations as a potential biomarker of resistance to topoisomerase-targeting regimens

Abstract Background: Antibody-drug conjugates (ADCs) deliver cytotoxic agents, such as topoisomerase I inhibitors, directly to tumor cells. Sacituzumab govitecan (SG) and trastuzumab deruxtecan (T-DXd) are FDA-approved ADCs with topoisomerase I payloads, specifically SG for pretreated triple-negative and HR-positive breast cancers, and T-DXd for HER2-expressing malignancies. Although ADCs have shown clinical efficacy across multiple solid tumors, mechanisms of resistance, particularly to topoisomerase payload–containing ADCs, remain poorly defined. Emerging data suggest that acquired mutations in DNA topoisomerase I (TOP1) may contribute to resistance. In this study, we investigated the incidence and molecular features of TOP1 mutations in patients progressing on ADCs with topoisomerase payloads or camptothecin-based chemotherapy. Methods: We retrospectively analyzed frequency of TOP1 mutations in 17,092 patients with solid tumors who underwent next-generation sequencing (NGS) at The University of Texas MD Anderson Cancer Center via MDA MAPP sequencing platform (tumor and/or liquid biopsy [LB]) between January 2019 and January 2025. We then focused on patients treated with topoisomerase inhibitor–based ADCs (SG, T-DXd, and datopotamab deruxtecan [Dato-DXd]) or irinotecan/topotecan-containing chemotherapy (n = 1807). Patients with paired pre-/post-treatment NGS were included in our study (n = 343). We assessed for emergence of TOP1 mutations, changes in variant allele frequency (VAF) in tumors that progressed on these regimens, and in silico analysis (ClinVar and InterVar) with review of literature for mutation annotation. Results: Among the 17,092 patients with available NGS data, 160 patients (0.94%) had TOP1 mutations. These included 14 of 2,040 patients (0.68%) with LB NGS only, 18 of 1,324 patients (1.35%) with both LB and tumor NGS, and 128 of 13,728 patients (0.93%) with tumor NGS only. We identified nine distinct TOP1 mutations—G363S, G365V, G365S, R364C, K333fs, R434Q, R84K, A670G, and R364H at time of disease progression. These alterations were observed in 3.4% (5/145) of patients who received ADC therapy and 2.1% (4/193) treated with irinotecan-based chemotherapy. The G365S and R364H variants have been reported as pathogenic, associated with resistance to camptothecin in vitro, and ADC resistance (R364H). Notably, one breast cancer patient treated with SG for 126 days before progression had three TOP1 alterations: G365V (VAF 23%), G365S (12%), and R364C (8%) at end of treatment. Additionally, four colorectal cancer patients treated with FOLFIRI plus bevacizumab or panitumumab had emergence of distinct TOP1 mutations at disease progression. Conclusions: The emergence of TOP1 mutations following treatment with ADCs with topoisomerase payload or irinotecan-based chemotherapy may represent a potential mechanism of resistance in a subset of patients. Given the limited number of cases and the current unknown impact of these mutations on TOP1 function or antitumor efficacy, additional studies are needed to clarify their clinical significance. Citation Format: Tejaswini P. Reddy, Lei Kang, Hung Le, Senthil Damodaran, Kanwal Raghav, Scott Kopetz, Jordi Rodon Ahnert, Ecaterina E. Dumbrava, Timothy A. Yap, Stephen Williams, Mark J. Routbort, Keyur P. Patel, Funda Meric-Bernstam. Emergence of TOP1 mutations as a potential biomarker of resistance to topoisomerase-targeting regimens [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr A041.