TOP1 Mutations and Cross-Resistance to Antibody-Drug Conjugates in Patients with Metastatic Breast Cancer

Abstract Purpose: Antibody-drug conjugates (ADCs) harboring topoisomerase I (TOP1) inhibitor payloads have improved survival for patients with metastatic breast cancer (MBC). However, knowledge of ADC resistance mechanisms and potential impact on sequential use of ADCs is limited. Here, we report the incidence and characterization of TOP1 mutations arising in the setting of ADC resistance in MBC. Methods: Patients with MBC treated with ADCs with available post-treatment plasma-based genotyping were included. TOP1 mutation incidence, mutant allele frequency (MAF) and functional characterization were assessed, and incidence was compared to that in MBC patients not receiving ADC treatment and in The Cancer Genome Atlas (TCGA). Results: Plasma-based genotyping identified distinct TOP1 mutations (S57C, R364H, W401C, G359E) in 12.9% of patients (4/31) at time of disease progression on ADC, compared to 0.7% (3/420) in non-ADC treated MBC patients and 0.5% reported in TCGA. Appearance of mutations was associated with clinical cross-resistance, as median duration on first ADC was 455 days versus 52 days for second ADC. Functional characterization of three novel TOP1 mutant proteins demonstrated that all exhibited reduced enzymatic activity, attenuated covalent DNA binding, and resistance to TOP1 inhibitor ADC payloads SN38 and Deruxtecan. Conclusions: We describe the recurrent emergence of functionally altered, resistance-associated TOP1 mutations in vivo under selective pressure from ADCs, and the potential impact on mediating cross-resistance to sequential ADCs. TOP1 mutation may represent a biomarker of resistance in this setting, and additional work is needed to optimize biomarkers and ADC payload design to improve outcomes for sequential use of ADCs.