Abstract PS13-09: Mechanisms of Resistance to Trastuzumab Deruxtecan in Breast Cancer Elucidated by Multi-omic Molecular Profiling

Abstract Trastuzumab deruxtecan is widely used as a treatment for metastatic HER-2 low and HER2-positive breast cancer, and preclinical studies have suggested multiple potential mechanisms of resistance. There have, however, been few large population-based studies of resistance. Following the course of trastuzumab deruxtecan (T-DXd) through the cancer cell, we combined Next Generation Sequencing (NGS), immunohistochemistry (IHC) and claims data to evaluate clinically relevant mechanisms of resistance to this agent. A total of 1220 T-DXd-treated breast cancer samples tested at Caris Life Sciences (Phoenix, AZ) underwent whole transcriptome sequencing (Illumina, NovaSeq). HER2 IHC was performed (4B5) and scored following ASCO/CAP guidelines. Real-world clinical data were obtained from insurance claims. Time-on-treatment (TOT) and post-treatment overall survival (OS) were determined as the interval from the T-DXd initiation to the end of treatment and the last recorded clinical activity, respectively. RNA expression of 86 genes linked to numerous reported ADC resistance mechanisms were investigated for association with clinical outcome, including antigen/dimerization partners (N=5), ABC transporters (N=38), lysosomal genes (N=16), genes involved in ADCC pathway (N=9), endocytosis, intracellular trafficking and cytoskeleton organization pathways (N=6), topoisomerase isoforms (N=4), tubulin isoforms (N=5) and well-established prognostic markers in breast cancer (N=3). Multivariate analysis was conducted using RNA transcript per million (TPM) inputs as continuous variables in a Cox-Proportional Hazard model, with significance determined at p<0.05. In the multivariate analyses performed in 1144 tumors collected prior to T-DXd start, associating expression levels of the 86 genes with TOT and OS revealed ERBB2 as the strongest positive predictor of TOT (p<0.0001; FDR adjusted p =0.0011) and OS (p<0.0001; FDR p =0.011); conversely, ABCC1 expression (MRP1, multidrug-resistance associated protein 1) emerged as the strongest negative predictor of TOT (p=0.0009, FDR p=0.030) and OS (p=0.0004, FDR p =0.011). Notably, MKI67 (p=0.0099), TUBB3 (p=0.005) were negatively associated with OS, not with TOT. Using the top quartile of ABCC1 expression (35 TPM) as cutoff, T-DXd outcome was better in ABCC1-low vs. ABCC1-high tumors (TOT: 6.0m vs. 5.2m p=0.09; OS: 24 vs. 15m, p=0.0005). When combined with ERBB2 RNA expression (using median of 63 TPM as a cutoff), ABCC1-high tumors showed significantly shorter TOT compared to ABCC1-low in both the ERBB2-high (TOT: 4.7m, 95% CI [3.9-5.1] vs. 9.1m, 95% CI [7.3-10.7m]) and ERBB-low group (TOT: 3m [2.3-4.3] vs. 6.3 [5.1-7], p<0.0001); similar differences were observed for OS. When ABCC1 RNA expression was combined with ERBB2 IHC, amongst all subgroups, tumors with HER2 IHC 0+ and ABCC1-high showed the shortest TOT (2.3m, [1.6-3.5m]) and OS (10.7m, [6-30.1m]) while tumors with HER2 IHC 3+ and ABCC1-low showed the longest TOT (10.7m [7.7-13.4m]) and OS (30.8 [24.1-not reached]). Patient age was not significantly associated with TOT or OS in our analyses. As expected, ERBB2 RNA expression was strongly associated with HER2 IHC results: median ERBB2 = 31 TPM in IHC intensity of 0+, 48 TPM in IHC of 1+; 84 TPM in IHC of 2+, and 445 TPM of IHC of 3+ (p<0.0001). Using a multi-omic approach, we thoroughly surveyed gene expressions on pathways associated with antibody-drug conjugate resistance mechanisms. By examining clinical outcome data from 1144 breast cancer patients treated with T-DXd, our data suggest that at an intracellular level TDXd outcome is a function of drug concentration influx and time to efflux. Citation Format: George Sledge, Joanne Xiu, Reshma L. Mahtani, Ana C. Sandoval Leon, Matthew J. Oberley, Milan Radovich, David Spetzle. Mechanisms of Resistance to Trastuzumab Deruxtecan in Breast Cancer Elucidated by Multi-omic Molecular Profiling [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr PS13-09.