Abstract Background: Anti-HER2 antibody-drug conjugate (HER2-ADC) therapies, such as trastuzumab emtansine (T-DM1) and trastuzumab deruxtecan (T-DXd), significantly prolong survival in patients with HER2-positive metastatic breast cancer (BC) compared to physician’s choice of chemotherapy with trastuzumab (The EMILIA, TH3RESA, and DESTINY-Breast clinical trials). Intrinsic or acquired resistance to HER2-ADC therapies remains a substantial clinical challenge since there is no established standard of care following progression on T-DXd. This study aimed to elucidate novel therapeutic targets that can overcome resistance to HER2-ADC therapies using unbiased approaches with synthetic lethal kinome RNA interference screening. Methods: We conducted targeted DNA sequencing (n=15) and whole transcriptome sequencing (n=11) to investigate genetic aberrations following anti-HER2 and/or HER2-ADC therapy (T-DM1 or T-DXd) in BC patient tissue samples. We generated HER2-positive human BC cell lines resistant to T-DM1 or T-DXd. To determine the effect of the T-DM1 and T-DXd on the ERBB2 gene and HER2 protein expression, we used fluorescence in situ hybridization, droplet digital PCR, and Western blotting assay. To discern resistance mechanisms of T-DXd and identify kinase targets whose inhibition might synergistically enhance the efficacy of T-DXd, we conducted whole-genome sequencing, cDNA microarray analysis, and synthetic lethal kinome RNA interference screening using T-DXd resistant HER2-positive BC cell lines. To determine the synergistic antitumor effect of T-DXd combined with targeted therapy, we conducted Bliss synergy analysis, colony formation, and xenograft assays by mammary fat pad injection of T-DM1- or T-DXd-resistant BC cells in nude mice. Results: Increased amplification of DNA repair-related genes (TOP2A, RAD21, RAD52, and CDK12) was found in patient tissue samples after progression to HER2 antibodies, T-DM1, or T-DXd. Significant enrichment of DNA damage repair-related gene sets was observed in the transcriptome of post-treatment human samples. Further, ERBB2 gene or HER2 protein expression was reduced compared to levels before such treatment. In HER2-ADC-resistant HER2-positive BC cell lines, we had similar upregulation of DNA repair-related genes (PCNA, ATM, RAD52) and reduction of ERBB2 gene and HER2 protein expression. By synthetic lethal kinome RNA interference screening, this non-bias screening identified the PI3 kinase, cell cycle, and DNA repair canonical pathways as potential targets to enhance the efficacy of T-DXd therapy in HER2-ADC–resistant HER2-positive BC. We confirmed that ectopic HER2 expression does not improve the efficacy of HER2 ADC in HER2-ADC–resistant HER2-positive BC. After further screening all potential targets, we found that the drugs targeting the DNA damage repair pathway were the most effective in enhancing the efficacy of T-DXd. Indeed, ATR inhibitor elimusertib led to significant HER2-ADC–resistant BC cell death in vitro (Bliss synergy score >5.0, P<0.01) and in four xenografts in vivo (P<0.01) compared to cell death with T-DXd alone. Importantly, we further observed the synergy of elimusertib and T-DXd in parental HER2-positive BC cell lines, ensuring the observed effects are not limited to resistant cell lines only. Conclusions: Our findings indicate that resistance to HER2-ADC therapies is associated with increased DNA repair-related genes. By non-biased screening, this study provides robust evidence that targeting DNA repair pathways can significantly enhance the efficacy of T-DXd in HER2-ADC-resistant HER2-positive BC. The potential of combining ATR inhibitors with T-DXd to overcome resistance and improve patient outcomes is a promising avenue that warrants further exploration in a clinical trial for patients with HER2-ADC-resistant- HER2-positive BC. Citation Format: Jangsoon Lee, Kumiko Kida, JiwonKoh, Huey Liu, GanirajuC. Manyam, Young JinGi, Dileep Reddy, Asha S. Multani, Jing Wang, Gitanjali Jayachandran, Dae-Won Lee, James M. Reuben, AysegulSahin, Lei Huo, DebuTripathy, Seock-Ah Im, and Naoto T. Ueno. Enhancing T-DXd Efficacy in HER2-positive Breast Cancer Resistant to HER2 ADC by Non-biased Kinase-related Target Screening [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 PS13-07.
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