Abstract PS3-04-13: Identifying recurrent gene amplifications in breast cancer for antibody drug conjugate development

Abstract Background: We hypothesized genes with frequent copy number amplifications in breast cancer resulting in overexpression of membrane proteins could serve as potential targets for novel antibody drug conjugates (ADC). Methods: DNA copy number aberrations (CNA) and mRNA expression data was retrieved from cBioPortal (https://www.cbioportal.org/) for 3,970 patients with breast cancer. We defined gene amplification as CNA value >2. Chi-square or Fisher’s Exact test was used to test for significant difference in amplification frequency between 3 clinical subtypes ER+ (n=2474), HER2+ (n=712), and TNBC (n=632). Wilcoxon signed-rank test was used to test if gene mRNA expression is higher in cancers with amplification compared to wild type. We shortlisted amplified genes as candidates if amplification has led to overexpression and the gene encoded a membrane protein based on information in the Protein Data Bank (https://www.rcsb.org/) and Human Protein Atlas (https://www.proteinatlas.org/). We retrieved normal tissue mRNA expression data from GTEx (https://www.gtexportal.org/home/) covering 21 different tissue types and compared candidate ADC target expression in cancer versus normal tissues using DESeq2. We prioritized ADC candidates by the following criteria (i) CNA frequency > 15% across all breast cancers or within a subtype (FDR<.0001) (ii) higher expression in amplified cancers (FDR<0.001), (iii) mean Log2 Fold expression > 1.5 in cancer compared to each normal tissue one by ones, and (iv) known membrane protein that is primarily located in the cell membrane and ability for internalization. Results: 963 unique genes were recurrently amplified and showed higher gene expression in amplified cancers across all breast cancers (722 genes) and/or significantly amplified only in ER+ (206 4 genes), HER2+ (216 200 genes), and TNBC (114 37 genes), and. how many were amplified in all subtypes?. Of the amplified and overexpressed genes, ⋯N=?...154 genes were membrane proteins. were membrane proteins. Among these membrane membrane proteins, 9 genes had higher expression in breast cancer than in normal tissues and primary located on cell membrane with ability for internalization. They (including HER2) are highlighted in Table 1 met all 4 criteria as potential novel ADC targets⋯N=?... had higher expression in breast cancer than in normal tissues. Nine genes (including HER2) highlighted in bold in Table 1 met all 4 criteria as potential novel ADC targets. Conclusion: We have identified several novel potential targets for ADC development in breast cancer. Citation Format: H. Lin, Y. Wang, J. Dai, L. Pusztai. Identifying recurrent gene amplifications in breast cancer for antibody drug conjugate development [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-04-13.