A comprehensive strategy for investigating HER2 isoform diversity in breast cancer. (A) Five-step approach to characterize HER2 splicing isoforms in breast cancer patients and cell cultures: (1) identification of HER2 splicing isoforms, (2) in silico characterization of HER2 protein variants, (3) HER2 isoform expression profiling by breast cancer subtype, (4) analysis of antibody–drug conjugate (ADC) sensitivity across HER2 isoform profiles, and (5) examination of HER2 isoform switches in ADC-induced resistance. (B) RNA-sequenced sample selection and stratification based on technical (e.g., distinct library preparation strategies and low number of mapped reads) and biological characteristics (e.g., male samples were excluded, and tumors with same HR status and HER2 expression levels were grouped).
