HER2 proteoforms promote therapeutic resistance and aggressiveness in HER2-positive breast cancer, yet their epigenetic consequences remain poorly defined. Here, we establish EpiBlot, a joint assay incorporating a customized plateATAC-seq workflow that minimizes sample inputs with single-cell western blotting to concurrently profile chromatin accessibility with protein and proteoform expression in breast cancer MCF7 cells. Engineered MCF7 cells expressing HER2 proteoforms - full-length p185HER2 or truncated 611-CTF - were evaluated on the impact of such proteoforms after lapatinib or doxorubicin exposure. Expression of 611-CTF elicits pervasive chromatin remodeling, whereas p185HER2 provokes only modest accessibility shifts under the same treatments. Lapatinib treatment produces limited global effects but unmasks proteoform-specific responses, while treatment with doxorubicin drives extensive genome-wide accessibility changes. Concordance between chromatin accessibility and protein abundance is moderate, underscoring complex regulatory coupling. Extending this dual-modality approach to HER2-low patient-derived organoids uncovers distinct chromatin states and reveals a subpopulation of triple-negative breast-cancer cells expressing truncated HER2 proteoforms. These findings highlight the value of multimodal profiling with proteoform identification for dissecting tumor heterogeneity and therapeutic response in HER2-positive breast cancer.
Khartchenko et al. (Sat,) studied this question.
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