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bioRxiv · 10.1101/2025.09.25.678463

Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems

Fomitcheva Khartchenko, A.·Lam, T.·Goldhammer, N.·Bont, M.·Warhadpande, S.·Rosenbluth, J.·Herr, A.
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Abstract

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. We applied our method to engineered MCF7 cells expressing HER2 proteoforms - full-length p185HER2 or truncated 611-CTF -, where we evaluated the impact of such proteoforms on the epigenetic and protein profiles after lapatinib or doxorubicin exposure. Expression of 611-CTF elicits pervasive chromatin remodeling, whereas p185HER2 provokes only modest accessibility shifts under the same treatments. EpiBlot reveals that treatment with doxorubicin drives extensive genome-wide accessibility changes, while lapatinib treatment produces limited global effects but unmasks proteoform-specific responses. 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. We anticipate that EpiBlot will highlight the value of multimodal profiling with proteoform identification for dissecting tumor heterogeneity and therapeutic response in cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/678463v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@673263org.highwire.dtl.DTLVardef@11d28c5org.highwire.dtl.DTLVardef@15fa336org.highwire.dtl.DTLVardef@1d4426b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Fomitcheva Khartchenko, A., Lam, T., Goldhammer, N., Bont, M., Warhadpande, S., Rosenbluth, J., Herr, A.. 2025-09-27. Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems. https://doi.org/10.1101/2025.09.25.678463

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