Impact of Trastuzumab and Pertuzumab on HER2 Localization and the Estrogen Receptor Cistrome in ER+/HER2+ Breast Cancer

Background: Although anti-HER2 monoclonal antibody therapy with trastuzumab and pertuzumab is highly effective for HER2-positive breast cancer, co-expression of estrogen receptor (ER) significantly reduces pathologic complete response rates. Objective: We investigated how HER2-targeted inhibition affects HER2 cellular localization and ER genomic binding in ER-positive, HER2-positive breast cancer. Methods: We evaluated HER2 localization in a tissue microarray of treatment-naive patients. Using cellular fractionation, immunofluorescence, chromatin immunoprecipitation, and genome-wide profiling (CUT&RUN), we evaluated HER2 localization and ER genomic binding following acute anti-HER2 treatment and in models of treatment resistance. The treatment-induced ER-bound gene signature was assessed for associations with pathologic complete response and survival in breast cancer clinical cohorts. Results: In treatment-naive primary breast tumors, nuclear HER2 inversely correlated with ER levels. In cell models, treatment with trastuzumab and pertuzumab induced nuclear and chromatin accumulation of HER2. Concurrently, acute anti-HER2 treatment displaced ER from canonical estrogen response elements at classical target genes, yet genome-wide profiling revealed redistribution of ER binding toward non-canonical zinc finger motifs adjacent to pro-survival Wnt and RAGE pathway genes (FZD8, RELA). Expression of a drug-induced ER-bound gene signature was significantly higher in tumors of individuals who did not achieve pathologic complete response following neoadjuvant anti-HER2 therapy and significantly correlated with reduced distant metastasis-free survival in clinical cohorts. Conclusions: Anti-HER2 targeted therapy causes dynamic cistromic reprogramming of ER from classical estrogen pathways toward alternative pro-survival networks. These findings implicate ER redistribution as a possible mediator of resistance and highlight novel therapeutic targets in ER-positive, HER2-positive breast cancer.