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Simple Summary: Breast cancer patients often receive anti-hormonal treatment if their tumor is positive for the Estrogen Receptor (ER), but tumors may become resistant to this therapy and still metastasize. We studied 101 of such metastatic lesions and investigated these lesions for mutated genes and mutation patterns, in combination with the level of expression of relevant genes. Our aim was to better understand the mechanisms that are involved in the resistance to anti-hormonal treatment. The analyses showed two distinct groups of patients, each with specific mutations. One group clearly showed an ongoing, active ER and its associated signal route; these patients probably still would benefit from ER-targeting agents. We advocate for combining mutation and expression analyses on metastatic lesions, to maximize the group of patients that still may benefit from existing or new anti-hormonal treatments targeting ER or its signaling network. Mutations in the estrogen receptor gene (ESR1), its transcriptional regulators, and the mitogen-activated protein kinase (MAPK) pathway are enriched in patients with endocrine-resistant metastatic breast cancer (MBC). Here, we integrated whole genome sequencing with RNA sequencing data from the same samples of 101 ER-positive/HER2-negative MBC patients who underwent a tumor biopsy prior to the start of a new line of treatment for MBC (CPCT-02 study, NCT01855477) to analyze the downstream effects of DNA alterations previously linked to endocrine resistance, thereby gaining a better understanding of the associated mechanisms. Hierarchical clustering was performed using expression of ESR1 target genes. Genomic alterations at the DNA level, gene expression levels, and last administered therapy were compared between the identified clusters. Hierarchical clustering revealed two distinct clusters, one of which was characterized by increased expression of ESR1 and its target genes. Samples in this cluster were significantly enriched for mutations in ESR1 and amplifications in FGFR1 and TSPYL. Patients in the other cluster showed relatively lower expression levels of ESR1 and its target genes, comparable to ER-negative samples, and more often received endocrine therapy as their last treatment before biopsy. Genes in the MAPK-pathway, including NF1, and ESR1 transcriptional regulators were evenly distributed. In conclusion, RNA sequencing identified a subgroup of patients with clear expression of ESR1 and its downstream targets, probably still benefiting from ER-targeting agents. The lower ER expression in the other subgroup might be partially explained by ER activity still being blocked by recently administered endocrine treatment, indicating that biopsy timing relative to endocrine treatment needs to be considered when interpreting transcriptomic data. [ABSTRACT FROM AUTHOR]