在患有内分泌耐药性转移性乳腺癌(MBC)的患者中，雌激素受体基因(ESR1)，其转录调控因子以及丝裂原活化蛋白激酶(MAPK)通路的突变情况较为集中。我们在本研究中综合了全基因组测序和RNA测序数据，这些数据来自101名ER阳性/HER2阴性MBC患者的同一样本，在开始新一线MBC治疗之前进行了肿瘤活检( CPCT-02研究，NCT01855477 )，以分析之前与内分泌耐药性相关的DNA突变的下游效应，从而更好地了解相关机制。我们使用ESR1靶基因的表达进行了分层聚类。比较了被识别出的聚类之间的DNA水平的基因组改变、基因表达水平以及最后一次治疗。分层聚类显示出两个明显的簇，一个以ESR1和其靶基因表达增加为特征。该簇中的样本中ESR1突变和FGFR1及TSPYL扩增的情况显著增多。另一个簇的患者ESR1和其靶基因的表达水平相对较低，与ER阴性样本相当，并且在活检前更常接受内分泌治疗作为最后一次治疗。MAPK通路中的NF1和ESR1转录调控因子的基因分布均匀。总之，RNA测序确定了一个具有明显ESR1及其下游靶点表达的患者亚群，可能仍然受益于靶向ER的药物。在另一个亚群中ER表达较低，这可能部分解释了最近接受内分泌治疗导致ER活性仍然被阻断，这表明在解读转录组数据时需要考虑活检与内分泌治疗的时间关系。

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.