Novel Drivers of Hormonal Resistance in HRPBC. Homo sapiens

We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n=11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role in vitro, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors. Severe alterations were recurrently found in 18 genes in the pairs. However, only MYC, DNAH5, CSFR1, EPHA7, ARID1B, and KMT2C preserved an independent prognosis impact and/or showed a significantly different incidence of alterations between relapsed and non-relapsed cases in the TCGA series. The signature composed of MYC, KMT2C, and EPHA7 best discriminated the clinical course, (overall survival 90,7 vs. 144,5 months; p=0.0001). Having an alteration in any of the genes of the signature implied a hazard ratio of death of 3.25 (p<0.0001), and early relapse during the adjuvant hormonal treatment. The presence of the D348N mutation in KMT2C and/or the T666I mutation in the kinase domain of EPHA7 conferred hormonal resistance in vitro. Novel inactivating mutations in KMT2C and EPHA7, which confer hormonal resistance, are linked to adverse clinical course in HRPBC.

本研究旨在鉴定与激素受体阳性乳腺癌（hormone-receptor positive breast cancer, HRPBC）的疾病复发及内分泌治疗耐药相关的遗传变异。我们对一系列伴远处复发的HRPBC样本进行分析，以>800倍的测序深度对11对肿瘤样本（原发灶与转移灶）开展测序，同时还进行了比较基因组杂交（Comparative genomic hybridization）实验。基于变异发生频率与变异严重程度筛选出的候选变异热点，在癌症基因组图谱（TCGA, The Cancer Genome Atlas）队列中进行了验证。我们对构建最简约预后标志物所需的基因开展体外（in vitro）功能研究：在激素剥夺条件（模拟芳香化酶抑制剂（aromatase inhibitors）治疗场景）下进行细胞生长实验，以评估其功能作用。在上述肿瘤样本对中，18个基因频繁出现严重变异。然而在TCGA队列中，仅MYC、DNAH5、CSFR1、EPHA7、ARID1B及KMT2C保留了独立的预后影响，且/或在复发与未复发病例间的变异发生率存在显著差异。由MYC、KMT2C及EPHA7构成的标志物可最佳区分患者临床结局：两组总生存期分别为90.7与144.5个月（p=0.0001）。该标志物涵盖基因中任意一个发生变异的患者，其死亡风险比为3.25（p<0.0001），且会在辅助内分泌治疗期间出现早期复发。在体外实验中，KMT2C基因的D348N突变以及/或EPHA7激酶结构域的T666I突变可引发内分泌耐药。KMT2C与EPHA7中全新的失活突变可引发内分泌耐药，并与HRPBC患者的不良临床结局相关。