Interpheron-? signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer [ChIP-seq]

Purpose: Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC). We assessed responses to histone deacetylase inhibitors (HDACi) and performed genome-wide RNA and chromatin immunoprecipitation (ChIP)-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation) and UWB1.289 transduced with wild type BRCA1. Experimental Design: Gene expression profiles of cells harboring mutated vs. functional BRCA1 and treated with the HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation (H3K9ac, H3K27ac) at active promoters and enhancers. Key pathways found deregulated in BRCA1 mutated cells were validated. Results: Gene networks activated in BRCA1-mutated vs. BRCA1+ OC cells relate to Cellular Movement, Cellular Development, Cellular Growth and Proliferation and shared upstream regulators included TGFb1, TNF, and IFN-g. The IFN-g pathway was significantly altered in response to HDACi in BRCA1+ vs. BRCA1-mutated cells and in BRCA1-mutated/or low vs. BRCA1-normal ovarian tumors profiled in the TCGA database. Key IFN-?-induced genes upregulated at baseline in BRCA1-mutated vs. BRCA1+ OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 to the promoters of these genes was observed in BRCA1-mutated cells, resulting in diminished cellular responses to IFN-? or to STAT1 knockdown. The IFN-g signature was associated with improved survival among tumors profiled by the TCGA. Conclusions: Transcriptomic changes affecting IFN-? response are associated with inactivating BRCA1 mutations in OC. These alterations could contribute to diminished anti-tumor immunity in BRCA1 mutated cells or tumors. Overall design: H3K9ac and H3K27ac levels were compared between BRCA1-null UWB1.289 ovarian cancer cells and UWB1.289 cells with BRCA1 restored.

研究目的：乳腺癌1型易感蛋白（breast cancer type 1 susceptibility protein, BRCA1）的功能丧失性突变与乳腺癌（breast cancer, BC）及卵巢癌（ovarian cancer, OC）的发生发展密切相关。本研究评估了细胞对组蛋白去乙酰化酶抑制剂（histone deacetylase inhibitors, HDACi）的应答情况，并在同基因卵巢癌细胞系UWB1.289（携带BRCA1突变）以及转导野生型BRCA1的UWB1.289细胞中开展了全基因组RNA测序及染色质免疫共沉淀（chromatin immunoprecipitation, ChIP）测序分析。

实验设计：将携带BRCA1突变与BRCA1功能正常的细胞经HDACi处理后的基因表达谱，与活性启动子及增强子区域的组蛋白H3赖氨酸9或27乙酰化（H3K9ac、H3K27ac）的染色质图谱进行整合分析，并对BRCA1突变细胞中失调的关键通路进行验证。

研究结果：BRCA1突变型与BRCA1正常型卵巢癌细胞中激活的基因网络涉及细胞运动、细胞发育、细胞生长与增殖，共有的上游调控因子包括转化生长因子β1（Transforming Growth Factor beta 1, TGFβ1）、肿瘤坏死因子（Tumor Necrosis Factor, TNF）及干扰素γ（Interferon-gamma, IFN-γ）。相较于BRCA1突变型细胞，BRCA1正常型细胞经HDACi处理后，IFN-γ通路发生显著改变；该通路在TCGA（The Cancer Genome Atlas，癌症基因组图谱）数据库收录的BRCA1突变/低表达与BRCA1正常的卵巢肿瘤样本中同样存在显著差异。BRCA1突变型相较于BRCA1正常型卵巢癌及乳腺癌细胞，其基线状态下上调的IFN-γ诱导关键基因包括CXCL10、CXCL11及IFI16。研究观察到BRCA1突变型细胞中，信号转导与转录激活因子1（Signal Transducer and Activator of Transcription 1, STAT1）在上述基因启动子区域的富集水平升高，导致细胞对IFN-γ或STAT1敲低的应答减弱。此外，IFN-γ特征基因集与TCGA数据库收录肿瘤患者的良好生存率呈显著相关。

研究结论：影响IFN-γ应答的转录组学改变与卵巢癌中BRCA1失活性突变密切相关。这类改变可能会削弱BRCA1突变细胞或肿瘤的抗肿瘤免疫能力。

整体实验设计：比较了BRCA1缺失型UWB1.289卵巢癌细胞与恢复BRCA1功能的UWB1.289细胞的H3K9ac及H3K27ac修饰水平。