Rewiring of master transcription factor cistrome during high-grade serous ovarian cancer development. Rewiring of master transcription factor cistrome during high-grade serous ovarian cancer development

The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors. Overall design: CUT&RUN or CUT&TAG of H3K27ac, H3K27me3, MECOM, PAX8 and SOX17 for cell lines and primary ex vivo cultures. ATAC-seq of cell lines.

转录因子MECOM、PAX8、SOX17与WT1是高级别浆液性“卵巢”癌（high-grade serous ovarian cancer, HGSC）的候选核心调控因子，然而它们在假说的肿瘤起源组织——输卵管分泌上皮（fallopian tube secretory epithelium, FTSEC）中的协同调控作用仍不明晰。本研究生成了26组表观基因组（CUT&TAG、CUT&RUN、ATAC-seq及HiC）数据集，并获取了24组在FTSEC与HGSC模型中经转录因子敲降后行RNA测序的表达谱，以此阐明这四种因子在顺式与反式调控模式下的结合位点及其调控的基因集。研究结果显示，MECOM、PAX8、SOX17与WT1属于谱系富集、与超级增强子相关联的核心调控因子，其协同DNA结合模式与靶基因在肿瘤发生进程中发生了重编程。四种转录因子均对HGSC的克隆形成能力与细胞存活不可或缺，但仅敲降PAX8与WT1会损伤FTSEC细胞的存活。这四种转录因子仅在HGSCs中可被转录抑制剂实现药理学靶向抑制，而在FTSECs中则无此效应。综上，本研究数据表明肿瘤特异性表观遗传重塑与MECOM、PAX8、SOX17及WT1的活性密切相关，且这些转录因子可通过转录抑制剂以肿瘤特异性的方式成为可靶向的治疗靶点。整体实验设计：针对细胞系与原代离体培养物，开展H3K27ac、H3K27me3、MECOM、PAX8及SOX17的CUT&RUN或CUT&TAG实验；针对细胞系开展ATAC-seq实验。