Table3_High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma.csv

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant mortality and frequent recurrence. Prior efforts to transcriptionally classify HNSCC into groups of varying prognoses have identified four accepted molecular subtypes of the disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigate the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identify samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to the AT subtype are more resistant to enhancer-blocking bromodomain inhibitors (BETi). Examination of nascent transcripts reveals that both AT TCGA tumors and cell lines express higher levels of enhancer RNA (eRNA) transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, investigation of higher-order chromatin structure suggests more enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways are upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with higher enhancer activity, resistance to enhancer blockade, and increased signaling through pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.

头颈部鳞状细胞癌（HNSCC）是一种异质性疾病，具有显著的死亡率和频繁的复发率。先前对HNSCC进行转录分类，以将其划分为具有不同预后组的努力，已识别出四种被广泛接受的临床分子亚型：非典型（AT）、基底（BA）、经典（CL）和间充质（MS）。在本研究中，我们利用代表性的HNSCC细胞系，对这些亚型的活跃增强子景观进行了探究，并发现属于AT亚型的样本相较于其他三种HNSCC亚型，其增强子活性显著增加。属于AT亚型的细胞系对增强子阻断溴结构域抑制剂（BETi）的抵抗力更强。对新生转录本的检查显示，AT TCGA肿瘤和细胞系中，控制BETi耐药途径（如脂质代谢和MAPK信号通路）的增强子RNA（eRNA）转录本水平较高。此外，对高级别染色质结构的调查表明，AT亚型中存在更多的增强子-启动子（E-P）相互作用，包括在eRNA分析中确定的基因。一致的是，已知BETi耐药途径在暴露于这些抑制剂后会被上调。总之，我们的研究结果揭示了HNSCC的AT亚型与更高的增强子活性、对增强子阻断的抵抗性以及通过可能作为未来治疗靶点的信号通路增加的信号传导有关。