Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer [HiCHIP]

Heterogeneity between tumors is a major barrier to the treatment of small cell lung cancer (SCLC). Identification of molecular markers to characterize and classify tumors can facilitate the diagnosis and development of targeted therapies. Here, we analyzed genomic regions, called super enhancers (SE), across multiple SCLC cell lines and patient-derived xenograft models, and find SE enrichment is sufficient to classify SCLC models into recently defined SCLC molecular subtypes SCLC-A, SCLC-N, and SCLC-P defined by the transcription factors ASCL1, NEUROD1, and POU2F3, respectively. 3D chromatin structure analysis identified genes associated with the SE that assemble into subtype-specific tumor-signatures with genes functioning in diverse processes. Focusing on the SCLC-A subtype, transcription factors NKX2-1 and PROX1 were identified as ASCL1-interacting proteins. All three factors bind overlapping genomic regions within SEs in SCLC-A cell line models. Nevertheless, combined loss of all three factors suppresses growth of SCLC-A similar to that seen with ASCL1 loss alone, continuing to place ASCL1 as a key dependency factor in a subset of SCLC. Focusing on genes co-regulated by the three transcription factors, two SCLC-A subtype-specific cell surface proteins, SCN3A and KCNB2, were identified. Loss of either channel alone did not disrupt SCLC-A growth in vitro, but they may serve as diagnostic tools in subtyping SCLC. HiChIP of H3K27ac to map enhancer-promoter loops in small cell lung cancer cell lines

肿瘤间的异质性是小细胞肺癌（small cell lung cancer, SCLC）治疗的主要障碍。鉴定可用于表征与分类肿瘤的分子标志物，能够助力临床诊断及靶向治疗的开发。本研究分析了多株SCLC细胞系及患者来源异种移植模型中的超级增强子（super enhancers, SE）基因组区域，发现SE富集足以将SCLC模型归类为近年定义的SCLC分子亚型：分别由转录因子ASCL1、NEUROD1及POU2F3所定义的SCLC-A、SCLC-N与SCLC-P亚型。三维染色质结构分析鉴定出，与SE相关的基因可与参与多种生物学过程的基因共同组装为亚型特异性肿瘤特征标记。针对SCLC-A亚型，研究鉴定出转录因子NKX2-1与PROX1为ASCL1的互作蛋白。在SCLC-A细胞系模型中，这三种因子均可结合SE内部的重叠基因组区域。尽管如此，联合敲除这三种因子可抑制SCLC-A细胞的增殖，其效果与单独敲除ASCL1相当，进一步确立了ASCL1作为部分SCLC亚型关键依赖因子的地位。针对这三种转录因子共同调控的基因，研究鉴定出两种SCLC-A亚型特异性细胞表面蛋白：SCN3A与KCNB2。单独敲除任一此类通道蛋白的编码基因均无法在体外干扰SCLC-A细胞的生长，但二者可作为SCLC分型的诊断辅助工具。本研究还通过组蛋白H3赖氨酸27乙酰化（H3K27ac）的HiChIP技术，绘制了小细胞肺癌细胞系中的增强子-启动子环相互作用图谱。