Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.
Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden.
Clin Epigenetics. 2020 May 29;12(1):74. doi: 10.1186/s13148-020-00863-z.
The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types; however, the effects of mutations on epigenome organization, gene expression, and cell growth are not clear. A frequently recurring mutation in colorectal cancer (CRC) with microsatellite instability is a single nucleotide deletion within the exon 38 poly-A(9) repeat (c.8390delA) which results in frameshift preceding the functional carboxy-terminal SET domain. To study effects of KMT2C expression in CRC cells, we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous c.8390delA mutant.
Gene editing resulted in increased KMT2C expression, increased H3K4me1 levels, altered gene expression profiles, and subtle negative effects on cell growth, where higher dependence and stronger effects of KMT2C expression were observed in RKO compared to HCT116 cells. Surprisingly, we found that the two RKO and HCT116 CRC cell lines have distinct baseline H3K4me1 epigenomic profiles. In RKO cells, a flatter genome-wide H3K4me1 profile was associated with more increased H3K4me1 deposition at enhancers, reduced cell growth, and more differential gene expression relative to HCT116 cells when KMT2C was restored. Profiling of H3K4me1 did not indicate a highly specific regulation of gene expression as KMT2C-induced H3K4me1 deposition was found globally and not at a specific enhancer sub-set in the engineered cells. Although we observed variation in differentially regulated gene sets between cell lines and individual clones, differentially expressed genes in both cell lines included genes linked to known cancer signaling pathways, estrogen response, hypoxia response, and aspects of immune system regulation.
Here, KMT2C restoration reduced CRC cell growth and reinforced genome-wide H3K4me1 deposition at enhancers; however, the effects varied depending upon the H3K4me1 status of KMT2C deficient cells. Results indicate that KMT2C inactivation may promote colorectal cancer development through transcriptional dysregulation in several pathways with known cancer relevance.
组蛋白 3 赖氨酸 4（H3K4）单甲基转移酶 KMT2C 在多种癌症类型中发生突变；然而，突变对表观基因组组织、基因表达和细胞生长的影响尚不清楚。在具有微卫星不稳定性的结直肠癌（CRC）中，经常发生的突变是外显子 38 多聚 A（9）重复内的单个核苷酸缺失（c.8390delA），导致功能羧基末端 SET 结构域之前的移码。为了研究 KMT2C 在 CRC 细胞中的表达效应，我们在两个均为纯合 c.8390delA 突变的 CRC 细胞系 RKO 和 HCT116 中，将一个等位基因恢复为野生型 KMT2C。
基因编辑导致 KMT2C 表达增加，H3K4me1 水平升高，基因表达谱发生改变，对细胞生长产生轻微的负向影响，其中 RKO 细胞中 KMT2C 表达的依赖性和影响更强。令人惊讶的是，我们发现这两个 RKO 和 HCT116 CRC 细胞系具有不同的基线 H3K4me1 表观基因组特征。在 RKO 细胞中，全基因组 H3K4me1 图谱更为平坦，与增强子处更多的 H3K4me1 沉积、细胞生长减少以及与 HCT116 细胞相比，KMT2C 恢复时更多的差异基因表达相关。H3K4me1 分析并未表明基因表达受到高度特异性调控，因为在工程细胞中，KMT2C 诱导的 H3K4me1 沉积是全局性的，而不是在特定的增强子子集上。尽管我们观察到细胞系和单个克隆之间差异调节基因集的变化，但两个细胞系中差异表达的基因包括与已知癌症信号通路、雌激素反应、缺氧反应和免疫系统调节相关的基因。
在这里，KMT2C 恢复降低了 CRC 细胞的生长，并在增强子处加强了全基因组 H3K4me1 的沉积；然而，这些效应取决于 KMT2C 缺陷细胞的 H3K4me1 状态。结果表明，KMT2C 失活可能通过在多个具有已知癌症相关性的途径中促进转录失调，从而促进结直肠癌的发生。
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