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.

中文翻译：

---

人结肠直肠癌细胞中 KMT2C/MLL3 的恢复增强了全基因组 H3K4me1 谱并影响细胞生长和基因表达。

组蛋白 3 赖氨酸 4 (H3K4) 单甲基化酶 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。具有微卫星不稳定性的结直肠癌 (CRC) 中经常复发的突变是外显子 38 poly-A(9) 重复 (c.8390delA) 中的单核苷酸缺失，导致功能性羧基末端 SET 域之前的移码。为了研究 KMT2C 在 CRC 细胞中表达的影响，我们将两个 CRC 细胞系 RKO 和 HCT116 中的一个等位基因恢复为野生型 KMT2C，这两个细胞系都是纯合的 c.8390delA 突变体。基因编辑导致 KMT2C 表达增加、H3K4me1 水平增加、基因表达谱改变以及对细胞生长的微妙负面影响，与 HCT116 细胞相比，在 RKO 中观察到更高的依赖性和更强的 KMT2C 表达影响。令人惊讶的是，我们发现两个 RKO 和 HCT116 CRC 细胞系具有不同的基线 H3K4me1 表观基因组谱。在 RKO 细胞中，当 KMT2C 恢复时，更平坦的全基因组 H3K4me1 谱与增强子处的 H3K4me1 沉积增加、细胞生长减少以及相对于 HCT116 细胞更多的差异基因表达相关。H3K4me1 的分析并不表明基因表达的高度特异性调节，因为 KMT2C 诱导的 H3K4me1 沉积是在全球范围内发现的，而不是在工程细胞中的特定增强子子集中。尽管我们观察到细胞系和单个克隆之间差异调节基因组的变化，两种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方面相关的基因。在这里，KMT2C 恢复减少了 CRC 细胞的生长，并增强了增强子的全基因组 H3K4me1 沉积；然而，效果因 KMT2C 缺陷细胞的 H3K4me1 状态而异。结果表明，KMT2C 失活可能通过与已知癌症相关的几种途径中的转录失调来促进结直肠癌的发展。