Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression
Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression
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DOI：
10.1186/s13148-020-00863-z
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发表时间：
2020-05-29
影响因子：
5.7
通讯作者：
Sjoblom, Tobias
中科院分区：
文献类型：
--
作者：
Larsson, Chatarina;Cordeddu, Lina;Sjoblom, Tobias
组蛋白3赖氨酸4（H3 K4）单甲基化酶KMT 2C在几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 poly-A（9）重复（c.8390delA）内的单核苷酸缺失，其导致在功能性羧基末端SET结构域之前的移码。为了研究KMT 2C在CRC细胞中表达的影响，我们在两个CRC细胞系RKO和HCT 116中将一个等位基因恢复为野生型KMT 2C，这两个细胞系都是纯合的c.8390delA突变体。结果基因编辑导致KMT 2C表达增加，H3 K4 me 1水平增加，基因表达谱改变，对细胞生长产生轻微的负面影响，其中RKO细胞中KMT 2C表达的依赖性和影响较HCT 116细胞更强。令人惊讶的是，我们发现两种RKO和HCT 116 CRC细胞系具有不同的基线H3 K4 me 1表观基因组谱。在RKO细胞中，当KMT 2C恢复时，较平坦的全基因组H3 K4 me 1谱与增强子处更多增加的H3 K4 me 1沉积、减少的细胞生长以及相对于HCT 116细胞更多差异基因表达相关。H3 K4 me 1的分析没有表明基因表达的高度特异性调节，因为KMT 2C诱导的H3 K4 me 1沉积在全球范围内发现，而不是在工程化细胞中的特异性增强子亚组。虽然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，但两种细胞系中差异表达的基因包括与已知癌症信号传导途径、雌激素反应、缺氧反应和免疫系统调节方面相关的基因。结论在这里，KMT 2C恢复减少CRC细胞的生长和增强的全基因组H3 K4 me 1沉积在增强子;然而，效果取决于KMT 2C缺陷细胞的H3 K4 me 1状态。结果表明，KMT 2C失活可能会促进结直肠癌的发展，通过转录失调，在几个途径与已知的癌症相关。
Background 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 ofKMT2Cexpression in CRC cells, we restored one allele to wild typeKMT2Cin the two CRC cell lines RKO and HCT116, which both are homozygous c.8390delA mutant. Results Gene editing resulted in increasedKMT2Cexpression, increased H3K4me1 levels, altered gene expression profiles, and subtle negative effects on cell growth, where higher dependence and stronger effects ofKMT2Cexpression 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. Conclusions 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.