Multi-omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability.
Multi-omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability.
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Lynch综合征（LS）是一种遗传性疾病，可增加结直肠癌（CRC）和结肠外癌的风险，表现出微卫星不稳定性（MSI-H）。MSI-H是由错配修复缺陷（dMMR）驱动的，大约15%的非遗传性CRC也表现出MSI-H。在这里，我们旨在通过LS正常结肠类器官和MSI-H肿瘤的多组学分析更好地定义LS和MSI-H癌症中肿瘤起始的机制。将在LS和健康个体的常规结肠镜检查中从正常结肠活检产生的右（n = 35）和左（n = 23）结肠类器官经受Illumina EPIC阵列。通过DMR cate进行差异甲基化区域（DMR）分析。对右半结肠类器官子集进行RNA测序（n = 16）和亚硫酸氢盐测序（n = 15）。CRISPR-cas9介导的健康个体结肠类器官中MMR基因的编辑之后是MSH 4的定量PCR。在三个独立的肿瘤数据集中进一步探讨了MSH 4表达和肿瘤突变负荷之间的关系。我们在LS与健康对照的右侧和左侧结肠类器官中鉴定了MSH 4的高甲基化区域，我们使用亚硫酸氢盐测序进行了验证。在三个胃肠道和一个子宫内膜数据集中的DMR分析显示，与微卫星稳定（MSS）肿瘤相比，MSI-H中该区域也是高甲基化的。在四个RNA-seq和四个微阵列数据集中，LS与健康受试者的结肠类器官以及公开可用的MSI-H与MSS肿瘤中MSH 4表达增加。在正常结肠类器官中，MLH 1和MSH 2的CRISPR-cas9编辑，而不是MSH 6，显著增加了MSH 4的表达。在三个公开数据集中，MSH 4表达与肿瘤突变负荷显著相关。我们的研究结果暗示，DNA甲基化和基因表达差异的MSH 4作为一个标记的dMMR和作为一个潜在的新的生物标志物LS。我们对LS结肠类器官的研究支持了这样的假设，即在CRC之前LS受试者的结肠中存在dMMR。
Lynch syndrome (LS) is a hereditary condition that increases the risk of colorectal (CRC) and extracolonic cancers that exhibit microsatellite instability (MSI‐H). MSI‐H is driven by defective mismatch repair (dMMR), and approximately 15% of nonhereditary CRCs also exhibit MSI‐H. Here, we aimed to better define mechanisms underlying tumor initiation in LS and MSI‐H cancers through multi‐omic analyses of LS normal colon organoids and MSI‐H tumors. Right (n = 35) and left (n = 23) colon organoids generated from normal colon biopsies at routine colonoscopy of LS and healthy individuals were subjected to Illumina EPIC array. Differentially methylated region (DMR) analysis was performed by DMRcate. RNA‐sequencing (n = 16) and bisulfite‐sequencing (n = 15) were performed on a subset of right colon organoids. CRISPR‐cas9‐mediated editing of MMR genes in colon organoids of healthy individuals was followed by quantitative PCR of MSH4. The relationship between MSH4 expression and tumor mutational burden was further explored in three independent tumor data sets. We identified a hypermethylated region of MSH4 in both the right and left colon organoids of LS versus healthy controls, which we validated using bisulfite‐sequencing. DMR analysis in three gastrointestinal and one endometrial data set revealed that this region was also hypermethylated in MSI‐H versus microsatellite stable (MSS) tumors. MSH4 expression was increased in colon organoids of LS versus healthy subjects and in publicly available MSI‐H versus MSS tumors across four RNA‐seq and four microarray data sets. CRISPR‐cas9 editing of MLH1 and MSH2, but not MSH6, in normal colon organoids significantly increased MSH4 expression. MSH4 expression was significantly associated with tumor mutational burden in three publicly available data sets. Our findings implicate DNA methylation and gene expression differences of MSH4 as a marker of dMMR and as a potential novel biomarker of LS. Our study of LS colon organoids supports the hypothesis that dMMR exists in the colons of LS subjects prior to CRC.
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DOI：
10.1056/nejmoa2201445
发表时间：
2022-06-23
期刊：
The New England journal of medicine
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1016/j.jcmgh.2019.04.002
发表时间：
2019-01-01
影响因子：
7.2
作者：
Fennell, Lochlan;Dumenil, Troy;Whitehall, Vicki
通讯作者：
Whitehall, Vicki
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Colaprico A;Silva TC;Olsen C;Garofano L;Cava C;Garolini D;Sabedot TS;Malta TM;Pagnotta SM;Castiglioni I;Ceccarelli M;Bontempi G;Noushmehr H
通讯作者：
Noushmehr H
影响因子：
4.6
作者：
Bonneville R;Krook MA;Kautto EA;Miya J;Wing MR;Chen HZ;Reeser JW;Yu L;Roychowdhury S
通讯作者：
Roychowdhury S