Article(id=1322934751753011940, tenantId=1146029695717560320, journalId=1319373162502258839, issueId=1322934653228822704, articleNumber=null, orderNo=null, doi=10.16016/j.2097-0927.202407095, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1721664000000, receivedDateStr=2024-07-23, revisedDate=1723737600000, revisedDateStr=2024-08-16, acceptedDate=null, acceptedDateStr=null, onlineDate=1793341823756, onlineDateStr=2026-10-30, pubDate=1741968000000, pubDateStr=2025-03-15, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1793341823756, onlineIssueDateStr=2026-10-30, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1793341823756, creator=13701087609, updateTime=1793341823756, updator=13701087609, issue=Issue{id=1322934653228822704, tenantId=1146029695717560320, journalId=1319373162502258839, year='2025', volume='47', issue='5', pageStart='385', pageEnd='488', issueExtLink='null', onlineDate='null', pubDate='1741968000000', pubDateStr='2025-03-15', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1793341800267, creator='13701087609', updateTime=1793341800267, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext=null, issueFiles=null, downloadFileDto=null}, startPage=417, endPage=425, ext={EN=ArticleExt(id=1322934753548174053, articleId=1322934751753011940, tenantId=1146029695717560320, journalId=1319373162502258839, language=EN, title=Remodeling characteristics of H3K27me3-marked silencers in gastric signet-ring cell carcinoma and its transcriptional regulatory function, columnId=1320442291748192970, journalTitle=Journal of Army Medical University, columnName=Monographic Reports, runingTitle=null, highlight=null, articleAbstract=
Objective‍

To draw the genome-wide distribution and remodeling characteristics of H3K27me3 silencers in signet-ring cell carcinoma of the stomach (SRCC) through epigenetic sequencing technology, and to investigate their roles in transcriptional regulation in order to elucidate the regulatory mechanism of SRCC malignant progression.

Methods‍

The study was conducted on 35 gastric samples obtained by gastroendoscopic biopsy (15 normal and 20 SRCC tissues) from Department of Gastroenterology of Army Medical Center of PLA between January 2021 and December 2023. Multi-omics analyses, including assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), cleavage under targets and tagmentation (CUT&Tag) and transcriptome sequencing (RNA-seq), were performed to identify chromatin accessibility, H3K27me3 silencer regions, and transcriptional changes, with aid of Illumina NovaSeq 6000. H3K27me3 related differentially expressed genes (|Log2FC|>1, FDR<0.05) were screened using DESeq2. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to analyze the enrichment function, and Homer was employed to identify transcription factor motifs. A regulatory network was constructed using Cytoscape, and then validated using immunohistochemistry to explore its regulatory mechanism.

Results

H3K27me3 silencers were primarily located in distal intergenic regions (37.06%) in SRCC. Compared with the normal tissues, SRCC showed a significant reduction in H3K27me3 silencer signals (95%CI:1.34~2.30, P=0.007) with 6 257 lost sites (FDR<0.01). Integrating CUT&Tag and RNA-seq revealed 380 up-regulated immune-related genes, particularly in T cell receptor signaling (OR=4.2, 95%CI: 2.8~6.3, P=0.002). Immunohistochemistry confirmed elevated expression of transcription factor EHF (P<0.05).

Conclusion‍

There is the remodeling of H3K27me3 silencers in SRCC, and EHF may potentially play a crucial role in the SRCC malignant progression.

, authors=Aibei DU1, 2, Yuanfeng REN2, Zhaole CHU2, Biying LIU2, Xianfeng LI2, Junyu XIANG2, Dongfeng CHEN2, Tao WANG2, Bin WANG2, Haiying GUO1, Xuan ZHANG3, Yuhong LI1, authorsList=Aibei DU, Yuanfeng REN, Zhaole CHU, Biying LIU, Xianfeng LI, Junyu XIANG, Dongfeng CHEN, Tao WANG, Bin WANG, Haiying GUO, Xuan ZHANG, Yuhong LI, authorCompany=null, correspAuthors=Xuan ZHANG, Yuhong LI, authorNote=null, correspAuthorsNote=null, copyrightStatement=© 2025 Journal of Army Medical University, copyrightOwner=Editorial Office of Journal of Army Medical University, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1322934755343336174, articleId=1322934751753011940, tenantId=1146029695717560320, journalId=1319373162502258839, language=CN, title=胃印戒细胞癌的H3K27me3沉默子重塑特征及转录调控功能, columnId=1322190423666315871, journalTitle=陆军军医大学学报, columnName=专题报道, runingTitle=null, highlight=null, articleAbstract=
目的

通过表观遗传组学技术,解析胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)的H3K27me3沉默子的全基因组特征及其对基因转录的调控作用,以阐明SRCC恶性进展的表观调控机制。

方法

采集2021年1月至2023年12月陆军特色医学中心消化内科35例胃镜样本(正常胃窦/胃体15例,SRCC 20例)。采用以下多组学分析:染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)检测染色质开放区域;染色质靶向捕获测序(cleavage under targets and tagmentation,CUT&Tag)捕获H3K27me3沉默子区域;转录组测序(transcriptome sequencing,RNA-seq)分析转录组。测序于Illumina NovaSeq 6000平台完成(符合深度标准)。通过DESeq2筛选H3K27me3相关差异基因(|Log2FC|>1,FDR<0.05),并通过基因本体论(Gene Oncology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)分析进行功能富集,Homer鉴定转录因子基序,Cytoscape构建调控网络,并使用免疫组化进行验证,探讨其调控机制。

结果

SRCC沉默子主要分布于基因组远端基因间区(占37.06%)。与正常组织相比,SRCC中H3K27me3沉默子信号显著降低(95%CI:1.34~2.30,P=0.007),共鉴定出6 257个丢失位点(FDR<0.01)。CUT&Tag和RNA-seq整合分析显示,380个因沉默子丢失而上调的基因显著富集于免疫相关通路,如T细胞受体信号通路(OR=4.2,95%CI:2.8~6.3,P=0.002)。免疫组化验证表明,转录因子EHF表达显著升高(P<0.05)。

结论

SRCC中存在H3K27me3沉默子重塑现象,转录因子EHF可能在SRCC恶性进展中发挥关键作用。

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李玉红:
张璇:
LI Yuhong,E-mail:
ZHANG Xuan,E-mail:
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A:样本取材及测序流程图;B:H3K27me3 CUT&Tag文库质量的质控分析;C:RNA测序数据的质控分析 左:片段在基因编码区上的片段富集情况;右:转录组测序饱和曲线;D:H3K27me3沉默子信号在正常样本和SRCC样本基因组的分布

, figureFileSmall=HPwEuoFgz73dhdWrkBXxfQ==, figureFileBig=mnItbtNc4HtGuP8ehrzrqw==, tableContent=null), ArticleFig(id=1322934763899716418, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=EN, label=null, caption=null, figureFileSmall=F00Mh2XTtj6ONreszZjoVg==, figureFileBig=b+ZnBkEwbKhxBUPccymFjw==, tableContent=null), ArticleFig(id=1322934763983602499, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=CN, label=图2, caption=SRCC组织中H3K27me3沉默子信号重塑特征

A:各胃窦正常与SRCC组织样本主成分分析;B:胃窦正常与SRCC组织中沉默子信号强度的可视化分析;C:2组样本间差异的沉默子信号分布热图(差异倍数>1.5,FDR<0.05);D:沉默子重塑相关靶基因的KEGG富集分析

, figureFileSmall=F00Mh2XTtj6ONreszZjoVg==, figureFileBig=b+ZnBkEwbKhxBUPccymFjw==, tableContent=null), ArticleFig(id=1322934764046517060, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=EN, label=null, caption=null, figureFileSmall=xM/U/PtNLY1P7OAPf8aNJA==, figureFileBig=Qp/sdsFYztwR7oo9As/dXA==, tableContent=null), ArticleFig(id=1322934764113625925, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=CN, label=图3, caption=沉默子相关靶基因及生物学功能

A:胃窦正常组织与SRCC组织的RNA-seq主成分聚类分析;B:胃窦正常与SRCC组织的差异表达基因分析(FC>2,FDR<0.05);C:各基因的沉默子信号与表达水平;D:SRCC中可能受沉默子信号上调的基因KEGG分析;E:SRCC中可能受沉默子信号下调的基因KEGG分析;F:上调基因KEGG分析中的关键基因富集;G:关键基因通路可视化分析;H:关键基因沉默子信号及转录水平分析

, figureFileSmall=xM/U/PtNLY1P7OAPf8aNJA==, figureFileBig=Qp/sdsFYztwR7oo9As/dXA==, tableContent=null), ArticleFig(id=1322934764189123398, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=EN, label=null, caption=null, figureFileSmall=XiVnfBkz5GjneSFT5LVL9g==, figureFileBig=CnWrgevoPakkFP4BL5y/YA==, tableContent=null), ArticleFig(id=1322934764247843655, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, language=CN, label=图4, caption=沉默子相关转录因子IRF6和EHF基因调控机制

A:由沉默子信号丢失的基因组区域富集转录因子的motif基序图;B:沉默子相关转录因子IRF6和EHF表达水平分析(差异倍数>1.5,FDR<0.05);C:沉默子丢失基因调控网络图;D:EHF下游沉默子调控通路;E:EHF与IRF6潜在调控的沉默子丢失基因GO富集分析;F:正常组和SRCC组织中EHF免疫组化染色及评分 a:P<0.05,与正常组比较

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胃印戒细胞癌的H3K27me3沉默子重塑特征及转录调控功能
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杜艾贝 1, 2 , 任原锋 2 , 储召乐 2 , 刘碧颖 2 , 李先锋 2 , 向俊宇 2 , 陈东风 2 , 王涛 2 , 王斌 2 , 郭海英 1 , 张璇 3 , 李玉红 1
陆军军医大学学报 | 专题报道 2025,47(5): 417-425
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陆军军医大学学报 |专题报道 2025 , 47 (5) : 417 -425
胃印戒细胞癌的H3K27me3沉默子重塑特征及转录调控功能
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杜艾贝1, 2, 任原锋2, 储召乐2, 刘碧颖2, 李先锋2, 向俊宇2, 陈东风2, 王涛2, 王斌2, 郭海英1, 张璇3 , 李玉红1
作者信息
  • 1陆军军医大学基础医学院细胞生物学教研室,重庆
  • 2陆军特色医学中心(第三军医大学大坪医院)消化内科,消化系统肿瘤精准防治重庆市重点实验室,重庆
  • 3重庆市中医院肿瘤科,重庆
通讯作者:
LI Yuhong,E-mail:
ZHANG Xuan,E-mail:
Remodeling characteristics of H3K27me3-marked silencers in gastric signet-ring cell carcinoma and its transcriptional regulatory function
Aibei DU1, 2, Yuanfeng REN2, Zhaole CHU2, Biying LIU2, Xianfeng LI2, Junyu XIANG2, Dongfeng CHEN2, Tao WANG2, Bin WANG2, Haiying GUO1, Xuan ZHANG3 , Yuhong LI1
Affiliations
  • 1Department of Cell Biology,College of Basic Medical Sciences,Army Medical University (Third Military Medical University),Chongqing
  • 2Department of Gastroenterology,Chongqing Key Laboratory of Precise Prevention and Treatment of Digestive Malignancies,Army Medical Center of PLA/Daping Hospital of Third Military Medical University,Chongqing
  • 3Department of Oncology,Chongqing Hospital of Traditional Chinese Medicine,Chongqing,China
出版时间: 2025-03-15 doi: 10.16016/j.2097-0927.202407095
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目的

通过表观遗传组学技术,解析胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)的H3K27me3沉默子的全基因组特征及其对基因转录的调控作用,以阐明SRCC恶性进展的表观调控机制。

方法

采集2021年1月至2023年12月陆军特色医学中心消化内科35例胃镜样本(正常胃窦/胃体15例,SRCC 20例)。采用以下多组学分析:染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)检测染色质开放区域;染色质靶向捕获测序(cleavage under targets and tagmentation,CUT&Tag)捕获H3K27me3沉默子区域;转录组测序(transcriptome sequencing,RNA-seq)分析转录组。测序于Illumina NovaSeq 6000平台完成(符合深度标准)。通过DESeq2筛选H3K27me3相关差异基因(|Log2FC|>1,FDR<0.05),并通过基因本体论(Gene Oncology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)分析进行功能富集,Homer鉴定转录因子基序,Cytoscape构建调控网络,并使用免疫组化进行验证,探讨其调控机制。

结果

SRCC沉默子主要分布于基因组远端基因间区(占37.06%)。与正常组织相比,SRCC中H3K27me3沉默子信号显著降低(95%CI:1.34~2.30,P=0.007),共鉴定出6 257个丢失位点(FDR<0.01)。CUT&Tag和RNA-seq整合分析显示,380个因沉默子丢失而上调的基因显著富集于免疫相关通路,如T细胞受体信号通路(OR=4.2,95%CI:2.8~6.3,P=0.002)。免疫组化验证表明,转录因子EHF表达显著升高(P<0.05)。

结论

SRCC中存在H3K27me3沉默子重塑现象,转录因子EHF可能在SRCC恶性进展中发挥关键作用。

胃印戒细胞癌  /  表观遗传  /  组蛋白修饰  /  沉默子  /  H3K27me3
Objective‍

To draw the genome-wide distribution and remodeling characteristics of H3K27me3 silencers in signet-ring cell carcinoma of the stomach (SRCC) through epigenetic sequencing technology, and to investigate their roles in transcriptional regulation in order to elucidate the regulatory mechanism of SRCC malignant progression.

Methods‍

The study was conducted on 35 gastric samples obtained by gastroendoscopic biopsy (15 normal and 20 SRCC tissues) from Department of Gastroenterology of Army Medical Center of PLA between January 2021 and December 2023. Multi-omics analyses, including assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), cleavage under targets and tagmentation (CUT&Tag) and transcriptome sequencing (RNA-seq), were performed to identify chromatin accessibility, H3K27me3 silencer regions, and transcriptional changes, with aid of Illumina NovaSeq 6000. H3K27me3 related differentially expressed genes (|Log2FC|>1, FDR<0.05) were screened using DESeq2. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to analyze the enrichment function, and Homer was employed to identify transcription factor motifs. A regulatory network was constructed using Cytoscape, and then validated using immunohistochemistry to explore its regulatory mechanism.

Results

H3K27me3 silencers were primarily located in distal intergenic regions (37.06%) in SRCC. Compared with the normal tissues, SRCC showed a significant reduction in H3K27me3 silencer signals (95%CI:1.34~2.30, P=0.007) with 6 257 lost sites (FDR<0.01). Integrating CUT&Tag and RNA-seq revealed 380 up-regulated immune-related genes, particularly in T cell receptor signaling (OR=4.2, 95%CI: 2.8~6.3, P=0.002). Immunohistochemistry confirmed elevated expression of transcription factor EHF (P<0.05).

Conclusion‍

There is the remodeling of H3K27me3 silencers in SRCC, and EHF may potentially play a crucial role in the SRCC malignant progression.

signet-ring cell carcinoma of the stomach  /  epigenetics  /  histone modification  /  silencer  /  H3K27me3
杜艾贝, 任原锋, 储召乐, 刘碧颖, 李先锋, 向俊宇, 陈东风, 王涛, 王斌, 郭海英, 张璇, 李玉红. 胃印戒细胞癌的H3K27me3沉默子重塑特征及转录调控功能. 陆军军医大学学报, 2025 , 47 (5) : 417 -425 . DOI: 10.16016/j.2097-0927.202407095
Aibei DU, Yuanfeng REN, Zhaole CHU, Biying LIU, Xianfeng LI, Junyu XIANG, Dongfeng CHEN, Tao WANG, Bin WANG, Haiying GUO, Xuan ZHANG, Yuhong LI. Remodeling characteristics of H3K27me3-marked silencers in gastric signet-ring cell carcinoma and its transcriptional regulatory function[J]. Journal of Army Medical University, 2025 , 47 (5) : 417 -425 . DOI: 10.16016/j.2097-0927.202407095
胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)作为胃癌的特殊亚型之一,因肿瘤细胞内存在大量黏液将细胞核推向一侧,形似印戒而得名。该亚型占原发性胃癌的35%~45%,近年来发病率明显上升[1]。SRCC作为一种高度恶性的低分化癌,具有高转移复发、免疫疗法低响应的特征,晚期患者5年生存率仅28.6%,造成了极大的死亡风险和社会经济负担[2]。由于SRCC发生发展的内在机理尚未阐明,且具有免疫抑制性肿瘤微环境,导致临床上缺乏有效的靶向治疗策略[3],亟待深入研究SRCC恶性进展的具体分子调控机制。
表观遗传调控是一种在细胞DNA序列不变的情况下由染色质结构变化介导的可遗传调控形式,组蛋白修饰是其中一种重要调控方式[4]。近年来,有大量研究表明,组蛋白修饰异常促进恶性肿瘤发生发展[5],然而,组蛋白修饰在SRCC具体调控机制方面的研究仍相对匮乏[6]。沉默子是真核生物基因组中一类特殊的转录调控元件,由多梳抑制复合体2(polycomb repressive complex 2,PRC2)催化的组蛋白H3上第27位赖氨酸三甲基化(H3K27me3)修饰所标记[7]。而H3K27me3修饰后的沉默子可提供结合位点招募抑制性调节因子,达到抑制相应启动子从而遏制基因转录的作用[8]。动物细胞中有超过50%的基因组处于沉默状态,沉默子在决定细胞命运、调控胚胎发育等生理过程[9],以及肿瘤发生发展等病理过程中发挥重要作用[8]。相对于H3K27乙酰化标记的增强子在胃癌中广泛而深入的研究[10-12],沉默子作为重要的表观调控元件在SRCC发生发展过程中的作用较少有研究报道。
本研究利用H3K27me3修饰的染色质靶向捕获测序(cleavage under targets and tagmentation,CUT&Tag)和染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)技术,整合表观组测序数据及转录组测序数据,系统描绘SRCC中沉默子全基因组的分布状态,探讨其靶基因的功能特征,揭示发挥调控作用的关键转录因子,从表观组学角度揭示SRCC恶性进展的调控机制,为SRCC的预防及治疗策略提供新思路。
收集2021年1月至2023年12月就诊于陆军特色医学中心消化内科患者的人正常胃窦/胃体样本15例,以及20例符合病理学诊断标准的人SRCC样本。SRCC患者纳入标准:①就诊于陆军特色医学中心,并接受内镜下治疗的患者;②手术前经病理科研判,放大内镜表现及活检病理等多方面检测达到SRCC的病理诊断标准;③临床病理资料完整。排除标准:①有其他恶性肿瘤病史;②有家族性遗传性肿瘤病史。临床样本采集方案已经陆军特色医学中心伦理委员会审批通过[医研伦审(2021)第260号]。
根据omni-ATAC实验流程[13],取冻存组织提取细胞核。使用台盼蓝染色检查细胞核完整性,调整细胞数量至1×105个,用于后续CUT&Tag和ATAC-seq文库构建。
分别提取正常胃窦样本和SRCC样本总RNA并检测浓度和质量,然后进行文库构建。加入oligo dT磁珠结合mRNA从而获得mRNA,并进行片段化;反转录成双链cDNA,加接头后进行PCR扩增;PCR产物纯化后文库构建完成,上机测序。得到测序原始数据后使用FastQC工具对数据进行质控;利用Cutadapt工具过滤掉低质量片段,然后将基因比对后读取计数并标准化。
细胞核提取后加入Tn5转座酶插入测序接头,对提取的DNA纯化后进行文库构建,然后使用Illumina NovaSeq 6000平台进行高通量测序。获得原始测序数据后,首先使用FastQC和Cutadapt工具对数据进行质控和过滤;使用Bowtie2工具将过滤后数据读取映射到参考基因组上;使用SAMtools工具去除重复片段、非特异性映射和低质量映射;使用MACS2工具识别染色质开放区域。使用ChIPseeker进一步对信号峰进行后续注释和分析,利用IGV工具对信号峰进行可视化。
根据诺维赞公司TD903试剂盒说明书,细胞核提取后加入H3K27me3抗体孵育并加入二抗孵育,然后加入pA-Tn5转座酶对目标DNA序列进行捕获。再将产物进行PCR扩增并进行浓度测定,CUT&Tag文库构建完成。使用Illumina Hiseq-X测序仪进行测序。得到测序原始数据后,进行数据质控。首先,使用Fastp联合Cutadapt工具对接头进行去除;使用Hisat2工具将接头去除后的数据比对到基因组上,得到SAM文件;SAM文件再通过sambamba工具转换为BAM文件后,去除重复片段得到可用于后续分析的数据。使用MAnorm2对数据进行标准比,数据清洗后进行数据峰值可视化,利用MACS2工具对过滤后数据进行峰识别,绘制峰线图,再使用ChIPseeker工具对H3K27me3信号峰位置进行注释和标记。最后,对沉默子所在位置信息进行可视化。
整合分析ATAC-seq、CUT&Tag和转录组测序(transcriptome sequencing,RNA-seq)数据可以识别特定转录因子或组蛋白修饰如何影响基因表达,从而展示特定基因的调控网络。ATAC-seq数据用于排除未开放染色质区域,筛选开放区域进行后续沉默子调控分析。使用edgeR和DEseq2对处理后的CUT&Tag和RNA-seq数据进行差异分析,分别得到差异表达基因以及对应差异染色质表达区域。对沉默子信号强度削弱且转录表达上调的靶基因进行统计,并对沉默子信号强度增强且转录表达下调的靶基因进行统计,分别对其进行基因本体论(Gene Ontology,GO)富集分析和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)分析以揭示其在生物过程中的作用。
通过多组学整合分析,筛选出SRCC及正常组织的转录组差异表达基因,结合沉默子信号减弱区域,即SRCC中沉默子丢失进而发生基因表达变化的区域,作为用于预测关键转录因子调控基序的目的基因组区间。使用Homer工具对此区间的转录因子基序进行预测,根据计算出的Q-value由高到低依次对转录因子进行排序,展示预测的前10个转录因子基序,绘制SRCC转录因子调控网络图。
收集2022年6月到2024年6月经病理科诊断为SRCC的样本31例,正常胃黏膜组织样本30例,通过免疫组化方法检测组织中EHF表达水平。具体实验过程如下:将石蜡包埋的组织切片置于65 ℃的烤箱中脱蜡1 h,然后分别浸泡于3个二甲苯溶液缸中,每缸15 min完成脱蜡。依次用无水乙醇(Ⅰ、Ⅱ、Ⅲ缸)、95%乙醇和85%乙醇溶液处理,在每种溶液中浸泡5 min进行水化。切片水化后,用3%的H2O2封闭15 min,放入柠檬酸钠缓冲液(pH=7.2)中,高温高压加热5 min以完成抗原修复。待切片冷却至室温后,用H2O2再次封闭30 min,以阻断过氧化物酶活性。用含山羊血清的封闭液在37 ℃下封闭1 h,并滴加一抗(兔抗人EHF单克隆抗体,稀释比例1∶400),4 ℃孵育过夜。次日,利用兔二步法检测试剂盒(PV-9001)完成二抗孵育,并用DAB显色剂显色。显色结束后,用苏木精染剂对细胞核进行染色,并用中性树脂封片保存。免疫组化评分基于染色强度(无染色为0分,弱染色为1分,中度染色为2分,强染色为3分)和染色面积(阳性细胞比例:0%~5%为0分,>5%~25%为1分,>25%~50%为2分,>50%~75%为3分,>75%~100%为4分)两部分计算,最终评分范围为0~12分。
统计各切片免疫组化评分所得数据,使用Prism 9.0软件进行统计学分析。两组间数据比较使用Wilcoxon秩和检验分析,P<0.05表示差异具有统计学意义。
收集正常胃黏膜组织样本和SRCC组织样本,对样本进行CUT&Tag、ATAC-seq和RNA-seq联合测序(图1A)。首先对测序数据进行质控,分析结果显示,测序样本DNA片段数>1×106,基因组比对率>98%,说明样本DNA质量良好,测序准确;信号峰数量均>1×104,表明抗体特异性良好,H3K27me3信号富集;信号峰区域的DNA片段比例(fraction of reads in peaks,FRiP)是反映CUT&Tag实验特异性和敏感性的直接指标,样本的FRiP>20%表明捕获的H3K27me3信号明确,以上质控分析表明,样本DNA质量良好,抗体特异性高,文库复杂性好,数据满足后续分析需求(图1B)。RNA-seq数据质控分析表明目标片段显著富集,测序深度足够,可用于后续分析(图1C)。
对组蛋白H3K27me3信号全基因组分布情况可视化后显示,正常组和SRCC组分别有38.84%和37.06%的沉默子分布在远端基因间区,分别有21.76%和23.73%的沉默子分布在非编码内含子区域,符合远距离调控元件定位特征(图1D)。由此,正常胃黏膜样本和SRCC组织样本质量良好,测序质量高,沉默子信号分布图谱数据可靠。
H3K27me3信号主成分分析(principal component analysis,PCA)显示,SRCC样本和正常胃黏膜样本各自聚类,癌组织不同病例间的变异性较大,体现肿瘤表观异质性,并且SRCC沉默子特征与正常组织有显著差异(图2A)。在对沉默子信号强度进行分析后发现,SRCC样本的沉默子信号低于正常样本(图2B)。为进一步揭示SRCC沉默子丢失特征,使用MAnorm2工具标准化处理H3K27me3信号后,分析SRCC组相比正常组具有差异的H3K27me3修饰位点。结果共鉴定出6 257个在SRCC中丢失的沉默子信号位点和8 472个新获得的沉默子信号位点(图2C),提示大量沉默子重塑可能改变相关靶基因的转录状态,进而导致SRCC恶性进展。同时,这些靶基因主要富集在了胃癌相关信号通路中(图2D)。
RNA-seq主成分聚类分析显示,SRCC和正常组样本均各自聚类(图3A)。差异基因分析显示相比正常组织,SRCC中有2 065个上调差异基因,有2 929个下调差异基因(图3B)。沉默子是调控基因表达的一种重要表观调控机制,受调控的靶基因可能介导SRCC恶性表型,因此鉴定SRCC中由于沉默子信号丢失而转录激活的具体靶基因至关重要。
为筛选SRCC中可能受沉默子改变而差异表达的基因,整合分析CUT&Tag数据后发现有380个基因表达上调而H3K27me3信号下调,有997个基因表达下调而H3K27me3信号上调(图3C)。分别对上调及下调差异基因作通路富集分析后发现,可能由于沉默子丢失而表达上调的基因大量富集在了免疫相关通路,如淋巴细胞跨内皮迁移、NK细胞调控的细胞毒性、T细胞受体信号通路以及中性粒细胞胞外陷阱形成等(图3D)。
KEGG富集和可视化分析发现,多条免疫相关通路中均富集免疫调控关键基因PRKCB,提示SRCC免疫抑制微环境可能受沉默子重塑调控(图3F)。LCP2、IFNGR1和FCGR2A等免疫相关通路分子也被富集(图3G)。SRCC中对富集基因和沉默子H3K27me3信号强度作相关性分析发现呈负相关(图3H),提示SRCC沉默子重塑可能通过上调多种免疫抑制或异常激活基因,影响肿瘤微环境内免疫细胞功能,进而促进免疫逃逸和肿瘤进展。
沉默子信号丢失后,对应区域染色质开放性增加,有利于转录因子结合在此区域从而调控基因表达,分析沉默子丢失区域可能结合的转录因子有助于深入解析SRCC沉默子重塑对基因表达的调控作用。对SRCC鉴定出的沉默子丢失区域的转录因子结合基序进行分析,列举出预测排名前五的转录因子(图4A)。结合RNA测序数据发现转录因子EHF和IRF6在SRCC组织中上调(图4B),提示其在SRCC沉默子重塑过程中可能发挥转录调控作用。
构建沉默子相关靶基因调控网络,发现EHF位于调控网络中心,并且EHF和IRF6存在相互调控作用,多个转录因子构成复杂的转录调控网络(图4C)。SRCC沉默子重塑调控基因转录模式如图4D所示,基因组区域H3K27me3信号降低即沉默子丢失,则染色质开放性增加进而招募转录因子如EHF结合,进而激活下游基因PRKCB转录(图4D)。对EHF和IRF6可能调控的靶基因作GO富集分析后,发现这些靶基因参与白细胞激活及分化、T细胞激活及分化等生物学过程(图4E)。
进一步免疫组化结果表明,SRCC中存在EHF表达水平上调(P<0.05,图4F),提示SRCC进展过程发生沉默子重塑,大量沉默子信号丢失导致基因异常转录激活,其中IRF6和EHF可能作为基因调控网络中的关键转录因子发挥作用,可能诱导SRCC免疫抑制状态。
SRCC是一种低分化胃癌,具有很高的转移率和复发率,预后较差[14-15]。由于其显著区别于其他胃癌亚型,目前对于SRCC分子机制及治疗手段的认识还较为局限。表观修饰是重要的基因转录调控方式,沉默子是其中一类重要调控元件,由于既往研究方法局限,目前尚缺乏对SRCC沉默子图谱及调控方式的认识。传统ChIP-seq技术需要的样本量较大、步骤繁琐,较难实现大规模组织检测;本研究采用新开发的CUT&Tag测序技术,使用极少量细胞(低至数百个)和简便流程,通过抗体特异性标记不同的组蛋白修饰。本研究联合使用了ATAC-seq和CUT&Tag高通量表观组学测序技术,分析SRCC和正常组织染色质开放区域和组蛋白修饰状态,系统描绘SRCC沉默子重塑图谱,从沉默子角度展示了SRCC的表观重塑状态。
本研究发现,SRCC组织中存在沉默子重塑,大量位点H3K27me3即沉默子信号下降,可能广泛影响基因转录。已有研究报道SRCC存在免疫细胞克隆及分化抑制,导致免疫静息状态[10],分析发现,SRCC可能由于沉默子丢失而上调的靶基因大量富集在免疫相关通路,影响淋巴细胞、T细胞、NK细胞的激活和功能。近期单细胞测序揭示了SRCC存在异常激活的免疫应答通路并呈现免疫抑制性肿瘤微环境[16],并且肿瘤微环境内的CD4+和CD8+ T细胞处于静止状态[14]。本研究使用表观遗传测序方法分析SRCC沉默子特征,发现沉默子可能调控免疫抑制基因的转录状态从而影响免疫细胞功能,揭示了沉默子可能调控SRCC免疫微环境的表观机制。
SRCC发生发展过程中,沉默子信号丢失区域可能募集许多转录因子,分析发现转录因子EHF和IRF6可能结合在沉默子区域调控下游靶基因网络表达。EHF表达于上皮细胞,可能在调节上皮细胞分化和增殖中起重要作用,参与癌变过程,并和临床较差预后有关[17]。IRF6是干扰素家族调节因子中的一个成员,主要调节细胞抗病毒机制和细胞因子免疫响应,可能和SRCC异常免疫状态有关。本研究进一步揭示EHF和IRF6可能通过沉默子重塑的表观机制影响免疫微环境形成。另有研究报道,富集到的LCP2、IFNGR1和FCGR2A高表达可能通过促进淋巴结转移、免疫抑制、免疫逃逸等促进肿瘤恶性进展[18-21]。此外PLCG2、VAV3、VAV1等在免疫细胞激活过程中起关键作用的信号转导分子被多次富集,这些基因高表达可能导致免疫细胞功能异常,形成免疫抑制微环境[22-24]。
综上所述,SRCC存在沉默子重塑的表观异常修饰状态,沉默子信号的丢失可能招募转录因子如EHF和IRF6等形成基因表达调控网络,进而诱导免疫抑制性肿瘤微环境。以上结果揭示SRCC发生发展中的表观重塑状态及抑制性免疫微环境的可能成因,为开发相应靶向药物,治疗SRCC,改善患者预后提供新思路。

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doi: 10.16016/j.2097-0927.202407095
  • 接收时间:2024-07-23
  • 首发时间:2026-10-30
  • 出版时间:2025-03-15
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  • 收稿日期:2024-07-23
  • 修回日期:2024-08-16
基金
作者信息
    1陆军军医大学基础医学院细胞生物学教研室,重庆
    2陆军特色医学中心(第三军医大学大坪医院)消化内科,消化系统肿瘤精准防治重庆市重点实验室,重庆
    3重庆市中医院肿瘤科,重庆

通讯作者:

LI Yuhong,E-mail:
ZHANG Xuan,E-mail:
参考文献
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https://castjournals.cast.org.cn/joweb/ljjydxxb/CN/10.16016/j.2097-0927.202407095
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2种不同金属材料的力学参数
科
Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)
属
Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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