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 DU
1, 2, Yuanfeng REN
2, Zhaole CHU
2, Biying LIU
2, Xianfeng LI
2, Junyu XIANG
2, Dongfeng CHEN
2, Tao WANG
2, Bin WANG
2, Haiying GUO
1, Xuan ZHANG
3, Yuhong LI
1, 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。
, authors=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, authorsList=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, authorCompany=null, correspAuthors=张璇, 李玉红, authorNote=null, correspAuthorsNote=
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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, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1322934757872501501, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, authorId=1322934756068950777, language=CN, stringName=杜艾贝, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=
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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, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1322934755628548847, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, xref=1, ext=[AuthorCompanyExt(id=1322934755636937456, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, companyId=1322934755628548847, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=
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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)])]), Author(id=1322934757956387583, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, orderNo=1, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1322934758052856577, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, authorId=1322934757956387583, language=EN, stringName=Yuanfeng REN, firstName=Yuanfeng, middleName=null, lastName=REN, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=
2, address=
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, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1322934758128354050, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, authorId=1322934757956387583, language=CN, stringName=任原锋, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=
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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, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1322934755876012786, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, xref=2, ext=[AuthorCompanyExt(id=1322934755884401395, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, companyId=1322934755876012786, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=
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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)])]), Author(id=1322934758224823044, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, orderNo=2, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1322934758329680646, tenantId=1146029695717560320, journalId=1319373162502258839, articleId=1322934751753011940, authorId=1322934758224823044, language=EN, stringName=Zhaole CHU, firstName=Zhaole, middleName=null, lastName=CHU, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=
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2, address=
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2, address=
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2, address=
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CUT&Tag、ATAC-seq及RNA-seq测序数据质控和H3K27me3修饰的基因组分布特征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
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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
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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
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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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