Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma

doi:10.1016/j.csbj.2023.07.030

科研成果详情

题名	Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma
作者	Li, Xianfeng 1,2,3,4; Wang, Yan 1; Min, Qingjie 1; Zhang, Weimin 1; Teng, Huajing 5; Li, Chao 6; Zhang, Kun6; Shi, Leisheng 7; Wang, Bin 2,3,4; Zhan, Qimin 1
发表日期	2023
发表期刊	Computational and Structural Biotechnology Journal 影响因子和分区
语种	英语
原始文献类型	Journal article (JA)
关键词	Cell culture Chemical activation Diseases Histology Tumors Alternative splicing Cancer subtypes Comprehensive comparisons Esophageal adenocarcinoma Esophageal squamous cell carcinoma Gene fusion Polyadenylation Promoter activities Transcriptomes Tumor development
其他关键词	GENOME-WIDE ASSOCIATION ; GLOBAL CANCER STATISTICS ; LONG NONCODING RNA ; SUSCEPTIBILITY LOCI ; BARRETTS-ESOPHAGUS ; GENE ; POLYADENYLATION ; IDENTIFICATION ; SIGNATURE ; CLEAVAGE
摘要	Background: Esophageal cancers are primarily categorized as esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While various (epi) genomic alterations associated with tumor development in ESCC and EAC have been documented, a comprehensive comparison of the transcriptomes in these two cancer subtypes remains lacking. Methods: We collected 551 gene expression profiles from publicly available sources, including normal, ESCC, and EAC tissues or cell lines. Subsequently, we conducted a systematic analysis to compare the transcriptomes of these samples at various levels, including gene expression, promoter activity, alternative splicing (AS), alternative polyadenylation (APA), and gene fusion. Results: Seven distinct cluster gene expression patterns were identified among the differentially expressed genes in normal, ESCC, and EAC tissues. These patterns were enriched in the PI3K-Akt signaling pathway and the activation of extracellular matrix organization and exhibited repression of epidermal development. Notably, we observed additional genes or unique expression levels enriched in these shared pathways and biological processes related to tumor development and immune activation. In addition to the differentially expressed genes, there was an enrichment of lncRNA co-expression networks and downregulation of promoter activity associated with the repression of epidermal development in both ESCC and EAC. This indicates a common feature between these two cancer subtypes. Furthermore, differential AS and APA patterns in ESCC and EAC appear to partially affect the expression of host genes associated with bacterial or viral infections in these subtypes. No gene fusions were observed between ESCC and EAC, thus highlighting the distinct molecular mechanisms underlying these two cancer subtypes. Conclusions: We conducted a comprehensive comparison of ESCC and EAC transcriptomes and uncovered shared and distinct transcriptomic signatures at multiple levels. These findings suggest that ESCC and EAC may exhibit common and unique mechanisms involved in tumorigenesis. © 2023
资助项目	Beijing Municipal Commission of Health and Family Planning Project [PXM2018 026279 000005]; National Natural Science Foundation of China [81902879, 82273431, 81490753, 81502150]; China Post-doctoral Science Foundation [2018M641117]
出版者	Elsevier B.V.
ISSN	2001-0370
EISSN	2001-0370
卷号	21 页码:3841-3853
DOI	10.1016/j.csbj.2023.07.030
页数	13
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号	WOS:001052385900001
收录类别	EI ; PUBMED ; SCIE ; SCOPUS
在线发表日期	2023-08
EI入藏号	20233214490390
EI主题词	Gene expression
EI分类号	461.2 Biological Materials and Tissue Engineering ; 461.9 Biology ; 802.2 Chemical Reactions ; 804 Chemical Products Generally
URL	查看原文
PubMed ID	37564101
SCOPUSEID	2-s2.0-85166484424
通讯作者地址	[Zhan, Qimin]Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing),Laboratory of Molecular Oncology,Peking University Cancer Hospital & Institute,Beijing,100142,China
Scopus学科分类	Biotechnology;Biophysics;Structural Biology;Biochemistry;Genetics;Computer Science Applications
引用统计
文献类型	期刊论文
条目标识符	https://kms.wmu.edu.cn/handle/3ETUA0LF/182542
专题	基因组医学研究院
通讯作者	Zhan, Qimin
作者单位	1.Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing),Laboratory of Molecular Oncology,Peking University Cancer Hospital & Institute,Beijing,100142,China; 2.Department of Gastroenterology and Chongqing Key Laboratory of Digestive Malignancies,Daping Hospital,Army Medical University (Third Military Medical University),10# Changjiang Branch Road, Yuzhong District,Chongqing,400042,China; 3.Institute of Pathology and Southwest Cancer Center,Key Laboratory of Tumor Immunopathology of Ministry of Education of China,Southwest Hospital,Army Medical University (Third Military Medical University),Chongqing,400038,China; 4.Jinfeng Laboratory,Chongqing,401329,China; 5.Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing),Department of Radiation Oncology,Peking University Cancer Hospital & Institute,Beijing,100142,China; 6.Institute of Genomic Medicine,Wenzhou Medical University,Wenzhou,325035,China; 7.Key Laboratory of Genomic and Precision Medicine,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing,100101,China
推荐引用方式 GB/T 7714	Li, Xianfeng,Wang, Yan,Min, Qingjie,et al. Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma[J]. Computational and Structural Biotechnology Journal,2023,21:3841-3853.
APA	Li, Xianfeng., Wang, Yan., Min, Qingjie., Zhang, Weimin., Teng, Huajing., ... & Zhan, Qimin. (2023). Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma. Computational and Structural Biotechnology Journal, 21, 3841-3853.
MLA	Li, Xianfeng,et al."Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma".Computational and Structural Biotechnology Journal 21(2023):3841-3853.