Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma

Weiwei Wang; Chengguo Wei; Pan Li; Li Wang; Wencai Li; Kuisheng Chen; Jianying Zhang; Weijia Zhang; Guozhong Jiang

doi:10.1016/j.gene.2018.03.066

Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma

Gene. 2018 Jun 30:661:169-175. doi: 10.1016/j.gene.2018.03.066. Epub 2018 Mar 28.

Authors

Weiwei Wang¹, Chengguo Wei², Pan Li¹, Li Wang¹, Wencai Li¹, Kuisheng Chen¹, Jianying Zhang³, Weijia Zhang⁴, Guozhong Jiang⁵

Affiliations

¹ Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou 450002, China; Henan Key Laboratory for Tumor Pathology, Zhengzhou 450052, China.
² Divisions of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
³ Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China.
⁴ Divisions of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States. Electronic address: weijia.zhang@mssm.edu.
⁵ Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Department of Pathology, School of Basic Medicine, Zhengzhou University, Zhengzhou 450002, China; Henan Key Laboratory for Tumor Pathology, Zhengzhou 450052, China. Electronic address: guozhongjiang@zzu.edu.cn.

PMID: 29604464
DOI: 10.1016/j.gene.2018.03.066

Abstract

Systems biology approaches can help understand pathogenesis of complex human diseases like cancers for identification of potential new therapeutic targets. Here in this study, we performed genome-wide screening for mRNA and lncRNA profiles in esophageal cancer to identify the novel cancer-related mRNA and lncRNA in esophageal squamous cell carcinoma (ESCC). We identified 1260 up-regulated/1445 down-regulated mRNAs and 402 up-regulated/741 down-regulated lncRNAs. Further functional analysis revealed differentially expressed genes (DEGs) of mRNA and lncRNA are related to different pathways. mRNA pathways are mainly involved in cell cycles while lncRNA pathways are for regulation and metabolic procession. Differentially expressed mRNAs/lncRNAs were validated with qPCR. At last, mRNA and lncRNA co-expression network were built and highly-connected networks were identified, which may provide a mechanism of mRNA expression regulation by lncRNA. In together, we used next generation sequencing data to explore the co-expression networks of lncRNA and mRNA, which may elucidate the functions and mechanisms of lncRNA in ESCC.

Keywords: Esophageal squamous cell carcinoma; Genome-wide screening; lncRNA; mRNA.

MeSH terms

Carcinoma, Squamous Cell / genetics*
Cell Transformation, Neoplastic / genetics
Computational Biology
Esophageal Neoplasms / genetics*
Esophageal Squamous Cell Carcinoma
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
High-Throughput Nucleotide Sequencing
Humans
Oligonucleotide Array Sequence Analysis
Oncogenes / genetics*
RNA, Long Noncoding / analysis
RNA, Long Noncoding / genetics*
RNA, Messenger / analysis
RNA, Messenger / genetics*
Systems Biology

Substances

RNA, Long Noncoding
RNA, Messenger