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

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

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

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.

Original language	English
Pages (from-to)	169-175
Number of pages	7
Journal	Gene
Volume	661
DOIs	https://doi.org/10.1016/j.gene.2018.03.066
State	Published - 30 Jun 2018

Keywords

Esophageal squamous cell carcinoma
Genome-wide screening
lncRNA
mRNA

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10.1016/j.gene.2018.03.066

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title = "Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma",

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",

author = "Weiwei Wang and Chengguo Wei and Pan Li and Li Wang and Wencai Li and Kuisheng Chen and Jianying Zhang and Weijia Zhang and Guozhong Jiang",

note = "Publisher Copyright: {\textcopyright} 2018 Elsevier B.V.",

year = "2018",

month = jun,

day = "30",

doi = "10.1016/j.gene.2018.03.066",

language = "English",

volume = "661",

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TY - JOUR

T1 - Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma

AU - Wang, Weiwei

AU - Wei, Chengguo

AU - Li, Pan

AU - Wang, Li

AU - Li, Wencai

AU - Chen, Kuisheng

AU - Zhang, Jianying

AU - Zhang, Weijia

AU - Jiang, Guozhong

PY - 2018/6/30

Y1 - 2018/6/30

N2 - 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.

AB - 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.

KW - Esophageal squamous cell carcinoma

KW - Genome-wide screening

KW - lncRNA

KW - mRNA

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DO - 10.1016/j.gene.2018.03.066

M3 - Article

C2 - 29604464

AN - SCOPUS:85045042038

SN - 0378-1119

VL - 661

SP - 169

EP - 175

JO - Gene

JF - Gene

ER -

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

Abstract

Keywords

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