Coding and non-coding gene regulatory networks underlie the immune response in liver cirrhosis

Autor: Weihui Zhang, Zu-Hua Gao, Yuguo Zhang, Bo Gao, Zhengpeng Yang, Xueming Zhang, Dongbo Xue, Yongming Huang
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
Liver Cirrhosis
Cirrhosis
Gene regulatory network
Gene Identification and Analysis
lcsh:Medicine
Genetic Networks
Biochemistry
0302 clinical medicine
Gene expression
Databases
Genetic
Medicine and Health Sciences
Gene Regulatory Networks
lcsh:Science
Immune Response
Regulation of gene expression
Multidisciplinary
Liver Diseases
Liver Neoplasms
FOXP3
Nucleic acids
Gene Expression Regulation
Neoplastic
Liver
030220 oncology & carcinogenesis
RNA
Long Noncoding
Network Analysis
Research Article
Computer and Information Sciences
Carcinoma
Hepatocellular
Immunology
Gastroenterology and Hepatology
Biology
03 medical and health sciences
medicine
Genetics
Humans
RNA
Messenger
Non-coding RNA
Transcription factor
Biology and life sciences
Competing endogenous RNA
Gene Expression Profiling
lcsh:R
Computational Biology
medicine.disease
Immunity
Innate
Gene regulation
Gene expression profiling
MicroRNAs
030104 developmental biology
Cancer research
Long non-coding RNAs
RNA
lcsh:Q
Transcription Factors
Zdroj: PLoS ONE
PLoS ONE, Vol 12, Iss 3, p e0174142 (2017)
ISSN: 1932-6203
0000-0671
Popis: Liver cirrhosis is recognized as being the consequence of immune-mediated hepatocyte damage and repair processes. However, the regulation of these immune responses underlying liver cirrhosis has not been elucidated. In this study, we used GEO datasets and bioinformatics methods to established coding and non-coding gene regulatory networks including transcription factor-/lncRNA-microRNA-mRNA, and competing endogenous RNA interaction networks. Our results identified 2224 mRNAs, 70 lncRNAs and 46 microRNAs were differentially expressed in liver cirrhosis. The transcription factor -/lncRNA- microRNA-mRNA network we uncovered that results in immune-mediated liver cirrhosis is comprised of 5 core microRNAs (e.g., miR-203; miR-219-5p), 3 transcription factors (i.e., FOXP3, ETS1 and FOS) and 7 lncRNAs (e.g., ENTS00000671336, ENST00000575137). The competing endogenous RNA interaction network we identified includes a complex immune response regulatory subnetwork that controls the entire liver cirrhosis network. Additionally, we found 10 overlapping GO terms shared by both liver cirrhosis and hepatocellular carcinoma including "immune response" as well. Interestingly, the overlapping differentially expressed genes in liver cirrhosis and hepatocellular carcinoma were enriched in immune response-related functional terms. In summary, a complex gene regulatory network underlying immune response processes may play an important role in the development and progression of liver cirrhosis, and its development into hepatocellular carcinoma.
Databáze: OpenAIRE
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