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 |
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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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