Integrated analysis of hepatic mRNA and miRNA profiles identified molecular networks and potential biomarkers of NAFLD

Scientific Reports
Mingzhe ZhuGuang Ji

Abstract

To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD. MiRNA target genes (13565) were predicted by the miRWalk database. Using DAVID 6.8, the intersection (195 genes) of differentially expressed mRNAs and miRNA-predicted target genes were enriched in 47 gene ontology (GO) terms and 28 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Using Cytoscape, pathway interaction and protein-protein interaction (PPI) networks were constructed, and hub genes (e.g., Abcg8, Cyp1a1, Cyp51, Hmgcr, etc.) associated with NAFLD were obtained. Moreover, 673 miRNA-mRNA negative regulatory pairs were obtained, and networks were constructed. Finally, several representative miRNAs and mRNAs were validated by real-time qPCR. In conclusion, potential molecular mech...Continue Reading

References

Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jun 29, 2010·Metabolism: Clinical and Experimental·Bilge AktasErol Avsar
Oct 20, 2010·Laboratory Investigation; a Journal of Technical Methods and Pathology·Anna AlisiValerio Nobili
Jun 8, 2011·The Journal of Clinical Investigation·Katey J RaynerKathryn J Moore
Jul 9, 2011·Drug Metabolism and Disposition : the Biological Fate of Chemicals·April D LakeNathan J Cherrington
Feb 9, 2013·Toxicology and Applied Pharmacology·April D LakeNathan J Cherrington
May 25, 2013·Arteriosclerosis, Thrombosis, and Vascular Biology·Noemi RotllanCarlos Fernández-Hernando
Aug 6, 2013·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Cynthia A MoylanAnna Mae Diehl
Jun 24, 2014·Source Code for Biology and Medicine·Chuming ChenCathy H Wu
Sep 19, 2014·World Journal of Hepatology·Mehmet CelikbilekMehmet Yucesoy
Jan 7, 2015·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Yue Ying FengJun Fen Fu
Mar 13, 2015·Antioxidants & Redox Signaling·Mithun SinhaChandan K Sen
May 24, 2015·Translational Research : the Journal of Laboratory and Clinical Medicine·Fatjon LetiJohanna K DiStefano
Jan 12, 2016·Laboratory Investigation; a Journal of Technical Methods and Pathology·Terence N BukongPaul J Winwood
Jan 30, 2016·Metabolism: Clinical and Experimental·Elena BuzzettiEmmanuel A Tsochatzis
Mar 8, 2016·Liver International : Official Journal of the International Association for the Study of the Liver·Joel Vega-BadilloSamuel Canizales-Quinteros
Apr 22, 2016·European Heart Journal·Peter WilleitManuel Mayr
Apr 22, 2016·Hepatic Medicine : Evidence and Research·Yuqing MaoXiaoming Fan
Jun 6, 2016·Environmental Toxicology and Pharmacology·Chunhua WangXiuying Zhang
Jun 28, 2016·Molecular and Cellular Biochemistry·Rashid H OsmanTuoyu Geng
Sep 27, 2016·International Journal of Molecular Sciences·Teresa AuguetCristóbal Richart
Jun 1, 2017·Journal of Translational Medicine·Masood Abu-HalimaHashim Abdul-Khaliq
Jun 18, 2017·Biochemical and Biophysical Research Communications·Hyeon Hui KangHwa Sik Moon
Aug 10, 2017·Biochimica Et Biophysica Acta. Molecular Basis of Disease·Junrui ChengXiang-Dong Wang
Aug 13, 2017·Scientific Reports·Annelynn WallaertPieter Van Vlierberghe
Aug 16, 2017·Journal of Diabetes Research·Sâmia Cruz Tfaile CorbiRaquel Mantuaneli Scarel-Caminaga

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Citations

Nov 7, 2019·Archives of Physiology and Biochemistry·Mina ZareReza Meshkani
Jul 5, 2019·BMC Complementary and Alternative Medicine·Mingzhe ZhuGuang Ji
Jul 30, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mingxiang WenXianqing Shi
Dec 14, 2018·International Journal of Molecular Sciences·Paola DongiovanniAnna Ludovica Fracanzani
Jan 31, 2021·Animals : an Open Access Journal From MDPI·Yongliang FanZhangping Yang
Aug 25, 2021·Evidence-based Complementary and Alternative Medicine : ECAM·Mehdi ZobeiriMohammad Abdollahi

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Methods Mentioned

BETA
PCR
RNA-Seq

Software Mentioned

MCODE
Molecular Complex Detection ( MCODE )
Bowtie
CluePedia
DEM
DAVID
Cytoscape
ClueGO
miRWalk
DESeq

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