Deep sequencing analysis of microRNA expression in porcine serum-induced hepatic fibrosis rats

Annals of Hepatology

Volumn 13, Issue 4, 2014, Pages 439-449

  Ge, Shanfei ^a   Wang, Xiaowei ^b   Xie, Jianping ^a   Yi, Xin ^c   Liu, Fei ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b BGI Tianjin   (China)

^c BGI SHENZHEN   (China)

Author keywords

Fibrosis related genes; Liver fibrosis; microRNAs

Indexed keywords

MICRORNA; MICRORNA 146B; MICRORNA 27A; UNCLASSIFIED DRUG;

ADULT; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; FIBROGENESIS; FIBROSIS RELATED GENE; GENE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENE TARGETING; GENETIC ASSOCIATION; LIVER FIBROSIS; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; QUANTITATIVE ANALYSIS; RAT; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SIGNAL TRANSDUCTION; UPREGULATION; ANIMAL; DISEASE MODEL; EXPERIMENTAL LIVER CIRRHOSIS; GENE EXPRESSION REGULATION; GENETICS; PATHOLOGY; PROCEDURES; SEQUENCE ANALYSIS; SERUM; SPRAGUE DAWLEY RAT; SWINE;

ANIMALS; DISEASE MODELS, ANIMAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LIVER CIRRHOSIS, EXPERIMENTAL; MICRORNAS; RATS; RATS, SPRAGUE-DAWLEY; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; SERUM; SWINE; UP-REGULATION;

EID: 84902368953     PISSN: 16652681     EISSN: None     Source Type: Journal    
DOI: 10.1016/s1665-2681(19)30851-8     Document Type: Article

References (46)

1. Christopher JP, Motoki T, Richard AR. Molecular mechanisms of hepatic fibrogenesis. J Gastroenterol Hepatol 2007; 22: S79-S84.
2. Elisabetta M, Joseph G, Natalia N. Molecular pathogenesis of hepatic fibrosis and current therapeutic approaches. Chemico-biological interactions 2011; 193: 225-31.
3. Friedman SL. Hepatic fibrosis-overview. Toxicology 2008; 254: 120-9.
4. Yoshiki M, Hidenori T, Masami T, Masahiko K, Yoshinori H, Fumihiko M, Atsushi T, et al. The progression of liver fibrosis is related with overexpression of the miR-199 and 200 families. PLoS One 2011; 6: 16081.
5. Soyer MT, Ceballos R, Aldrete JS. Reversibility of severe hepatic damage caused by jejunoileal bypass after re-establishment of normal intestinal continuity. Surgery 1976; 79: 601.
6. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-97.
7. Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development 2005; 132: 4653-62.
8. Miska EA. How microRNAs control cell division, differentiation and death. Current opinion in genetics & development 2005; 15: 563-568.
9. Robert EL, Elisabeth SH, Andreas P, Robert P, Morten L, Martin EM, Sakari K, et al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 2010; 327: 198-201.
10. Roderburg C, Luedde T. The role of miRNAs in animal models of liver fibrosis. Drug Discovery Today: Disease Models 2012; 363: 1-6.
11. Janaiah K, Raghu RC, Kathryn AO, Erik AW, Chrystal LM, Hun-Way H, Tsung-Cheng C. et al. Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell 2009; 137: 1005-17.
12. Ashley ML, Nury MS, Tracy LW, Sriparna G, Ting L, Iain HM, Mark WR, et al. Inhibitory effects of microRNA 19b in hepatic stellate cell©\mediated fibrogenesis. Hepatology 2012; 56: 300-10.
13. Koziel M. The immunopathogenesis of HBV infection. Antiviral therapy 1998; 3: 13.
14. Wei-Qing L, Chao C, Mi-Die X, Jia G, Yi-Ming L, Qing-Mei X, Hui-Min L, et al. The rno©\miR©\34 family is upregulated and targets ACSL1 in dimethylnitrosamine©\induced hepatic fibrosis in rats. FEBS Journal 2011; 278: 1522-32.
15. Christoph R, Gerd-Willem U, Kira B, Mihael V, Henning Z, Sabine Schmidt, Jörn J, et al. Micro©\RNA profiling reveals a role for miR©\29 in human and murine liver fibrosis. Hepatology 2011; 53: 209-18.
16. Hasegawa-Baba Y, Doi K. Changes in TIMP-1 and-2 expression in the early stage of porcine serum-induced liver fibrosis in rats. Exp Toxicol Pathol 2011; 63: 357-61.
17. Osuna-Martínez U, Reyes-Esparza JA, L-Petricevich V, Hernandez-Pando R, Rodriguez-Fragoso L. Protective effect of thymic humoral factor on porcine serum-induced hepatic fibrosis and liver damage in Wistar rats. Ann Hepatol 2011; 10: 540.
18. Jan K, Nikolaus R, Ravi B, Kallanthottathil GR, Thomas T, Muthiah M, Markus S. Silencing of microRNAs in vivo with 'antagomirs'. Nature 2005; 438: 685-9.
19. Christine E, Scott D, Susan FM, Xing XY, Sanjay KP, Michael P, Lynnetta W, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell metabolism 2006; 3: 87-98.
20. Catherine LJ, MinKyung Y, Alissa ML, Stanley ML, Peter S. Modulation of hepatitis C virus RNA abundance by a liverspecific MicroRNA. Science 2005; 309: 1577-81.
21. Shimizu I, Mizobuchi Y, Yasuda M, Shiba M, Y-R M, Horie T, Liu F, et al. Inhibitory effect of oestradiol on activation of rat hepatic stellate cells in vivo and in vitro. Gut 1999; 44: 127-36.
22. Osuna-Martínez U, Reyes-Esparza JA, L-Petricevich V, Hernandez-Pando R, Rodriguez-Fragoso L. Protective effect of Thymic Humoral Factor on porcine serum induced hepatic fibrosis and liver dam age in Wistar rats. Ann Hepatol 2011; 10: 540-51.
23. Ruiqiang L, Chang Y, Yingrui L, Tak-Wah L, Siu-Ming Y, Karsten K, Jun W. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009; 25: 1966-7.
24. Piotr JB, Piero C, Carsten OD, Jun K, Yoshihide H, Werner VB, Christian B, et al. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol 2009; 10: 79.
25. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome research 1997; 7: 986-95.
26. Zhenbiao X, Maoshan C, Zhonggan R, Nian Z, Hanmei X, Xiao L, Geng T, et al., Deep sequencing identifies regulated small RNAs in Dugesia japonica. Molecular biology reports 2013; 1-7.
27. Harsh D, Carsten S, Priyanka P, Norbert G. miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Informatics 2011; 44: 839-47.
28. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120: 15-20.
29. Anton JE, Bino J, Ulrike G, Thomas T, Chris S, Debora SM. MicroRNA targets in Drosophila. Genome biology 2004; 5: R1.
30. Ana C, Stefan G, Juan MG, Javier T, Manuel T, Montserrat R. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005; 21: 3674-6.
31. Jia Y, Lin F, Hongkun Z, Yong Z, Jie C, Zengjin Z, Jing W, et al. WEGO: a web tool for plotting GO annotations. Nucleic acids research 2006; 34: W293-W297.
32. Glynn DJ, Brad TS, Douglas AH, Jun Y, Wei G, H CL, Richard AL. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 2003; 4: 3.
33. Xiaoyu F, Deming T, Zhouhua H, Zhiliang H, Guozhen L. miR-338-3p Is Down-Regulated by Hepatitis B Virus X and Inhibits Cell Proliferation by Targeting the 3'-UTR Region of CyclinD1. International Journal of molecular sciences 2012; 13: 8514-39.
34. Angela D, Jan P, Karen K, Donna C, Pranoti M, Arumugam V, Gyongyi S. MicroRNA Expression Profile in Lieber©\DeCarli Diet©\Induced Alcoholic and Methionine Choline Deficient Diet©\Induced Nonalcoholic Steatohepatitis Models in Mice. Alcoholism: Clinical and Experimental Research 2009; 33: 1704-10.
35. Can-Jie G, Qin P, Tao C, Bo J, Guang-Yu C, Ding-Guo L. Changes in microRNAs associated with hepatic stellate cell activation status identify signaling pathways. FEBS Journal 2009; 276: 5163-76.
36. Can-Jie G, Qin P, Ding-Guo L, Hua S, Bo-Wei L. miR-15b and miR-16 are implicated in activation of the rat hepatic stellate cell: An essential role for apoptosis. J Hepatol 2009; 50: 766-78.
37. Can-Jie G, Qin P, Bo J, Guang-Yu C, Ding-Guo L. Effects of upregulated expression of microRNA-16 on biological properties of culture-activated hepatic stellate cells. Apoptosis 2009; 14: 1331-40.
38. Jianjian Z, Zhuo L, Peihong D, Zhongqiu L, Shenmeng G, Xiaoqian C, Cunzao W, et al. Activation of hepatic stellate cells is suppressed by microRNA-150. International Journal of Molecular Medicine 2013; 32: 17.
39. Masashi I, Tomohiro O, Masaru E, Hiroyuki M, Katsutoshi Y, Kazuo I, Norifumi K. Induction of microRNA-214-5p in human and rodent liver fibrosis. Fibrogenesis Tissue Repair 2012; 5: 12.
40. Juling J, Jinsheng Z, Guangcun H, Jin Q, Xueqing W, Shuang M. Over-expressed microRNA-27a and 27b influence fat accumulation and cell proliferation during rat hepatic stellate cell activation. FEBS letters 2009; 583: 759-66.
41. Jiang X, Ning Q, Wang J. Angiotensin II induced differentially expressed microRNAs in adult rat cardiac fibroblasts. J Physiol Sciences 2013; 63: 31-8.
42. Yanyan L, Ying W, Lin Y, Cuiyun Sc, Degang C, Shizhu Y, Qian W, et al. miR-146b-5p inhibits glioma migration and invasion by targeting MMP16. Cancer letters 2013; 339: 260-9.
43. Richard F, Roland R, Thuy PL, Alexandra S, Ulrich W, Hans PD, Dieter H. Intercellular communication via gap junctions in activated rat hepatic stellate cells. Gastroenterology 2005; 128: 433-48.
44. Lim M, Maubach G, Zhuo L. TGF-beta1 down-regulates connexin 43 expression and gap junction intercellular communication in rat hepatic stellate cells. Eur J Cell Biol 2009; 88: 719.
45. Emma AK, Paulo RA, Gaurav A, Jin Y, Michael HN, Jonathan AD. Molecular basis for calcium signaling in hepatic stellate cells. American Journal of Physiology-Gastrointestinal and Liver Physiology 2007; 292: G975-G982.
46. An P, Tian Y, Dai J, Chen M, Luo H. Ca2+/Calmodulin-Dependent Protein Kinase II Mediates Platelet-Derived Growth Factor-Induced Human Hepatic Stellate Cell Proliferation. Digestive diseases and sciences 2012; 57: 935-42.