Viral genotype correlates with distinct liver gene transcription signatures in chronic hepatitis C virus infection

Liver International

Volumn 35, Issue 10, 2015, Pages 2256-2264

  Robinson, Mark W ^a,b   Aranday Cortes, Elihu ^a   Gatherer, Derek ^a,c   Swann, Rachael ^a,d   Liefhebber, Jolanda M P ^a   Filipe, Ana Da Silva ^a   Sigruener, Alex ^e   Barclay, Stephen T ^f   Mills, Peter R ^d   Patel, Arvind H ^a   Mclauchlan, John ^a  

^a MRC UNIVERSITY OF GLASGOW CENTRE FOR VIRUS RESEARCH   (United Kingdom)

^b TRINITY COLLEGE DUBLIN   (Ireland)

^c LANCASTER UNIVERSITY   (United Kingdom)

^d GARTNAVEL GENERAL HOSPITAL   (United Kingdom)

^e UNIVERSITY HOSPITAL REGENSBURG   (Germany)

^f GLASGOW ROYAL INFIRMARY   (United Kingdom)

Author keywords

HCV; Genotype; Interferon; ISGs; Transcriptomics

Indexed keywords

GAMMA INTERFERON; INTERFERON; IFNG PROTEIN, HUMAN; IFNL4 PROTEIN, HUMAN; INTERLEUKIN DERIVATIVE; TRANSCRIPTOME;

ARTICLE; CHRONIC HEPATITIS C; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENOTYPE; HEPATITIS C VIRUS GENOTYPE 1; HEPATITIS C VIRUS GENOTYPE 3; HUMAN; HUMAN CELL; LIVER BIOPSY; LIVER CELL; NONHUMAN; UPREGULATION; VIRUS TRANSCRIPTION; ADULT; CELL LINE; GENETICS; HEPATITIS C; HOST PATHOGEN INTERACTION; LIVER; MALE; METABOLISM; MIDDLE AGED; PATHOLOGY;

ADULT; CELL LINE; FEMALE; GENOTYPE; HEPATITIS C; HEPATITIS C, CHRONIC; HOST-PATHOGEN INTERACTIONS; HUMANS; INTERFERON-GAMMA; INTERLEUKINS; LIVER; MALE; MIDDLE AGED; POLYMORPHISM, GENETIC; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84942371513     PISSN: 14783223     EISSN: 14783231     Source Type: Journal    
DOI: 10.1111/liv.12830     Document Type: Article

References (38)

1. Smith DB, Bukh J, Kuiken C, et al. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014; 59: 318-27.
2. Thomas DL. Global control of hepatitis C: where challenge meets opportunity. Nat Med 2013; 19: 850-8.
3. Lawitz E, Mangia A, Wyles D, et al.Sofosbuvir for previously untreated chronic hepatitis C infection. N Engl J Med 2013; 368: 1878-87.
4. Kohli A, Shaffer A, Sherman A, Kottilil S. Treatment of Hepatitis C. JAMA 2014; 312: 631.
5. Swadling L, Klenerman P, Barnes E. Ever closer to a prophylactic vaccine for HCV. Expert Opin Biol Ther 2013; 13: 1109-24.
6. Messina JP, Humphreys I, Flaxman A, et al.Global distribution and prevalence of hepatitis C virus genotypes. Hepatology 2015; 66: 77-87.
7. Poynard T, Ratziu V, McHutchison J, et al.Effect of treatment with peginterferon or interferon alfa-2b and ribavirin on steatosis in patients infected with hepatitis C. Hepatology 2003; 38: 75-85.
8. Probst A, Dang T, Bochud M, et al. Role of hepatitis C virus genotype 3 in liver fibrosis progression-a systematic review and meta-analysis. J Viral Hepat 2011; 18: 745-59.
9. Zeuzem S, Berg T, Moeller B, et al.Expert opinion on the treatment of patients with chronic hepatitis C. J Viral Hepat 2009; 16: 75-90.
10. Su AI, Pezacki JP, Wodicka L, et al.Genomic analysis of the host response to hepatitis C virus infection. Proc Natl Acad Sci USA 2002; 99: 15669-74.
11. Bigger CB, Guerra B, Brasky KM, et al.Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees. J Virol 2004; 78: 13779-92.
12. Smith MW, Yue ZN, Korth MJ, et al.Hepatitis C virus and liver disease: global transcriptional profiling and identification of potential markers. Hepatology 2003; 38: 1458-67.
13. Helbig KJ, Lau DT-Y, Semendric L, Harley HAJ, Beard MR. Analysis of ISG expression in chronic hepatitis C identifies viperin as a potential antiviral effector. Hepatology 2005; 42: 702-10.
14. Chen L, Borozan I, Feld J, et al.Hepatic Gene Expression Discriminates Responders and Nonresponders in Treatment of Chronic Hepatitis C Viral Infection. Gastroenterology 2005; 128: 1437-44.
15. Sarasin-Filipowicz M, Oakeley EJ, Duong FHT, et al.Interferon signaling and treatment outcome in chronic hepatitis C. Proc Natl Acad Sci USA 2008; 105: 7034-9.
16. Jones DM, Domingues P, Targett-Adams P, McLauchlan J. Comparison of U2OS and Huh-7 cells for identifying host factors that affect hepatitis C virus RNA replication. J Gen Virol 2010; 91: 2238-48.
17. Trapnell C, Roberts A, Goff L, et al.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7: 562-78.
18. Prokunina-Olsson L, Muchmore B, Tang W, et al.A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 2013; 45: 164-71.
19. Lanford RE, Guerra B, Lee H, et al. Genomic response to interferon-alpha in chimpanzees: implications of rapid downregulation for hepatitis C kinetics. Hepatology 2006; 43: 961-72.
20. Metz P, Dazert E, Ruggieri A, et al.Identification of type I and type II interferon-induced effectors controlling hepatitis C virus replication. Hepatology 2012; 56: 2082-93.
21. Thomas DL, Thio CL, Martin MP, et al.Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature 2009; 461: 798-801.
22. Tanaka Y, Nishida N, Sugiyama M, et al.Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet 2009; 41: 1105-9.
23. Ge D, Fellay J, Thompson AJ, et al.Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009; 461: 399-401.
24. Dill MT, Duong FHT, Vogt JE, et al.Interferon-induced gene expression is a stronger predictor of treatment response than IL28B genotype in patients with hepatitis C. Gastroenterology 2011; 140: 1021-31.
25. Clark PJ, Thompson AJ, Vock DM, et al.Hepatitis C virus selectively perturbs the distal cholesterol synthesis pathway in a genotype-specific manner. Hepatology 2012; 56: 49-56.
26. Trinchieri G. Type I interferon: friend or foe? J Exp Med 2010; 207: 2053-63.
27. Cousens LP, Orange JS, Su HC, Biron CA. Interferon-alpha/beta inhibition of interleukin 12 and interferon-gamma production in vitro and endogenously during viral infection. Proc Natl Acad Sci USA 1997; 94: 634-9.
28. Kearney SJ, Delgado C, Eshleman EM, et al. Type I IFNs downregulate myeloid cell IFN-γ receptor by inducing recruitment of an early growth response 3/NGFI-A binding protein 1 complex that silences ifngr1 transcription. J Immunol 2013; 191: 3384-92.
29. Teles RMB, Graeber TG, Krutzik SR, et al.Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses. Science 2013; 339: 1448-53.
30. Asselah T, Bieche I, Narguet S, et al.Liver gene expression signature to predict response to pegylated interferon plus ribavirin combination therapy in patients with chronic hepatitis C. Gut 2008; 57: 516-24.
31. Makowska Z, Duong FHT, Trincucci G, Tough DF, Heim MH. Interferon-β and interferon-λ signaling is not affected by interferon-induced refractoriness to interferon-α in vivo. Hepatology 2011; 53: 1154-63.
32. Dill MT, Makowska Z, Duong FHT, et al.Interferon-γ-stimulated genes, but not USP18, are expressed in livers of patients with acute hepatitis C. Gastroenterology 2012; 143: 777-86.
33. Francois-Newton V, Livingstone M, Payelle-Brogard B, Uzé G, Pellegrini S. USP18 establishes the transcriptional and anti-proliferative interferon α/β differential. Biochem J 2012; 446: 509-16.
34. Strebovsky J, Walker P, Dalpke AH. Suppressor of cytokine signaling proteins as regulators of innate immune signaling. Front Biosci 2012; 17: 1627-39.
35. Robinson MW, Swann R, Sigruener A, et al.Elevated interferon-stimulated gene transcription in peripheral blood mononuclear cells occurs in patients infected with genotype 1 but not genotype 3 hepatitis C virus. J Viral Hepat 2015; 22: 384-90.
36. Duong FHT, Trincucci G, Boldanova T, et al.IFN-λ receptor 1 expression is induced in chronic hepatitis C and correlates with the IFN-λ3 genotype and with nonresponsiveness to IFN-α therapies. J Exp Med 2014; 211: 857-68.
37. McFarland AP, Horner SM, Jarret A, et al.The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat Immunol 2014; 15: 72-9.
38. Rauch A, Kutalik Z, Descombes P, et al.Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology 2010; 138: 1338-45.