Interferon lambda alleles predict innate antiviral immune responses and hepatitis C virus permissiveness

Cell Host and Microbe

Volumn 15, Issue 2, 2014, Pages 190-202

  Sheahan, Timothy ^a   Imanaka, Naoko ^a   Marukian, Svetlana ^a,b   Dorner, Marcus ^a   Liu, Peng ^a   Ploss, Alexander ^a   Rice, Charles M ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b HemoShear Therapeutics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON; INTERFERON LAMBDA; TRANSCRIPTOME; UNCLASSIFIED DRUG; ANTIVIRUS AGENT; LAMBDA INTERFERON;

ALLELE; ANTIGEN PRESENTATION; ARTICLE; CONTAMINATION; CONTROLLED STUDY; CULTURE MEDIUM; DNA LIBRARY; GENE INDUCTION; GENETIC VARIABILITY; GENOTYPE; GESTATIONAL AGE; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN CELL; IMMUNE RESPONSE; INNATE IMMUNITY; INTERFERON INDUCTION; KINETICS; LASER CAPTURE MICRODISSECTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN INDUCTION; QUALITY CONTROL; UPREGULATION; VIROLOGY; VIRUS VIRULENCE; DRUG RESPONSE; FETUS; GENE EXPRESSION; GENE LOCUS; GENE ONTOLOGY; HUMAN TISSUE; NUCLEOTIDE SEQUENCE; VIRAL GENETICS; VIRUS CELL INTERACTION; VIRUS IMMUNITY; VIRUS ISOLATION;

HEPATITIS C VIRUS;

ALLELES; CELLS, CULTURED; DISEASE SUSCEPTIBILITY; GENE EXPRESSION PROFILING; HEPACIVIRUS; HEPATITIS C; HEPATOCYTES; HUMANS; IMMUNITY, INNATE; INTERLEUKINS; TRANSCRIPTION, GENETIC;

EID: 84893948746     PISSN: 19313128     EISSN: 19346069     Source Type: Journal    
DOI: 10.1016/j.chom.2014.01.007     Document Type: Article

References (38)

1. H.J. Alter, and T.J. Liang Hepatitis C: the end of the beginning and possibly the beginning of the end Ann. Intern. Med. 156 2012 317 318
2. L. Andrus, S. Marukian, C.T. Jones, M.T. Catanese, T.P. Sheahan, J.W. Schoggins, W.T. Barry, L.B. Dustin, K. Trehan, and A. Ploss et al. Expression of paramyxovirus V proteins promotes replication and spread of hepatitis C virus in cultures of primary human fetal liver cells Hepatology 54 2011 1901 1912
3. S. Bibert, T. Roger, T. Calandra, M. Bochud, A. Cerny, N. Semmo, F.H. Duong, T. Gerlach, R. Malinverni, D. Moradpour Swiss Hepatitis C Cohort Study IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction J. Exp. Med. 210 2013 1109 1116
4. C.B. Bigger, K.M. Brasky, and R.E. Lanford DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection J. Virol. 75 2001 7059 7066
5. C.B. Bigger, B. Guerra, K.M. Brasky, G. Hubbard, M.R. Beard, B.A. Luxon, S.M. Lemon, and R.E. Lanford Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees J. Virol. 78 2004 13779 13792
6. S. Blackham, A. Baillie, F. Al-Hababi, K. Remlinger, S. You, R. Hamatake, and M.J. McGarvey Gene expression profiling indicates the roles of host oxidative stress, apoptosis, lipid metabolism, and intracellular transport genes in the replication of hepatitis C virus J. Virol. 84 2010 5404 5414
7. R.S. Brown Hepatitis C and liver transplantation Nature 436 2005 973 978
8. M.T. Dill, Z. Makowska, F.H. Duong, F. Merkofer, M. Filipowicz, T.F. Baumert, L. Tornillo, L. Terracciano, and M.H. Heim Interferon-γ- stimulated genes, but not USP18, are expressed in livers of patients with acute hepatitis C Gastroenterology 143 2012 777 e1-e6
9. V. Espina, J.D. Wulfkuhle, V.S. Calvert, A. VanMeter, W. Zhou, G. Coukos, D.H. Geho, E.F. Petricoin 3rd, and L.A. Liotta Laser-capture microdissection Nat. Protoc. 1 2006 586 603
10. U. Garaigorta, and F.V. Chisari Hepatitis C virus blocks interferon effector function by inducing protein kinase R phosphorylation Cell Host Microbe 6 2009 513 522
11. D. Ge, J. Fellay, A.J. Thompson, J.S. Simon, K.V. Shianna, T.J. Urban, E.L. Heinzen, P. Qiu, A.H. Bertelsen, and A.J. Muir et al. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance Nature 461 2009 399 401
12. M.H. Heim 25 years of interferon-based treatment of chronic hepatitis C: an epoch coming to an end Nat. Rev. Immunol. 13 2013 535 542
13. S.M. Horner, and M. Gale Jr. Regulation of hepatic innate immunity by hepatitis C virus Nat. Med. 19 2013 879 888
14. N. Jilg, W. Lin, J. Hong, E.A. Schaefer, D. Wolski, J. Meixong, K. Goto, C. Brisac, P. Chusri, and D.N. Fusco et al. Kinetic differences in the induction of interferon stimulated genes by interferon-α and IL28B are altered by Infection with Hepatitis C virus Hepatology 2013 10.1002/hep.26653 Published online August 1, 2013
15. C.T. Jones, M.T. Catanese, L.M. Law, S.R. Khetani, A.J. Syder, A. Ploss, T.S. Oh, J.W. Schoggins, M.R. MacDonald, S.N. Bhatia, and C.M. Rice Real-time imaging of hepatitis C virus infection using a fluorescent cell-based reporter system Nat. Biotechnol. 28 2010 167 171
16. J. Kaiser Biomedical research. NIH to phase out most chimp research Science 341 2013 17 18
17. K. Li, Z. Chen, N. Kato, M. Gale Jr., and S.M. Lemon Distinct poly(I-C) and virus-activated signaling pathways leading to interferon-beta production in hepatocytes J. Biol. Chem. 280 2005 16739 16747
18. Y. Liang, T. Shilagard, S.Y. Xiao, N. Snyder, D. Lau, L. Cicalese, H. Weiss, G. Vargas, and S.M. Lemon Visualizing hepatitis C virus infections in human liver by two-photon microscopy Gastroenterology 137 2009 1448 1458
19. B.D. Lindenbach, M.J. Evans, A.J. Syder, B. Wölk, T.L. Tellinghuisen, C.C. Liu, T. Maruyama, R.O. Hynes, D.R. Burton, J.A. McKeating, and C.M. Rice Complete replication of hepatitis C virus in cell culture Science 309 2005 623 626
20. S. Marukian, C.T. Jones, L. Andrus, M.J. Evans, K.D. Ritola, E.D. Charles, C.M. Rice, and L.B. Dustin Cell culture-produced hepatitis C virus does not infect peripheral blood mononuclear cells Hepatology 48 2008 1843 1850
21. S. Marukian, L. Andrus, T.P. Sheahan, C.T. Jones, E.D. Charles, A. Ploss, C.M. Rice, and L.B. Dustin Hepatitis C virus induces interferon-λ and interferon-stimulated genes in primary liver cultures Hepatology 54 2011 1913 1923
22. P. Metz, E. Dazert, A. Ruggieri, J. Mazur, L. Kaderali, A. Kaul, U. Zeuge, M.P. Windisch, M. Trippler, and V. Lohmann et al. Identification of type I and type II interferon-induced effectors controlling hepatitis C virus replication Hepatology 56 2012 2082 2093
23. S. Naggie, A. Osinusi, A. Katsounas, R. Lempicki, E. Herrmann, A.J. Thompson, P.J. Clark, K. Patel, A.J. Muir, and J.G. McHutchison et al. Dysregulation of innate immunity in hepatitis C virus genotype 1 IL28B-unfavorable genotype patients: impaired viral kinetics and therapeutic response Hepatology 56 2012 444 454
24. M. Noureddin, E.C. Wright, H.J. Alter, S. Clark, E. Thomas, R. Chen, X. Zhao, C. Conry-Cantilena, D.E. Kleiner, T.J. Liang, and M.G. Ghany Association of IL28B genotype with fibrosis progression and clinical outcomes in patients with chronic hepatitis C: A longitudinal analysis Hepatology 58 2013 1548 1557
25. H. Park, E. Serti, O. Eke, B. Muchmore, L. Prokunina-Olsson, S. Capone, A. Folgori, and B. Rehermann IL-29 is the dominant type III interferon produced by hepatocytes during acute hepatitis C virus infection Hepatology 56 2012 2060 2070
26. A. Ploss, S.R. Khetani, C.T. Jones, A.J. Syder, K. Trehan, V.A. Gaysinskaya, K. Mu, K. Ritola, C.M. Rice, and S.N. Bhatia Persistent hepatitis C virus infection in microscale primary human hepatocyte cultures Proc. Natl. Acad. Sci. USA 107 2010 3141 3145
27. L. Prokunina-Olsson, B. Muchmore, W. Tang, R.M. Pfeiffer, H. Park, H. Dickensheets, D. Hergott, P. Porter-Gill, A. Mumy, and I. Kohaar 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. 45 2013 164 171
28. Z. Raglow, C. Thoma-Perry, R. Gilroy, and Y.J. Wan IL28B genotype and the expression of ISGs in normal liver Liver Int. 33 2013 991 998
29. P.C. Sabeti, P. Varilly, B. Fry, J. Lohmueller, E. Hostetter, C. Cotsapas, X. Xie, E.H. Byrne, S.A. McCarroll, R. Gaudet International HapMap Consortium Genome-wide detection and characterization of positive selection in human populations Nature 449 2007 913 918
30. B. Sainz Jr., V. TenCate, and S.L. Uprichard Three-dimensional Huh7 cell culture system for the study of Hepatitis C virus infection Virol. J. 6 2009 103
31. M. Sarasin-Filipowicz, E.J. Oakeley, F.H. Duong, V. Christen, L. Terracciano, W. Filipowicz, and M.H. Heim Interferon signaling and treatment outcome in chronic hepatitis C Proc. Natl. Acad. Sci. USA 105 2008 7034 7039
32. T.D. Schmittgen, and K.J. Livak Analyzing real-time PCR data by the comparative C(T) method Nat. Protoc. 3 2008 1101 1108
33. J.W. Schoggins, S.J. Wilson, M. Panis, M.Y. Murphy, C.T. Jones, P. Bieniasz, and C.M. Rice A diverse range of gene products are effectors of the type I interferon antiviral response Nature 472 2011 481 485
34. A.I. Su, J.P. Pezacki, L. Wodicka, A.D. Brideau, L. Supekova, R. Thimme, S. Wieland, J. Bukh, R.H. Purcell, P.G. Schultz, and F.V. Chisari Genomic analysis of the host response to hepatitis C virus infection Proc. Natl. Acad. Sci. USA 99 2002 15669 15674
35. D.L. Thomas, C.L. Thio, M.P. Martin, Y. Qi, D. Ge, C. O'Huigin, J. Kidd, K. Kidd, S.I. Khakoo, and G. Alexander et al. Genetic variation in IL28B and spontaneous clearance of hepatitis C virus Nature 461 2009 798 801
36. E. Thomas, V.D. Gonzalez, Q. Li, A.A. Modi, W. Chen, M. Noureddin, Y. Rotman, and T.J. Liang HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons Gastroenterology 142 2012 978 988
37. T.J. Urban, A.J. Thompson, S.S. Bradrick, J. Fellay, D. Schuppan, K.D. Cronin, L. Hong, A. McKenzie, K. Patel, and K.V. Shianna et al. IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C Hepatology 52 2010 1888 1896
38. K.A. Walters, A.J. Syder, S.L. Lederer, D.L. Diamond, B. Paeper, C.M. Rice, and M.G. Katze Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes PLoS Pathog. 5 2009 e1000269