Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression

Hepatology

Volumn 59, Issue 4, 2014, Pages 1262-1272

  Bolen, Christopher R ^a   Ding, Siyuan ^b   Robek, Michael D ^b   Kleinstein, Steven H ^a,b  

^a YALE UNIVERSITY   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA INTERFERON; BETA INTERFERON; GAMMA INTERFERON INDUCIBLE PROTEIN 10; INTERFERON; INTERFERON REGULATORY FACTOR; INTERFERON REGULATORY FACTOR 1; INTERFERON REGULATORY FACTOR 2; INTERFERON REGULATORY FACTOR 6; INTERFERON REGULATORY FACTOR 7; INTERFERON REGULATORY FACTOR 9; INTERLEUKIN 28A; INTERLEUKIN 29; LAMBDA 3 INTERFERON; STAT1 PROTEIN; TUMOR NECROSIS FACTOR RELATED APOPTOSIS INDUCING LIGAND; UNCLASSIFIED DRUG;

ANTIVIRAL ACTIVITY; ANTIVIRAL THERAPY; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEEDBACK SYSTEM; GENE EXPRESSION; GENE EXPRESSION PROFILING; HEPATOMA CELL; HUMAN; HUMAN CELL; IMMUNE RESPONSE; IN VITRO STUDY; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; UPREGULATION;

CELL LINE, TUMOR; FEEDBACK; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HEPATOCYTES; HUMANS; INTERFERON TYPE I; INTERLEUKINS; PHOSPHORYLATION; STAT1 TRANSCRIPTION FACTOR; TIME FACTORS;

EID: 84896493961     PISSN: 02709139     EISSN: 15273350     Source Type: Journal    
DOI: 10.1002/hep.26657     Document Type: Article

References (33)

1. Sheppard P, Kindsvogel W, Xu W, Henderson K, Schlutsmeyer S, Whitmore TE, et al. IL-28, IL-29 and their class II cytokine receptor IL-28R. Nat Immunol 2003;4:63-68.
2. Kotenko SV, Gallagher G, Baurin VV, Lewis-Antes A, Shen M, Shah NK, et al. IFN-lambdas mediate antiviral protection through a distinct class II cytokine receptor complex. Nat Immunol 2003;4:69-77.
3. Doyle SE, Schreckhise H, Khuu-Duong K, Henderson K, Rosler R, Storey H, et al. Interleukin-29 uses a type 1 interferon-like program to promote antiviral responses in human hepatocytes. Hepatology 2006;44:896-906.
4. Meager A, Visvalingam K, Dilger P, Bryan D, Wadhwa M. Biological activity of interleukins-28 and -29: comparison with type I interferons. Cytokine 2005;31:109-118.
5. Ank N, West H, Bartholdy C, Eriksson K, Thomsen AR, Paludan SR. Lambda Interferon (IFN-λ), a type III IFN, is induced by viruses and IFNs and displays potent antiviral activity against select virus infections in vivo. J Virol 2006;80:4501-4509.
6. Pagliaccetti NE, Chu EN, Bolen CR, Kleinstein SH, Robek MD. Lambda and alpha interferons inhibit hepatitis B virus replication through a common molecular mechanism but with different in vivo activities. Virology 2010;401:197-206.
7. Marcello T, Grakoui A, Barba-Spaeth G, Machlin ES, Kotenko SV, Macdonald MR, et al. Interferons α and λ inhibit hepatitis C virus replication with distinct signal transduction and gene regulation kinetics. Gastroenterology 2006;131:1887-1898.
8. Marijanovic Z, Ragimbeau J, van der Heyden J, Uzé G, Pellegrini S. Comparable potency of IFNα2 and IFNβ on immediate JAK/STAT activation but differential down-regulation of IFNAR2. Biochem J 2007;407:141.
9. Uzé G, Schreiber G, Piehler J, Pellegrini S. The receptor of the type I interferon family. Curr Top Microbiol Immunol 2007;316:71-95.
10. 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;446:509-516.
11. Malakhova OA, Kim KI, Luo J-K, Zou W, Kumar KGS, Fuchs SY, et al. UBP43 is a novel regulator of interferon signaling independent of its ISG15 isopeptidase activity. EMBO J 2006;25:2358-2367.
12. Chen L, Borozan I, Feld J, Sun J, Tannis L-L, Coltescu C, et al. Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection. Gastroenterology 2005;128:1437-1444.
13. Dellgren C, Gad HH, Hamming OJ, Melchjorsen J, Hartmann R. Human interferon-[lambda]3 is a potent member of the type III interferon family. Genes Immun 2008;10:125-131.
14. Kim K, Kim KH, Kim HY, Cho HK, Sakamoto N, Cheong J. Curcumin inhibits hepatitis C virus replication via suppressing the Akt-SREBP-1 pathway. FEBS Lett 2010;584:707-712.
15. Schulze-Bergkamen H, Fleischer B, Schuchmann M, Weber A, Weinmann A, Krammer PH, et al. Suppression of Mcl-1 via RNA interference sensitizes human hepatocellular carcinoma cells towards apoptosis induction. BMC Cancer 2006;6:232.
16. Hung J-H, Lu Y-S, Wang Y-C, Ma Y-H, Wang D-S, Kulp SK, et al. FTY720 induces apoptosis in hepatocellular carcinoma cells through activation of protein kinase C delta signaling. Cancer Res 2008;68:1204-1212.
17. Dunning MJ, Smith ML, Ritchie ME, Tavaré S. Beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007;23:2183-2184.
18. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology [Internet]. 2004 [cited 2010 Oct 21];3. Available from: http://www.bepress.com/sagmb/vol3/iss1/art3.
19. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 1995;57:289-300.
20. Protzer U, Maini MK, Knolle PA. Living in the liver: hepatic infections. Nat Rev Immunol 2012;12:201-213.
21. Rehermann B, Nascimbeni M. Immunology of hepatitis B virus and hepatitis C virus infection. Nat Rev Immunol 2005;5:215-229.
22. Pagliaccetti NE, Eduardo R, Kleinstein SH, Mu XJ, Bandi P, Robek MD. Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. J Biol Chem 2008;283:30079-30089.
23. Chawla-Sarkar M, Leaman DW, Borden EC. Preferential induction of apoptosis by interferon (IFN)-beta compared with IFN-alpha2: correlation with TRAIL/Apo2L induction in melanoma cell lines. Clin Cancer Res 2001;7:1821-1831.
24. Leaman DW, Chawla-Sarkar M, Jacobs B, Vyas K, Sun Y, Ozdemir A, et al. Novel growth and death related interferon-stimulated genes (ISGs) in melanoma: greater potency of IFN-beta compared with IFN-alpha2. J Interferon Cytokine Res 2003;23:745-756.
25. Shen H, Zhang M, Minuk GY, Gong Y. Different effects of rat interferon alpha, beta and gamma on rat hepatic stellate cell proliferation and activation. BMC Cell Biol 2002;3:9.
26. Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, Bieniasz P, et al. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 2011;472:481-485.
27. Schmid S, Mordstein M, Kochs G, García-Sastre A, Tenoever BR. Transcription factor redundancy ensures induction of the antiviral state. J Biol Chem 2010;285:42013-42022.
28. Wen Z, Zhong Z, Darnell JE Jr. Maximal activation of transcription by Stat1 and Stat3 requires both tyrosine and serine phosphorylation. Cell 1995;82:241-250.
29. Kohli A, Zhang X, Yang J, Russell RS, Donnelly RP, Sheikh F, et al. Distinct and overlapping genomic profiles and antiviral effects of Interferon-λ and -α on HCV-infected and noninfected hepatoma cells. J Viral Hepat 2012;19:843-853.
30. Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, et al. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009;461:399-401.
31. Suppiah V, Moldovan M, Ahlenstiel G, Berg T, Weltman M, Abate ML, et al. IL28B is associated with response to chronic hepatitis C interferon-[alpha] and ribavirin therapy. Nat Genet 2009;41:1100-1104.
32. Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K, Sakamoto N, et al. Genome-wide association of IL28B with response to pegylated interferon-[alpha] and ribavirin therapy for chronic hepatitis C. Nat Genet 2009;41:1105-1109.
33. Uddin S, Sassano A, Deb DK, Verma A, Majchrzak B, Rahman A, et al. Protein kinase C-delta (PKC-delta) is activated by type I interferons and mediates phosphorylation of Stat1 on serine 727. J Biol Chem 2002;277:14408-14416.