Functional annotation of IFN-α-stimulated gene expression profiles from sensitive and resistant renal cell carcinoma cell lines

Journal of Interferon and Cytokine Research

Volumn 26, Issue 8, 2006, Pages 534-547

  Holko, Michelle ^a,b   Williams, Bryan R G ^a,b,c  

^a LERNER RESEARCH INSTITUTE   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA INTERFERON; RECOMBINANT ALPHA2B INTERFERON; STAT1 PROTEIN;

ANTIVIRAL ACTIVITY; APOPTOSIS; ARTICLE; CANCER CELL CULTURE; CANCER RESISTANCE; CARCINOMA CELL; CLUSTER ANALYSIS; CONTROLLED STUDY; DRUG RESPONSE; ENZYME ACTIVATION; GENE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE INDUCTION; HUMAN; HUMAN CELL; KIDNEY CARCINOMA; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ANTINEOPLASTIC AGENTS; ANTIVIRAL AGENTS; APOPTOSIS; CARCINOMA, RENAL CELL; CELL LINE, TUMOR; CELL PROLIFERATION; DRUG RESISTANCE, NEOPLASM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; INTERFERON-ALPHA; KIDNEY NEOPLASMS; KINETICS; STAT TRANSCRIPTION FACTORS; TRANS-ACTIVATION (GENETICS);

EID: 33747881700     PISSN: 10799907     EISSN: None     Source Type: Journal    
DOI: 10.1089/jir.2006.26.534     Document Type: Article

References (64)

1. Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD. How cells respond to interferons. Annu. Rev. Biochem. 1998;67:227-264.
2. Haque SJ, Williams BR. Signal transduction in the interferon system. Semin. Oncol. 1998;25(Suppl 1):14-22.
3. Goh KC, Haque SJ, Williams BR. p38 MAP kinase is required for Stat1 serine phosphorylation and transcriptional activation induced by interferons. EMBO J. 1999;18:5601-5608.
4. Li Y, Sassano A, Majchrzak B, Deb DK, Levy DE, Gaestel M, Nebreda AR, Fish EN, Platanias LC. Role of p38alpha MAP kinase in type I interferon signaling. J. Biol. Chem. 2004;279:970-979.
5. Du Z, Shen Y, Yang W, Mecklenbrauker I, Neel BG, Ivashkiv LB. Inhibition of IFN-alpha signaling by a PKC- and protein tyrosine phosphatase SHP-2-dependent pathway. Proc. Natl. Acad. Sci. USA 2005;102:10267-10272.
6. Luxon BA, Grace M, Brassard D, Bordens R. Pegylated interferons for the treatment of chronic hepatitis C infection. Clin. Ther. 2002;24:1363-1383.
7. Guilhot F, Roy L, Guilnot J, Millot F. Interferon therapy in chronic myelogenous leukemia. Hematol. Oncol. Clin. North Am. 2004;18:585-603.
8. Huland E, Heinzer H. Renal cell carcinoma: novel treatments for advanced disease. Curr. Opin. Urol. 2003;13:451-456.
9. Sabel MS, Sondak VK. Pros and cons of adjuvant interferon in the treatment of melanoma. Oncologist 2003;8:451-458.
10. Rieckmann P, Toyka KV, Bassetti C, Beer K, Beer S, Buettner U, Chofflon M, Gotschi-Fuchs M, Hess K, Kappos L, Kesselring J, Goebels N, Ludin HP, Mattle H, Schluep M, Vaney C, Baumhackl U, Berger T, Deisenhammer F, Fazekas F, Freimuller M, Kollegger H, Kristoferitsch W, Lassmann H, Markut H, Strasser-Fuchs S, Vass K, Altenkirch H, Bamborschke S, Baum K, Benecke R, Bruck W, Dommasch D, Elias WG, Gass A, Gehlen W, Haas J, Haferkamp G, Hanefeld F, Hartung HP, Heesen C, Heidenreich F, Heitmann R, Hemmer B, Hense T, Hohlfeld R, Janzen RW, Japp G, Jung S, Jugelt E, Koehler J, Kolmel W, Konig N, Lowitzsch K, Manegold U, Melms A, Merlin J, Oschmann P, Petereit HF, Pette M, Pohlau D, Pohl D, Poser S, Sailer M, Schmidt S, Schock G, Schulz M, Schwarz S, Seidel D, Sommer N, Stangel M, Stark E, Steinbrecher A, Tumani H, Voltz R, Weber F, Weinrich W, Weissert R, Wiendl H, Wietholter H, Wildemann U, Zettl UK, Zipp F, Zschenderlein R, Izquierdo G, Kirjazovas A, Packauskas L, Miller D, Koncan Vracko B, Millers A, Orologas A, Panellus M, Sindic CJ, Bratic M, Svraka A, Vella NR, Stelmasiak Z, Selmaj K, Bartosik-Psujik H, Mitosek-Szewczyk K, Belniak E, Mochecka A, Bayas A, Chan A, Flachenecker P, Gold R, Kallmann B, Leussink V, Maurer M, Ruprecht K, Stoll G. Escalating immunotherapy of multiple sclerosis-new aspects and practical application. J. Neurol. 2004;251:1329-1339.
11. Kim KH, Yavel RM, Gross VL, Brody N. Intralesional interferon alpha-2b in the treatment of basal cell carcinoma and squamous cell carcinoma: revisited. Dermatol. Surg. 2004;30:116-120.
12. Burchert A, Neubauer A. Interferon alpha and T-cell responses in chronic myeloid leukemia. Leuk. Lymphoma 2005;46:167-175.
13. Mickisch GH. Chemoresistance of renal cell carcinoma: 1986-1994. World J. Urol. 1994;12:214-223.
14. Glaspy JA. Therapeutic options in the management of renal cell carcinoma. Semin. Oncol. 2002;29(Suppl 7):41-46.
15. Motzer RJ, Russo P, Nanus DM, Berg WJ. Renal cell carcinoma. Curr. Probl. Cancer 1997;21:185-232.
16. Yasumura S, Lin WC Weidmann E, Hebda P, Whiteside TL. Expression of interleukin 2 receptors on human carcinoma cell lines and tumor growth inhibition by interleukin 2. Int. J. Cancer 1994;59:225-234.
17. Thiounn N, Mathiot C, Dorval T, Flam TA, Tartour E, Mosseri V, Zerbib M, Fridman WH, Debre B. Lack of efficacy of low-dose subcutaneous recombinant interleukin-2 and interferon-alpha in the treatment of metastatic renal cell carcinoma. Br. J. Urol. 1995;75:586-589.
18. Atkins MB, Regan M, McDermott D. Update on the role of interleukin 2 and other cytokines in the treatment of patients with stage IV renal carcinoma. Clin. Cancer Res. 2004;10:63425-63465.
19. Atzpodien J, Schmitt E, Gertenbach U, Fornara P, Heynemann H, Maskow A, Ecke M, Woltjen HH, Jentsch H, Wieland W, Wandert T, Reitz M. Adjuvant treatment with interleukin-2- and interferon-alpha2a-based chemoimmunotherapy in renal cell carcinoma post tumour nephrectomy: results of a prospectively randomised trial of the German Cooperative Renal Carcinoma Chemoimmunotherapy Group (DGCIN). Br. J. Cancer 2005;92:843-846.
20. Mancuso A, Sternberg CN. New treatments for metastatic kidney cancer. Can. J. Urol. 2005;12(Suppl 1):66-70.
21. Virtanen I, Lehto VP. Progression of malignancy in clear cell renal cell carcinomas. Scand. J. Surg. 2004;93:112-117.
22. de Veer MJ, Holko M, Frevel M, Walker E, Der S, Paranjape JM, Silverman RH, Williams BRG. Functional classification of interferon-stimulated genes identified using microarrays. J. Leukoc. Biol. 2001;69:912-920.
23. Bromberg JF, Horvath CM, Wen Z, Schreiber RD, Darnell JE Jr. Transcriptionally active Stat1 is required for the antiproliferative effects of both interferon alpha and interferon gamma. Proc. Natl. Acad. Sci. USA 1996;93:7673-7678.
24. Dupuis S, Jouanguy E, Al-Hajjar S, Fieschi C, Al Mohsen IZ, Al Jumaah S, Yang K, Chapgier A, Eidenschenk C, Eid P, Al Ghonaium A, Tufenkeji H, Frayha H, Al Gazlan S, Al Rayes H, Schreiber RD, Gresser I, Casanova JL. Impaired response to interferon-alpha/beta and lethal viral disease in human Stat1 deficiency. Nat. Genet. 2003;33:388-391.
25. Brinckmann A, Axer S, Jakschies D, Dallmann I, Grosse J, Patzelt T, Bernier T, Emmendoerffer A, Atzpodien J. Interferon-alpha resistance in renal carcinoma cells is associated with defective induction of signal transducer and activator of transcription 1, which can be restored by a supernatant of phorbol 12-myristate 13-acetate stimulated peripheral blood mononuclear cells. Br. J. Cancer 2002;86:449-455.
26. Sturzebecher S, Wandinger KP, Rosenwald A, Sathyamoorthy M, Tzou A, Mattar P, Frank JA, Staudt L, Martin R, McFarland HF. Expression profiling identifies responder and non-responder phenotypes to interferon-beta in multiple sclerosis. Brain 2003;126:1419-1429.
27. Wittnebel S, Jalil A, Thiery J, DaRocha S, Viey E, Escudier B, Chouaib S, Caignard A. The sensitivity of renal cell carcinoma cells to interferon alpha correlates with p53-induction and involves Bax. Eur. Cytokine Netw. 2005;16:123-127.
28. Khabar KS, Al-Haj L, Al-Zoghaibi F, Marie M, Dhalla M, Polyak SJ, Williams BR. Expressed gene clusters associated with cellular sensitivity and resistance towards anti-viral and anti-proliferative actions of interferon. J. Mol. Biol. 2004;342:833-846.
29. Campbell CE, Kuriyan NP, Rackley RR, Caulfield MJ, Tubbs R, Finke J, Williams BR. Constitutive expression of the Wilms tumor suppressor gene (WT1) in renal cell carcinoma. Int. J. Cancer 1998;78:182-188.
30. Der SD, Zhou A, Williams BR, Silverman RH. Identification of genes differentially regulated by interferon alpha, beta, or gamma using oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 1998;95:15623-15628.
31. Frevel MA, Bakheet T, Silva AM, Hissong JG, Khabar KS, Williams BR. p38 mitogen-activated protein kinase-dependent and -independent signaling of mRNA stability of AU-rich element-containing transcripts. Mol. Cell. Biol. 2003;23:425-436.
32. Sledz CA, Williams BR. RNA interference and double-stranded-RNA-activated pathways. Biochem. Soc. Trans. 2004;32:952-956.
33. Dennis G Jr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4:P3.
34. Shindo M, Okuno T. Genomic variations in precore and cytotoxic T lymphocyte regions in chronic hepatitis B in relationship to interferon responsiveness. Liver 2000;20:136-142.
35. Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG. Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J. Virol. 2003;77:6367-6375.
36. Gouilleux-Gruart V, Gouilleux F, Desaint C, Claisse JF, Capiod JC, Delobel J, Weber-Nordt R, Dusanter-Fourt I, Dreyfus F, Groner B, Prin L. Stat-related transcription factors are constitutively activated in peripheral blood cells from acute leukemia patients. Blood 1996;87:1692-1697.
37. Basturk B, Yavascaoglu I, Vuruskan H, Goral G, Oktay B, Oral HB. Cytokine gene polymorphisms as potential risk and protective factors in renal cell carcinoma. Cytokine 2005;30:41-45.
38. Zhu H, Nelson DR, Crawford JM, Liu C. Defective Jak-Stat activation in hepatoma cells is associated with hepatitis C viral IFN-αresistance. J. Interferon Cytokine Res. 2005;25:528-539.
39. Wong YF, Selvanayagam ZE, Wei N, Porter J, Vittal R, Hu R, Lin Y, Liao J, Shih JW, Cheung TH, Lo KW, Yim SF, Yip SK, Ngong DT, Siu N, Chan LK, Chan CS, Kong T, Kutlina E, McKinnon RD, Denhardt DT, Chin KV, Chung TK. Expression genomics of cervical cancer: molecular classification and prediction of radiotherapy response by DNA microarray. Clin. Cancer Res. 2003;9:5486-5492.
40. Talpaz M, Chernajovsky Y, Troutman-Worden K, Wetzler M, Kantarjian H, Gutterman JU, Kurzrock R. Interferon-stimulated genes in interferon-sensitive and -resistant chronic myelogenous leukemia patients. Cancer Res. 1992;52:1087-1090.
41. Naito M, Matsui A, Inao M, Nagoshi S, Nagano M, Ho N, Egashira T, Hashimoto M, Mishiro S, Mochida S, Fujiwara K. SNPs in the promoter region of the osteopontin gene as a marker predicting the efficacy of interferon-based therapies in patients with chronic hepatitis C. J. Gastroenterol. 2005;40:381-388.
42. Dandoy F, De Maeyer-Guignard J, Bailey D, De Maeyer E. Mouse genes influence antiviral action of interferon in vivo. Infect. Immun. 1982;38:89-93.
43. Ohno R, Nakamura Y. Prediction of response to imatinib by cDNA microarray analysis. Semin. Hematol 2003;40(Suppl 2):42-49.
44. Bosinger SE, Hosiawa KA, Cameron MJ, Persad D, Ran L, Xu L, Boulassel MR, Parenteau M, Fournier J, Rud EW, Kelvin DJ. Gene expression profiling of host response in models of acute HIV infection. J. Immunol. 2004;173:6858-6863.
45. Takata R, Katagiri T, Kanehira M, Tsunoda T, Shuin T, Miki T, Namiki M, Kohri K, Matsushita Y, Fujioka T, Nakamura Y. Predicting response to methotrexate, vinblastine, doxorubicin, and cisplatin neoadjuvant chemotherapy for bladder cancers through genome-wide gene expression profiling. Clin. Cancer Res. 2005;11:2625-2636.
46. Modlich O, Prisack HB, Munnes M, Audretsch W, Bojar H. Predictors of primary breast cancers responsiveness to preoperative epirubicin/ cyclophosphamide-based chemotherapy: translation of microarray data into clinically useful predictive signatures. J. Transl. Med. 2005;3:32-49.
47. Sherlock G. Analysis of large-scale gene expression data. Curr. Opin. Immunol. 2000;12:201-205.
48. Sakao E, Ishihara A, Horikawa K, Akiyama M, Arai M, Kato M, Seki N, Fukunaga K, Shimizu-Yabe A, Iwase K, Ohtsuka S, Sato T, Kohno Y, Shibata S, Takiguchi M. Two-peaked synchronization in day/night expression rhythms of the fibrinogen gene cluster in the mouse liver. J. Biol. Chem. 2003;278:30450-30457.
49. Klevecz RR, Bolen J, Forrest G, Murray DB. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl. Acad. Sci. USA 2004;101:1200-1205.
50. Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biol. 2001;2:RESEARCH0055.
51. Naef F, Hacker CR, Patil N, Magnasco M. Characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol. 2002;3:PREPRINT0001.
52. Dozmorov I, Knowlton N. Tang Y, Centola M. Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. BMC BioEnformatics 2004;5:53-61.
53. Carter DE, Robinson JF, Allister EM, Huff MW, Hegele RA. Quality assessment of microarray experiments. Clin. Biochem. 2005;38:639-642.
54. Pfeffer LM, Wang C, Constantinescu SN, Croze E, Blatt LM, Albino AP, Nanus DM. Human renal cancers resistant to IFN's antiproliferative action exhibit sensitivity to IFN's gene-inducing and antiviral actions. J. Urol. 1996;156:1867-1871.
55. Piekarz RL, Robey R, Sandor V, Bakke S, Wilson WH, Dahmoush L, Kingma DM, Turner ML, Altemus R, Bates SE. Inhibitor of histone deacetylation, depsipeptide (FR901228), in the treatment of peripheral and cutaneous T-cell lymphoma: a case report. Blood 2001;98:2865-2868.
56. Sandor V, Bakke S, Robey RW, Kang MH, Blagosklonny MV, Bender J, Brooks R, Piekarz RL, Tucker E, Figg WD, Chan KK, Goldspiel B, Fojo AT, Balcerzak SP, Bates SE. Phase I trial of the histone deacetylase inhibitor, depsipeptide (FR901228, NSC 630176), in patients with refractory neoplasms. Clin. Cancer Res. 2002;8:718-728.
57. Vigushin DM, Coombes RC. Histone deacetylase inhibitors in cancer treatment. Anticancer Drugs 2002;13:1-13.
58. La Thangue NB. Histone deacetylase inhibitors and cancer therapy. J. Chemother. 2004;16(Suppl 4):64-67.
59. Byrd JC, Marcucci G, Parthun MR, Xiao JJ, Klisovic RB, Moran M, Lin TS, Liu S, Sklenar AR, Davis ME, Lucas DM, Fischer B, Shank R, Tejaswi SL, Binkley P, Wright J, Chan KK, Grever MR. A phase I and pharmacodynamic study of depsipeptide (FK228) in chronic lymphocytic leukemia and acule myeloid leukemia. Blood 2005;105:959-967.
60. Chinnaiyan P, Vallabhaneni G, Armstrong E, Huang SM, Harari PM. Modulation of radiation response by histone deacetylase inhibition. Int. J. Radiat. Oncol. Biol. Phys. 2005;62:223-229.
61. Kelly WK, O'Connor OA, Krug LM, Chiao JH, Heaney M, Curley T, MacGregore-Cortelli B, Tong W, Secrist JP, Schwartz L, Richardson S, Chu E, Olgac S, Marks PA, Scher H, Richon VM. Phase I study of an oral histone deacetylase inhibitor, suberoylanilide hydroxamic acid, in patients with advanced cancer. J. Clin. Oncol. 2005;23:3923-3931.
62. Ryan QC, Headlee D, Acharya M, Sparreboom A, Trepel JB, Ye J, Figg WD, Hwang K, Chung EJ, Murgo A, Melillo G, Elsayed Y, Monga M, Kalnitskiy M, Zwiebel J, Sausville EA. Phase I and pharmacokinetic study of MS-275, a histone deacetylase inhibitor, in patients with advanced and refractory solid tumors or lymphoma. J. Clin. Oncol. 2005;23:3912-3922.
63. Nusinzon I, Horvath CM. Interferon-stimulated transcription and innate antiviral immunity require deacetylase activity and histone deacetylase 1. Proc. Natl. Acad. Sci. USA 2003;100:14742-14747.
64. Chang HM, Paulson M. Holko M, Rice CM, Williams BR, Marie I, Levy DE. Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity. Proc. Natl. Acad. Sci. USA 2004;101:9578-9583.