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Volumn 9, Issue 10, 2014, Pages

Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; INTERFERON; OSTEOCLAST DIFFERENTIATION FACTOR;

EID: 84907994039     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0109760     Document Type: Article
Times cited : (143)

References (40)
  • 1
    • 84890814629 scopus 로고    scopus 로고
    • Cancer Immunotherapy
    • Couzin-Frankel J (2013) Cancer Immunotherapy. Science 342: 1432-1433. doi:10.1126/science.342.6165.1432.
    • (2013) Science , vol.342 , pp. 1432-1433
    • Couzin-Frankel, J.1
  • 2
    • 84880706152 scopus 로고    scopus 로고
    • Oncology meets immunology: The cancer-immunity cycle
    • Chen DS, Mellman I (2013) Oncology meets immunology: the cancer-immunity cycle. Immunity 39: 1-10. doi:10.1016/j.immuni.2013.07.012.
    • (2013) Immunity , vol.39 , pp. 1-10
    • Chen, D.S.1    Mellman, I.2
  • 3
    • 84884870085 scopus 로고    scopus 로고
    • Use of ipilimumab in the treatment of melanoma
    • Acharya UH, Jeter JM (2013) Use of ipilimumab in the treatment of melanoma. Clin Pharmacol Adv Appl 5: 21-27. doi:10.2147/CPAA.S45884.
    • (2013) Clin Pharmacol Adv Appl , vol.5 , pp. 21-27
    • Acharya, U.H.1    Jeter, J.M.2
  • 4
    • 82155168544 scopus 로고    scopus 로고
    • A prospective phase II trial exploring the association between tumor microenvironment biomarkers and clinical activity of ipilimumab in advanced melanoma
    • Hamid O, Schmidt H, Nissan A, Ridolfi L, Aamdal S, et al. (2011) A prospective phase II trial exploring the association between tumor microenvironment biomarkers and clinical activity of ipilimumab in advanced melanoma. J Transl Med 9: 204. doi:10.1186/1479-5876-9-204.
    • (2011) J Transl Med , vol.9 , pp. 204
    • Hamid, O.1    Schmidt, H.2    Nissan, A.3    Ridolfi, L.4    Aamdal, S.5
  • 5
    • 84880704621 scopus 로고    scopus 로고
    • The continuum of cancer immunosurveillance: Prognostic, predictive, and mechanistic signatures
    • Galon J, Angell HK, Bedognetti D, Marincola FM (2013) The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. Immunity 39: 11-26. doi:10.1016/j.immuni.2013.07.008.
    • (2013) Immunity , vol.39 , pp. 11-26
    • Galon, J.1    Angell, H.K.2    Bedognetti, D.3    Marincola, F.M.4
  • 8
    • 46749152178 scopus 로고    scopus 로고
    • A modular analysis framework for blood genomics studies: Application to systemic lupus erythematosus
    • Chaussabel D, Quinn C, Shen J, Patel P, Glaser C, et al. (2008) A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29: 150-164. doi:10.1016/j.immuni.2008.05.012.
    • (2008) Immunity , vol.29 , pp. 150-164
    • Chaussabel, D.1    Quinn, C.2    Shen, J.3    Patel, P.4    Glaser, C.5
  • 9
    • 78651486442 scopus 로고    scopus 로고
    • Densely interconnected transcriptional circuits control cell states in human hematopoiesis
    • Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, et al. (2011) Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144: 296-309. doi:10.1016/j.cell.2011.01.004.
    • (2011) Cell , vol.144 , pp. 296-309
    • Novershtern, N.1    Subramanian, A.2    Lawton, L.N.3    Mak, R.H.4    Haining, W.N.5
  • 10
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323. doi:10.1186/1471-2105-12-323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 11
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
    • Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41: D808-815. doi:10.1093/nar/gks1094.
    • (2013) Nucleic Acids Res , vol.41 , pp. D808-D815
    • Franceschini, A.1    Szklarczyk, D.2    Frankild, S.3    Kuhn, M.4    Simonovic, M.5
  • 12
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504. doi:10.1101/gr.1239303.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5
  • 13
    • 84855199947 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing. Vienna, Austria. Available
    • R Core Team (2013) A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. Available: http://www.R-project.org/.
    • (2013) A Language and Environment for Statistical Computing
  • 15
    • 37249026668 scopus 로고    scopus 로고
    • Reshaping Data with the reshape Package
    • Wickham H (2007) Reshaping Data with the reshape Package. J Stat Softw 21: 1-20.
    • (2007) J Stat Softw , vol.21 , pp. 1-20
    • Wickham, H.1
  • 20
    • 84859371920 scopus 로고    scopus 로고
    • Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections
    • Banchereau R, Jordan-Villegas A, Ardura M, Mejias A, Baldwin N, et al. (2012) Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections. PloS One 7: e34390. doi:10.1371/journal.pone.0034390.
    • (2012) PloS One , vol.7 , pp. e34390
    • Banchereau, R.1    Jordan-Villegas, A.2    Ardura, M.3    Mejias, A.4    Baldwin, N.5
  • 21
    • 77951923670 scopus 로고    scopus 로고
    • Vitiligo is an independent favourable prognostic factor in stage III and IV metastatic melanoma patients: Results from a single-institution hospital-based observational cohort study
    • Quaglino P, Marenco F, Osella-Abate S, Cappello N, Ortoncelli M, et al. (2010) Vitiligo is an independent favourable prognostic factor in stage III and IV metastatic melanoma patients: results from a single-institution hospital-based observational cohort study. Ann Oncol Off J Eur Soc Med Oncol ESMO 21: 409-414. doi:10.1093/annonc/mdp325.
    • (2010) Ann Oncol off J Eur Soc Med Oncol ESMO , vol.21 , pp. 409-414
    • Quaglino, P.1    Marenco, F.2    Osella-Abate, S.3    Cappello, N.4    Ortoncelli, M.5
  • 22
    • 32644454916 scopus 로고    scopus 로고
    • Prognostic significance of autoimmunity during treatment of melanoma with interferon
    • Gogas H, Ioannovich J, Dafni U, Stavropoulou-Giokas C, Frangia K, et al. (2006) Prognostic significance of autoimmunity during treatment of melanoma with interferon. N Engl J Med 354: 709-718. doi:10.1056/NEJMoa053007.
    • (2006) N Engl J Med , vol.354 , pp. 709-718
    • Gogas, H.1    Ioannovich, J.2    Dafni, U.3    Stavropoulou-Giokas, C.4    Frangia, K.5
  • 23
    • 84874235143 scopus 로고    scopus 로고
    • Conservation and divergence in the transcriptional programs of the human and mouse immune systems
    • Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, et al. (2013) Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A 110: 2946-2951. doi:10.1073/pnas.1222738110.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 2946-2951
    • Shay, T.1    Jojic, V.2    Zuk, O.3    Rothamel, K.4    Puyraimond-Zemmour, D.5
  • 24
    • 77954234849 scopus 로고    scopus 로고
    • Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome
    • Jönsson G, Busch C, Knappskog S, Geisler J, Miletic H, et al. (2010) Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome. Clin Cancer Res Off J Am Assoc Cancer Res 16: 3356-3367. doi:10.1158/1078-0432.CCR-09-2509.
    • (2010) Clin Cancer Res off J Am Assoc Cancer Res , vol.16 , pp. 3356-3367
    • Jönsson, G.1    Busch, C.2    Knappskog, S.3    Geisler, J.4    Miletic, H.5
  • 25
    • 84862769116 scopus 로고    scopus 로고
    • An immuneactive tumor microenvironment favors clinical response to ipilimumab
    • Ji R-R, Chasalow SD, Wang L, Hamid O, Schmidt H, et al. (2012) An immuneactive tumor microenvironment favors clinical response to ipilimumab. Cancer Immunol Immunother CII 61: 1019-1031. doi:10.1007/s00262-011-1172-6.
    • (2012) Cancer Immunol Immunother CII , vol.61 , pp. 1019-1031
    • Ji, R.-R.1    Chasalow, S.D.2    Wang, L.3    Hamid, O.4    Schmidt, H.5
  • 26
    • 84872595484 scopus 로고    scopus 로고
    • BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in patients with stage III melanoma
    • Mann GJ, Pupo GM, Campain AE, Carter CD, Schramm S-J, et al. (2013) BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in patients with stage III melanoma. J Invest Dermatol 133: 509-517. doi:10.1038/jid.2012.283.
    • (2013) J Invest Dermatol , vol.133 , pp. 509-517
    • Mann, G.J.1    Pupo, G.M.2    Campain, A.E.3    Carter, C.D.4    Schramm, S.-J.5
  • 28
    • 84873111794 scopus 로고    scopus 로고
    • Type I interferon response and innate immune sensing of cancer
    • Fuertes MB, Woo S-R, Burnett B, Fu Y-X, Gajewski TF (2013) Type I interferon response and innate immune sensing of cancer. Trends Immunol 34: 67-73. doi:10.1016/j.it.2012.10.004.
    • (2013) Trends Immunol , vol.34 , pp. 67-73
    • Fuertes, M.B.1    Woo, S.-R.2    Burnett, B.3    Fu, Y.-X.4    Gajewski, T.F.5
  • 29
    • 22144465860 scopus 로고    scopus 로고
    • A critical function for type I interferons in cancer immunoediting
    • Dunn GP, Bruce AT, Sheehan KCF, Shankaran V, Uppaluri R, et al. (2005) A critical function for type I interferons in cancer immunoediting. Nat Immunol 6: 722-729. doi:10.1038/ni1213.
    • (2005) Nat Immunol , vol.6 , pp. 722-729
    • Dunn, G.P.1    Bruce, A.T.2    Sheehan, K.C.F.3    Shankaran, V.4    Uppaluri, R.5
  • 30
    • 68149179663 scopus 로고    scopus 로고
    • Genome-wide association study identifies three loci associated with melanoma risk
    • Bishop DT, Demenais F, Iles MM, Harland M, Taylor JC, et al. (2009) Genome-wide association study identifies three loci associated with melanoma risk. Nat Genet 41: 920-925. doi:10.1038/ng.411.
    • (2009) Nat Genet , vol.41 , pp. 920-925
    • Bishop, D.T.1    Demenais, F.2    Iles, M.M.3    Harland, M.4    Taylor, J.C.5
  • 31
    • 80051959840 scopus 로고    scopus 로고
    • Comprehensive field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma
    • Chatzinasiou F, Lill CM, Kypreou K, Stefanaki I, Nicolaou V, et al. (2011) Comprehensive field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma. J Natl Cancer Inst 103: 1227-1235. doi:10.1093/jnci/djr219.
    • (2011) J Natl Cancer Inst , vol.103 , pp. 1227-1235
    • Chatzinasiou, F.1    Lill, C.M.2    Kypreou, K.3    Stefanaki, I.4    Nicolaou, V.5
  • 32
    • 68149100807 scopus 로고    scopus 로고
    • Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi
    • Falchi M, Bataille V, Hayward NK, Duffy DL, Bishop JAN, et al. (2009) Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. Nat Genet 41: 915-919. doi:10.1038/ng.410.
    • (2009) Nat Genet , vol.41 , pp. 915-919
    • Falchi, M.1    Bataille, V.2    Hayward, N.K.3    Duffy, D.L.4    Bishop, J.A.N.5
  • 33
    • 84870284054 scopus 로고    scopus 로고
    • Influence of genetic variants in type I interferon genes on melanoma survival and therapy
    • Lenci RE, Bevier M, Brandt A, Bermejo JL, Sucker A, et al. (2012) Influence of genetic variants in type I interferon genes on melanoma survival and therapy. PloS One 7: e50692. doi:10.1371/journal.pone.0050692.
    • (2012) PloS One , vol.7 , pp. e50692
    • Lenci, R.E.1    Bevier, M.2    Brandt, A.3    Bermejo, J.L.4    Sucker, A.5
  • 34
    • 0030999555 scopus 로고    scopus 로고
    • A breakpoint map of recurrent chromosomal rearrangements in human neoplasia
    • Mitelman F, Mertens F, Johansson B (1997) A breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Nat Genet 15: 417-474. doi:10.1038/ng0497supp-417.
    • (1997) Nat Genet , vol.15 , pp. 417-474
    • Mitelman, F.1    Mertens, F.2    Johansson, B.3
  • 35
    • 41749114987 scopus 로고    scopus 로고
    • Characterization of 9p21 copy number alterations in human melanoma by fluorescence in situ hybridization
    • Rákosy Z, Vízkeleti L, Ecsedi S, Bégány A, Emri G, et al. (2008) Characterization of 9p21 copy number alterations in human melanoma by fluorescence in situ hybridization. Cancer Genet Cytogenet 182: 116-121. doi:10.1016/j.cancergencyto.2008.01.008.
    • (2008) Cancer Genet Cytogenet , vol.182 , pp. 116-121
    • Rákosy, Z.1    Vízkeleti, L.2    Ecsedi, S.3    Bégány, A.4    Emri, G.5
  • 37
    • 0026683968 scopus 로고
    • Molecular analysis of deletions of the short arm of chromosome 9 in human gliomas
    • Olopade OI, Jenkins RB, Ransom DT, Malik K, Pomykala H, et al. (1992) Molecular analysis of deletions of the short arm of chromosome 9 in human gliomas. Cancer Res 52: 2523-2529.
    • (1992) Cancer Res , vol.52 , pp. 2523-2529
    • Olopade, O.I.1    Jenkins, R.B.2    Ransom, D.T.3    Malik, K.4    Pomykala, H.5
  • 38
    • 84899050715 scopus 로고    scopus 로고
    • Functional network pipeline reveals genetic determinants associated with in situ lymphocyte proliferation and survival of cancer patients
    • Mlecnik B, Bindea G, Angell HK, Sasso MS, Obenauf AC, et al. (2014) Functional network pipeline reveals genetic determinants associated with in situ lymphocyte proliferation and survival of cancer patients. Sci Transl Med 6: 228ra37. doi:10.1126/scitranslmed.3007240.
    • (2014) Sci Transl Med , vol.6 , pp. 228ra37
    • Mlecnik, B.1    Bindea, G.2    Angell, H.K.3    Sasso, M.S.4    Obenauf, A.C.5
  • 39
    • 84873870755 scopus 로고    scopus 로고
    • Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon a-kinoid
    • Lauwerys BR, Hachulla E, Spertini F, Lazaro E, Jorgensen C, et al. (2013) Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon a-kinoid. Arthritis Rheum 65: 447-456. doi:10.1002/art.37785.
    • (2013) Arthritis Rheum , vol.65 , pp. 447-456
    • Lauwerys, B.R.1    Hachulla, E.2    Spertini, F.3    Lazaro, E.4    Jorgensen, C.5
  • 40
    • 33749677657 scopus 로고    scopus 로고
    • Unbiased Recursive Partitioning: A Conditional Inference Framework
    • Hothorn T, Hornik K, Zeileis A (2006) Unbiased Recursive Partitioning: A Conditional Inference Framework. J Comput Graph Stat 15: 651-674.
    • (2006) J Comput Graph Stat , vol.15 , pp. 651-674
    • Hothorn, T.1    Hornik, K.2    Zeileis, A.3


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