Integrated molecular analysis of adult T cell leukemia/lymphoma

Nature Genetics

Volumn 47, Issue 11, 2015, Pages 1304-1315

  Kataoka, Keisuke ^a   Nagata, Yasunobu ^a   Kitanaka, Akira ^b   Shiraishi, Yuichi ^c   Shimamura, Teppei ^d   Yasunaga, Jun Ichirou ^e   Totoki, Yasushi ^f   Chiba, Kenichi ^c   Sato Otsubo, Aiko ^a   Nagae, Genta ^g   Ishii, Ryohei ^c   Muto, Satsuki ^c   Kotani, Shinichi ^a   Watatani, Yosaku ^a   Takeda, June ^a   Sanada, Masashi ^a,h   Tanaka, Hiroko ^c   Suzuki, Hiromichi ^a   Sato, Yusuke ^a   Shiozawa, Yusuke ^a   Yoshizato, Tetsuichi ^a   Yoshida, Kenichi ^a   Makishima, Hideki ^a   Iwanaga, Masako ⁱ   Ma, Guangyong ^e   Nosaka, Kisato ^j   Hishizawa, Masakatsu ^a   Itonaga, Hidehiro ^k   Imaizumi, Yoshitaka ^l   Munakata, Wataru ^m   Ogasawara, Hideaki ⁿ   Sato, Toshitaka ⁿ   Sasai, Ken ⁿ   Muramoto, Kenzo ⁿ   Penova, Marina ^a   Kawaguchi, Takahisa ^a   Nakamura, Hiromi ^f   Hama, Natsuko ^f   Shide, Kotaro ^b   Kubuki, Yoko ^b   Hidaka, Tomonori ^b   Kameda, Takuro ^b   Nakamaki, Tsuyoshi ^o   Ishiyama, Ken ^p   Miyawaki, Shuichi ^q   Yoon, Sung Soo ^r   Tobinai, Kensei ^m   Miyazaki, Yasushi ^l   Takaori Kondo, Akifumi ^a   Matsuda, Fumihiko ^a   Takeuchi, Kengo ^s   Nureki, Osamu ^c   Aburatani, Hiroyuki ^g   Watanabe, Toshiki ^c   Shibata, Tatsuhiro ^c,f   Matsuoka, Masao ^e   Miyano, Satoru ^c   Shimoda, Kazuya ^b   Ogawa, Seishi ^a   more..

^a KYOTO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b UNIVERSITY OF MIYAZAKI   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^e KYOTO UNIVERSITY   (Japan)

^f NATIONAL CANCER CENTER RESEARCH INSTITUTE   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h NATIONAL HOSPITAL ORGANIZATION NAGOYA MEDICAL CENTER   (Japan)

ⁱ NAGASAKI UNIVERSITY GRADUATE SCHOOL OF BIOMEDICAL SCIENCES   (Japan)

^j KUMAMOTO UNIV SCHOOL OF MEDICINE   (Japan)

^k Sasebo Shiritsu Sogo Hospital   (Japan)

^l NAGASAKI UNIVERSITY   (Japan)

^m NATIONAL CANCER CENTER HOSPITAL   (Japan)

ⁿ Kanazawa University Hospital ^*  (Japan)

^o SHOWA UNIVERSITY   (Japan)

^p KANAZAWA UNIVERSITY HOSPITAL   (Japan)

^q Tokyo Metropolitan Ohtsuka Hospital   (Japan)

^r Seoul National University College of Medicine   (South Korea)

^s CANCER INSTITUTE   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN KINASE II; CD28 ANTIGEN; CHEMOKINE RECEPTOR CCR4; CHEMOKINE RECEPTOR CCR7; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; DNA METHYLTRANSFERASE 3A; G PROTEIN COUPLED RECEPTOR; GUANINE NUCLEOTIDE EXCHANGE FACTOR; I KAPPA B KINASE BETA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 4; IONOMYCIN; JANUS KINASE 3; NOTCH1 RECEPTOR; PHORBOL 13 ACETATE 12 MYRISTATE; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN KINASE FYN; PROTEIN SERINE THREONINE KINASE; PROTEIN TYROSINE PHOSPHATASE; RNA BINDING PROTEIN; STAT3 PROTEIN; T LYMPHOCYTE RECEPTOR; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTOME; TAX PROTEIN; TAX PROTEIN, HUMAN T-LYMPHOTROPHIC VIRUS 1;

ADULT; ARTICLE; CLINICAL FEATURE; CONTROLLED STUDY; COPY NUMBER VARIATION; CPG ISLAND; DNA INTEGRATION; DNA METHYLATION; EXOME; GENE EXPRESSION; GENE FUSION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HUMAN T-LYMPHOTROPIC VIRUS 1; IMMUNOSURVEILLANCE; INDEL MUTATION; LEUKOCYTE MIGRATION; MAJOR CLINICAL STUDY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SOMATIC MUTATION; T CELL LEUKEMIA; T CELL LYMPHOMA; AMINO ACID SEQUENCE; DNA SEQUENCE; GENETICS; HEK293 CELL LINE; HOST PATHOGEN INTERACTION; HUMAN GENOME; JURKAT CELL LINE; METABOLISM; MOLECULAR GENETICS; MUTATION; PHYSIOLOGY; PROCEDURES; SEQUENCE HOMOLOGY; SURVIVAL ANALYSIS; T LYMPHOCYTE; VIROLOGY;

ADULT; AMINO ACID SEQUENCE; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; EXOME; GENE PRODUCTS, TAX; GENOME, HUMAN; HEK293 CELLS; HOST-PATHOGEN INTERACTIONS; HUMAN T-LYMPHOTROPIC VIRUS 1; HUMANS; JURKAT CELLS; LEUKEMIA-LYMPHOMA, ADULT T-CELL; MOLECULAR SEQUENCE DATA; MUTATION; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; SURVIVAL ANALYSIS; T-LYMPHOCYTES; TRANSCRIPTOME;

EID: 84945344219     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3415     Document Type: Article

References (61)

1. Ishitsuka, K., & Tamura, K. Human T-cell leukaemia virus type I and adult T-cell leukaemia-lymphoma. Lancet Oncol. 15, e517-e526 (2014).
2. Matsuoka, M., & Jeang, K.T. Human T-cell leukaemia virus type 1 (HTLV-1) infectivity and cellular transformation. Nat. Rev. Cancer 7, 270-280 (2007).
3. Yamagishi, M., & Watanabe, T. Molecular hallmarks of adult T cell leukemia. Front. Microbiol. 3, 334 (2012).
4. Nakagawa, M., et al. Gain-of-function CCR4 mutations in adult T cell leukemia/lymphoma. J. Exp. Med. 211, 2497-2505 (2014).
5. Swerdllow, S., Campo, E., & Harris, N.L WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (IARC Press, 2008).
6. Chiu, Y.L., & Greene, W.C. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu. Rev. Immunol. 26, 317-353 (2008).
7. Zhang, J., et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157-163 (2012).
8. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059-2074 (2013).
9. Boxus, M., et al. The HTLV-1 Tax interactome. Retrovirology 5, 76 (2008).
10. Thome, M., Charton, J.E., Pelzer, C., & Hailfinger, S. Antigen receptor signaling to NF-?B via CARMA1, BCL10, and MALT1. Cold Spring Harb. Perspect. Biol. 2, a003004 (2010).
11. Vallabhapurapu, S., & Karin, M. Regulation and function of NF-?B transcription factors in the immune system. Annu. Rev. Immunol. 27, 693-733 (2009).
12. Paul, S., & Schaefer, B.C. A new look at T cell receptor signaling to nuclear factor-?B. Trends Immunol. 34, 269-281 (2013).
13. Chen, L., & Flies, D.B. Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat. Rev. Immunol. 13, 227-242 (2013).
14. Bidère, N., et al. Casein kinase 1a governs antigen-receptor-induced NF-?B activation and human lymphoma cell survival. Nature 458, 92-96 (2009).
15. Orel, L., Neumeier, H., Hochrainer, K., Binder, B.R., & Schmid, J.A. Crosstalk between the NF-?B activating IKK-complex and the CSN signalosome. J. Cell. Mol. Med. 14, 1555-1568 (2010).
16. Phillips-Mason, P.J., Kaur, H., Burden-Gulley, S.M., Craig, S.E., & Brady-Kalnay, S.M. Identification of phospholipase C ?1 as a protein tyrosine phosphatase μ substrate that regulates cell migration. J. Cell. Biochem. 112, 39-48 (2011).
17. Wall, K.A., Pierce, J.D., & Elbein, A.D. Inhibitors of glycoprotein processing alter T-cell proliferative responses to antigen and to interleukin 2. Proc. Natl. Acad. Sci. USA 85, 5644-5648 (1988).
18. Fu, J., et al. The tumor suppressor gene WWOX links the canonical and noncanonical NF-?B pathways in HTLV-I Tax-mediated tumorigenesis. Blood 117, 1652-1661 (2011).
19. Koss, H., Bunney, T.D., Behjati, S., & Katan, M. Dysfunction of phospholipase C? in immune disorders and cancer. Trends Biochem. Sci. 39, 603-611 (2014).
20. Antal, C.E., et al. Cancer-Associated protein kinase C mutations reveal kinase's role as tumor suppressor. Cell 160, 489-502 (2015).
21. Leonard, T.A., Rozycki, B., Saidi, L.F., Hummer, G., & Hurley, J.H. Crystal structure and allosteric activation of protein kinase C bII. Cell 144, 55-66 (2011).
22. Shaffer, A.L. III, Young, R.M., & Staudt, L.M. Pathogenesis of human B cell lymphomas. Annu. Rev. Immunol. 30, 565-610 (2012).
23. Sommer, K., et al. Phosphorylation of the CARMA1 linker controls NF-?B activation. Immunity 23, 561-574 (2005).
24. Palomero, T., et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat. Genet. 46, 166-170 (2014).
25. Bustelo, X.R. Regulatory and signaling properties of the Vav family. Mol. Cell. Biol. 20, 1461-1477 (2000).
26. Rudd, C.E., Taylor, A., & Schneider, H. CD28 and CTLA-4 coreceptor expression and signal transduction. Immunol. Rev. 229, 12-26 (2009).
27. Griffith, J.W., Sokol, C.L., & Luster, A.D. Chemokines and chemokine receptors: positioning cells for host defense and immunity. Annu. Rev. Immunol. 32, 659-702 (2014).
28. Bangham, C.R., & Osame, M. Cellular immune response to HTLV-1. Oncogene 24, 6035-6046 (2005).
29. Bhatia, A., & Kumar, Y. Cellular and molecular mechanisms in cancer immune escape: a comprehensive review. Expert Rev. Clin. Immunol. 10, 41-62 (2014).
30. Asanuma, S., et al. Adult T-cell leukemia cells are characterized by abnormalities of Helios expression that promote T cell growth. Cancer Sci. 104, 1097-1106 (2013).
31. Zhang, Z., et al. Expression of a non-DNA-binding isoform of Helios induces T-cell lymphoma in mice. Blood 109, 2190-2197 (2007).
32. Melino, G., De Laurenzi, V., & Vousden, K.H. p73: friend or foe in tumorigenesis. Nat. Rev. Cancer 2, 605-615 (2002).
33. Supek, F., Minana, B., Valcarcel, J., Gabaldon, T., & Lehner, B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 156, 1324-1335 (2014).
34. Feschotte, C., & Gilbert, C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat. Rev. Genet. 13, 283-296 (2012).
35. Najafabadi, H.S., et al. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat. Biotechnol. 33, 555-562 (2015).
36. Oeckinghaus, A., Hayden, M.S., & Ghosh, S. Crosstalk in NF-?B signaling pathways. Nat. Immunol. 12, 695-708 (2011).
37. Tong, X., et al. Ataxin-1 and Brother of ataxin-1 are components of the Notch signalling pathway. EMBO Rep. 12, 428-435 (2011).
38. Hodson, D.J., et al. Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemia. Nat. Immunol. 11, 717-724 (2010).
39. Litchfield, D.W. Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. Biochem. J. 369, 1-15 (2003).
40. Perissi, V., Aggarwal, A., Glass, C.K., Rose, D.W., & Rosenfeld, M.G. A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors. Cell 116, 511-526 (2004).
41. Childs, K.S., & Goodbourn, S. Identification of novel co-repressor molecules for Interferon Regulatory Factor-2. Nucleic Acids Res. 31, 3016-3026 (2003).
42. Kaida, D., Schneider-Poetsch, T., & Yoshida, M. Splicing in oncogenesis and tumor suppression. Cancer Sci. 103, 1611-1616 (2012).
43. Mallory, M.J., et al. Signal-And development-dependent alternative splicing of LEF1 in T cells is controlled by CELF2. Mol. Cell. Biol. 31, 2184-2195 (2011).
44. Ramsay, A.J., et al. POT1 mutations cause telomere dysfunction in chronic lymphocytic leukemia. Nat. Genet. 45, 526-530 (2013).
45. You, J.S., & Jones, P.A Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22 9-20 2012).
46. Kinpara, S., et al. Involvement of double-stranded RNA-dependent protein kinase and antisense viral RNA in the constitutive NF?B activation in adult T-cell leukemia/lymphoma cells. Leukemia 29, 1425-1429 (2015).
47. Mackay, H.J., & Twelves, C.J. Targeting the protein kinase C family: are we there yet? Nat. Rev. Cancer 7, 554-562 (2007).
48. Tsukasaki, K., et al. Definition, prognostic factors, treatment, and response criteria of adult T-cell leukemia-lymphoma: a proposal from an international consensus meeting. J. Clin. Oncol. 27, 453-459 (2009).
49. Iwanaga, M., et al. Human T-cell leukemia virus type I (HTLV-1) proviral load and disease progression in asymptomatic HTLV-1 carriers: a nationwide prospective study in Japan. Blood 116, 1211-1219 (2010).
50. Yoshida, K., et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64-69 (2011).
51. Sato, Y., et al. Integrated molecular analysis of clear-cell renal cell carcinoma. Nat. Genet. 45, 860-867 (2013).
52. Subramanian, A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).
53. Nannya, Y., et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 65, 6071-6079 (2005).
54. Yamamoto, G., et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of Affymetrix single-nucleotide-polymorphism genotyping microarrays. Am. J. Hum. Genet. 81, 114-126 (2007).
55. Van Loo, P., et al. Allele-specific copy number analysis of tumors. Proc. Natl. Acad. Sci. USA 107, 16910-16915 (2010).
56. Mermel, C.H., et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
57. Shiraishi, Y., et al. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res. 41, e89 (2013).
58. Haferlach, T., et al. Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia 28, 241-247 (2014).
59. Lawrence, M.S., et al. Mutational heterogeneity in cancer and the search for new cancer-Associated genes. Nature 499, 214-218 (2013).
60. Accomando, W.P., Wiencke, J.K., Houseman, E.A., Nelson, H.H., & Kelsey, K.T. Quantitative reconstruction of leukocyte subsets using DNA methylation. Genome Biol. 15, R50 (2014).
61. Teschendorff, A.E., et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29, 189-196 (2013).