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PMID: 21430775 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Initial genome sequencing and analysis of multiple myeloma.

Nature ·Vol. 471 ·No. 7339 ·2011-03-24 ·Pages 467-72

Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR

Abstract

Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.

MeSH Terms
Amino Acid Sequence Blood Coagulation/genetics CpG Islands/genetics DNA Mutational Analysis DNA Repair/genetics Exons/genetics Exosome Multienzyme Ribonuclease Complex Genome, Human/genetics Genomics Histones/metabolism Homeodomain Proteins/genetics Homeostasis/genetics Humans Methylation Models, Molecular Molecular Sequence Data Multiple Myeloma/drug therapy,enzymology,genetics,metabolism Mutation/genetics NF-kappa B/metabolism Oncogenes/genetics Open Reading Frames/genetics Protein Biosynthesis/genetics Protein Conformation Proto-Oncogene Proteins B-raf/antagonists & inhibitors,genetics,metabolism RNA Processing, Post-Transcriptional/genetics Ribonucleases/chemistry,genetics Signal Transduction/genetics Transcription, Genetic/genetics
Chemicals
Histones Homeodomain Proteins NF-kappa B homeobox protein HOXA9 BRAF protein, human Proto-Oncogene Proteins B-raf Exosome Multienzyme Ribonuclease Complex Ribonucleases DIS3 protein, human
Authors & Affiliations
50 authors, click to expand affiliations / ORCID
Chapman Michael A
The Eli and Edythe L. Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02412, USA.
Lawrence Michael S
Keats Jonathan J
Cibulskis Kristian
Sougnez Carrie
Schinzel Anna C
Harview Christina L
Brunet Jean-Philippe
Ahmann Gregory J
Adli Mazhar
Anderson Kenneth C
Ardlie Kristin G
Auclair Daniel
Baker Angela
Bergsagel P Leif
Bernstein Bradley E
Drier Yotam
Fonseca Rafael
Gabriel Stacey B
Hofmeister Craig C
Jagannath Sundar
Jakubowiak Andrzej J
Krishnan Amrita
Levy Joan
Liefeld Ted
Lonial Sagar
Mahan Scott
Mfuko Bunmi
Monti Stefano
Perkins Louise M
Onofrio Robb
Pugh Trevor J
Rajkumar S Vincent
Ramos Alex H
Siegel David S
Sivachenko Andrey
Stewart A Keith
Trudel Suzanne
Vij Ravi
Voet Douglas
Winckler Wendy
Zimmerman Todd
Carpten John
Trent Jeff
Hahn William C
Garraway Levi A
Meyerson Matthew
Lander Eric S
Getz Gad
Golub Todd R
References (46)
46 references, click to expand
  1. BLIMP1 is a tumor suppressor gene frequently disrupted in activated B cell-like diffuse large B cell lymphoma.
    Cancer Cell. 2010 Dec 14;18(6):568-79 PMID: 21156281
  2. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
    Nat Genet. 2008 Jun;40(6):722-9 PMID: 18438408
  3. Inhibition of murine melanoma experimental metastasis by recombinant desulfatohirudin, a highly specific thrombin inhibitor.
    Cancer Res. 1991 Sep 1;51(17):4549-56 PMID: 1873799
  4. Genome remodelling in a basal-like breast cancer metastasis and xenograft.
    Nature. 2010 Apr 15;464(7291):999-1005 PMID: 20393555
  5. Mutations of the BRAF gene in human cancer.
    Nature. 2002 Jun 27;417(6892):949-54 PMID: 12068308
  6. RNA recognition by 3'-to-5' exonucleases: the substrate perspective.
    Biochim Biophys Acta. 2008 Apr;1779(4):256-65 PMID: 18078842
  7. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
    Nature. 2008 Nov 6;456(7218):66-72 PMID: 18987736
  8. Frequent engagement of the classical and alternative NF-kappaB pathways by diverse genetic abnormalities in multiple myeloma.
    Cancer Cell. 2007 Aug;12(2):115-30 PMID: 17692804
  9. Molecular pathogenesis and a consequent classification of multiple myeloma.
    J Clin Oncol. 2005 Sep 10;23(26):6333-8 PMID: 16155016
  10. Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.
    BMC Genomics. 2007 Sep 22;8:332 PMID: 17888167
  11. Determination of key residues for catalysis and RNA cleavage specificity: one mutation turns RNase II into a "SUPER-ENZYME".
    J Biol Chem. 2009 Jul 31;284(31):20486-98 PMID: 19458082
  12. Polycomb group genes as epigenetic regulators of normal and leukemic hemopoiesis.
    Exp Hematol. 2003 Jul;31(7):567-85 PMID: 12842702
  13. The mutation spectrum revealed by paired genome sequences from a lung cancer patient.
    Nature. 2010 May 27;465(7297):473-7 PMID: 20505728
  14. Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma.
    Cancer Cell. 2007 Aug;12(2):131-44 PMID: 17692805
  15. A comprehensive catalogue of somatic mutations from a human cancer genome.
    Nature. 2010 Jan 14;463(7278):191-6 PMID: 20016485
  16. Frequent somatic hypermutation of the 5' noncoding region of the BCL6 gene in B-cell lymphoma.
    Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12520-4 PMID: 8618933
  17. A single subunit, Dis3, is essentially responsible for yeast exosome core activity.
    Nat Struct Mol Biol. 2007 Jan;14(1):15-22 PMID: 17173052
  18. Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells.
    Cell. 1994 Apr 22;77(2):297-306 PMID: 8168136
  19. IRF4 addiction in multiple myeloma.
    Nature. 2008 Jul 10;454(7201):226-31 PMID: 18568025
  20. Cloning of the gene containing mutations that cause PARK8-linked Parkinson's disease.
    Neuron. 2004 Nov 18;44(4):595-600 PMID: 15541308
  21. The molecular classification of multiple myeloma.
    Blood. 2006 Sep 15;108(6):2020-8 PMID: 16728703
  22. CHOP-independent apoptosis and pathway-selective induction of the UPR in developing plasma cells.
    Mol Immunol. 2010 Mar;47(6):1356-65 PMID: 20044139
  23. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology.
    Neuron. 2004 Nov 18;44(4):601-7 PMID: 15541309
  24. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer.
    Nat Genet. 2009 May;41(5):521-3 PMID: 19330029
  25. The development of proteasome inhibitors as anticancer drugs.
    Cancer Cell. 2004 May;5(5):417-21 PMID: 15144949
  26. A small-cell lung cancer genome with complex signatures of tobacco exposure.
    Nature. 2010 Jan 14;463(7278):184-90 PMID: 20016488
  27. Array-based comparative genomic hybridization in early-stage mycosis fungoides: recurrent deletion of tumor suppressor genes BCL7A, SMAC/DIABLO, and RHOF.
    Genes Chromosomes Cancer. 2008 Dec;47(12):1067-75 PMID: 18663754
  28. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
    Nat Genet. 2003 Jul;34(3):267-73 PMID: 12808457
  29. The exosome: a multipurpose RNA-decay machine.
    Trends Biochem Sci. 2008 Oct;33(10):501-10 PMID: 18786828
  30. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  31. Molecular cloning of complex chromosomal translocation t(8;14;12)(q24.1;q32.3;q24.1) in a Burkitt lymphoma cell line defines a new gene (BCL7A) with homology to caldesmon.
    Blood. 1996 Apr 15;87(8):3124-34 PMID: 8605326
  32. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF.
    Cell. 2004 Mar 19;116(6):855-67 PMID: 15035987
  33. The differentiation and stress response factor XBP-1 drives multiple myeloma pathogenesis.
    Cancer Cell. 2007 Apr;11(4):349-60 PMID: 17418411
  34. Blockade of the MEK/ERK signalling cascade by AS703026, a novel selective MEK1/2 inhibitor, induces pleiotropic anti-myeloma activity in vitro and in vivo.
    Br J Haematol. 2010 May;149(4):537-49 PMID: 20331454
  35. Managing and exploiting stress in the antibody factory.
    FEBS Lett. 2007 Jul 31;581(19):3652-7 PMID: 17475256
  36. 'Unfolding' pathways in neurodegenerative disease.
    Trends Neurosci. 2003 Aug;26(8):407-10 PMID: 12900170
  37. Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma.
    J Exp Med. 2006 Feb 20;203(2):311-7 PMID: 16492805
  38. The mammalian epigenome.
    Cell. 2007 Feb 23;128(4):669-81 PMID: 17320505
  39. Blimp-1 orchestrates plasma cell differentiation by extinguishing the mature B cell gene expression program.
    Immunity. 2002 Jul;17(1):51-62 PMID: 12150891
  40. Blimp-1 is required for the formation of immunoglobulin secreting plasma cells and pre-plasma memory B cells.
    Immunity. 2003 Oct;19(4):607-20 PMID: 14563324
  41. The exosome subunit Rrp44 plays a direct role in RNA substrate recognition.
    Mol Cell. 2007 Jul 20;27(2):324-31 PMID: 17643380
  42. Thrombin generation and the pathogenesis of cancer.
    Semin Thromb Hemost. 2006 Apr;32 Suppl 1:61-8 PMID: 16673267
  43. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
    Nature. 2009 Oct 8;461(7265):809-13 PMID: 19812674
  44. The endoplasmic reticulum stress response in immunity and autoimmunity.
    Nat Rev Immunol. 2008 Sep;8(9):663-74 PMID: 18670423
  45. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.
    Proc Natl Acad Sci U S A. 2005 May 17;102(20):7203-8 PMID: 15883364
  46. Determinants of protein function revealed by combinatorial entropy optimization.
    Genome Biol. 2007;8(11):R232 PMID: 17976239
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2011-03-24
Pages
467-72
Language
English
Region
England
NLM ID
0410462
PMCID
PMC3560292
Subset
IM
Grants
NCI NIH HHS · R01 CA133115 · United States
NHGRI NIH HHS · U54 HG003067 · United States
NCI NIH HHS · R01 CA133115-04 · United States
NCI NIH HHS · R01 CA133966-03 · United States
NCI NIH HHS · K12 CA133250 · United States
NCI NIH HHS · R01 CA133966 · United States
NIA NIH HHS · R01 AG020686-07 · United States
NIA NIH HHS · R01 AG020686 · United States
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