Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

Genome Biology

Volumn 16, Issue 1, 2015, Pages

  Mathelier, Anthony ^a   Lefebvre, Calvin ^b,c   Zhang, Allen W ^a,c   Arenillas, David J ^a   Ding, Jiarui ^b,c   Wasserman, Wyeth W ^a   Shah, Sohrab P ^b,c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSIS; ARTICLE; B CELL LYMPHOMA; BINDING SITE; BURKITT LYMPHOMA; CARCINOGENESIS; CELL GROWTH; CELL PROLIFERATION; COHORT ANALYSIS; CONTROLLED STUDY; EXON; FOLLICULAR LYMPHOMA; GENE DISRUPTION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; HUMAN; LARGE CELL LYMPHOMA; MAJOR CLINICAL STUDY; MIXED CELL LYMPHOMA; PRIMARY MEDIASTINAL LARGE B CELL LYMPHOMA; PROMOTER REGION; SOMATIC MUTATION; BIOLOGY; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDY; GENETICS; HUMAN GENOME; METABOLISM; MUTATION; REGULATORY SEQUENCE;

PROTEIN BINDING; TRANSCRIPTION FACTOR;

BINDING SITES; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; EXONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC ASSOCIATION STUDIES; GENOME, HUMAN; HUMANS; LYMPHOMA, B-CELL; MUTATION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

EID: 84939172630     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0648-7     Document Type: Article

References (63)

1. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013; 502:333-9. doi:10.1038/nature12634.
2. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014; 505:495-501.
3. Mathelier A, Shi W, Wasserman WW. Identification of altered cis-regulatory elements in human disease. Trends Genet. 2015; 31:67-76.
4. Reijnen MJ, Sladek FM, Bertina RM, Reitsma PH. Disruption of a binding site for hepatocyte nuclear factor 4 results in hemophilia B Leyden. Proc Natl Acad Sci. 1992; 89:6300-3.
5. Ludlow LB, Schick BP, Budarf ML, Driscoll DA, Zackai EH, Cohen A, et al. Identification of a mutation in a GATA binding site of the platelet glycoprotein ib β promoter resulting in the Bernard-Soulier syndrome. J Biol Chem. 1996; 271:22076-80. doi:10.1074/jbc.271.36.22076.
6. Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA, et al. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013; 339:957-9. doi:10.1126/science.1229259.
7. Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, et al. TERT promoter mutations in familial and sporadic melanoma. Science. 2013; 339:959-61. doi:10.1126/science.1230062.
8. Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat Genet. 2014; 46:1258-63.
9. Kapeller J, Houghton LA, Monnikes H, Walstab J, Moller D, Bonisch H, et al. First evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3e gene with diarrhea predominant irritable bowel syndrome. Hum Mol Genet. 2008; 17:2967-77. doi:10.1093/hmg/ddn195.
10. VanderMeer JE, Ahituv N. Cis-regulatory mutations are a genetic cause of human limb malformations. Dev Dyn. 2011; 240:920-30. doi:10.1002/dvdy.22535.
11. Spielmann M, Brancati F, Krawitz PM, Robinson P, Ibrahim DM, Franke M, et al. Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. Am J Hum Genet. 2012; 91:629-35. doi:10.1016/j.ajhg.2012.08.014.
12. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013; 342:1235587. doi:10.1126/science.1235587.
13. Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W. Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014; 11:1160-5. doi:10.1038/ng.3101.
14. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, et al. Divergence of transcription factor binding sites across related yeast species. Science. 2007; 317:815-9. doi:10.1126/science.1140748.
15. Andersen MC, Engstrãum PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, et al. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol. 2008; 4:5. doi:10.1371/journal.pcbi.0040005.
16. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, et al. Variation in transcription factor binding among humans. Science. 2010; 328:232-5. doi:10.1126/science.1183621.
17. Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, et al. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 2012; 13:49.
18. Chen C-C, Xiao S, Xie D, Cao X, Song C-X, Wang T, et al. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput Biol. 2013; 9:1003367. doi:10.1371/journal.pcbi.1003367.
19. Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 2014; 10:1004226. doi:10.1371/journal.pgen.1004226.
20. Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 2013; 23:800-11. doi:10.1101/gr.144899.112.
21. McVean GA, Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491:56-65. doi:10.1038/nature11632.
22. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007; 316:1497-502. doi:10.1126/science.1141319.
23. Sikora-Wohlfeld W, Ackermann M, Christodoulou EG, Singaravelu K, Beyer A. Assessing computational methods for transcription factor target gene identification based on ChIP-seq data. PLoS Comput Biol. 2013; 9:1003342. doi:10.1371/journal.pcbi.1003342.
24. The ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA elements) project. Science. 2004; 306:636-40. doi:10.1126/science.1105136.
25. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, et al. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013; 122:1256. doi:10.1182/blood-2013-02-483727.
26. Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, et al. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012; 44:1316-20. doi:10.1038/ng.2469.
27. Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, et al. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics. 2012; 28:167-75. doi:10.1093/bioinformatics/btr629.
28. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2013; 42:142-7. doi:10.1093/nar/gkt997.
29. Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C, et al. COSMIC (the catalogue of somatic mutations in cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 2010; 38:652-7. doi:10.1093/nar/gkp995.
30. Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, et al. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012; 3:1308-19.
31. Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128.
32. Ding J, McConechy MK, Horlings HM, Ha G, Fong CC, Funnell T, et al. Systematic analysis of somatic mutations impacting gene expression in twelve tumor types. Submitted.
33. Pelengaris S, Khan M, Evan G. c-MYC: more than just a matter of life and death. Nat Rev Cancer. 2002; 2:764-76. doi:10.1038/nrc904.
34. Bonner AE, Lemon WJ, You M. Gene expression signatures identify novel regulatory pathways during murine lung development: implications for lung tumorigenesis. J Med Genet. 2003; 40:408-17.
35. Xian J, Aitchison A, Bobrow L, Corbett G, Pannell R, Rabbitts T, et al. Targeted disruption of the 3p12 gene, DUTT1/ROBO1, predisposes mice to lung adenocarcinomas and lymphomas with methylation of the gene promoter. Cancer Res. 2004; 64:6432-7. doi:10.1158/0008-5472.CAN-04-2561.
36. Parray A, Siddique HR, Kuriger JK, Mishra SK, Rhim JS, Nelson HH, et al. ROBO1, a tumor suppressor and critical molecular barrier for localized tumor cells to acquire invasive phenotype: study in African-American and Caucasian prostate cancer models. Int J Cancer. J Int Du Cancer. 2014; 135:2493-506. doi:10.1002/ijc.28919.
37. Orton RJ, Sturm OE, Gormand A, Wolch W, Gilbert DR. Computational modelling reveals feedback redundancy within the epidermal growth factor receptor/extracellular-signal regulated kinase signalling pathway. IET Syst Biol. 2008; 2:173-83. doi:10.1049/iet-syb:20070066.
38. Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan G-C, Frank DA, et al. STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6. Mol Cell Biol. 2013; 33:2879-90. doi:10.1128/MCB.01620-12.
39. UCSC hgTables. http://genome.ucsc.edu/cgi-bin/hgTables .
40. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014; 507:455-61. doi:10.1038/nature12787.
41. ICGC Malignant Lymphoma webpage. https://dcc.icgc.org/projects/MALY-DE .
42. Lawrence M, Huber W, Pagãis H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9:1003118. doi:10.1371/journal.pcbi.1003118.
43. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5:80. doi:10.1186/gb-2004-5-10-r80.
44. Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA, et al. Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013; 41:545-52. doi:10.1093/nar/gks1066.
45. MutationSeq webpage. http://compbio.bccrc.ca/software/mutationseq/ .
46. Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R, et al. Dindel: Accurate indel calls from short-read data. Genome Res. 2011; 21:961-73. doi:10.1101/gr.112326.110.
47. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009; 25:2865-71. doi:10.1093/bioinformatics/btp394.
48. Picard webpage. http://broadinstitute.github.io/picard .
49. Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001; 29:308-11. doi:10.1093/nar/29.1.308.
50. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26:841-42. doi:10.1093/bioinformatics/btq033.
51. Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, et al. PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol. 2007; 8:207.
52. Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004; 5:276-87. doi:10.1038/nrg1315.
53. Lenhard B, Wasserman WW. TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 2002; 18:1135-6. doi:10.1093/bioinformatics/18.8.1135.
54. Kwon AT, Arenillas DJ, Hunt RW, Wasserman WW. oPOSSUM-3: Advanced analysis of regulatory motif over-representation across genes or ChIP-seq datasets. G3; Genes|Genomes|Genet. 2012; 2:987-1002. doi:10.1534/g3.112.003202.
55. Lenhard B, Sandelin A, Mendoza L, Engstrãum P, Jareborg N, Wasserman WW, et al. Identification of conserved regulatory elements by comparative genome analysis. J Biol. 2003; 2:13.
56. MANTA source code. https://github.com/wassermanlab/manta .
57. MANTA webpage. http://manta.cmmt.ubc.ca/manta/ .
58. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012; 6:80-92. doi:10.4161/fly.19695.
59. xseq webpage. http://compbio.bccrc.ca/software/xseq/ .
60. xseq source code. https://bitbucket.org/MO_BCCRC/xseq .
61. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19:1639-45. doi:10.1101/gr.092759.109.
62. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13:2498-504. doi:10.1101/gr.1239303.
63. R webpage. http://www.R-project.org .