Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients

设为首页

收藏本站

网站地图 | English | 公务邮箱

About the library

Background
History
Leadership
Organization

Readers' Guide

Opening Hours
Collections
Help Via Email

Publications

Electronic Information Resources

Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients

详细信息查看全文

作者：Emilia L Lim (1) Diane L Trinh (1) David W Scott (3) Andy Chu (1) Martin Krzywinski (1) Yongjun Zhao (1) A Gordon Robertson (1) Andrew J Mungall (1) Jacqueline Schein (1) Merrill Boyle (3) Anja Mottok (3) (5) Daisuke Ennishi (3) Nathalie A Johnson (3) Christian Steidl (3) Joseph M Connors (3) Ryan D Morin (1) (4) Randy D Gascoyne (3) (5) Marco A Marra (1) (2)
刊名：Genome Biology
出版年：2015
出版时间：December 2015
年：2015
卷：16
期：1
全文大小：3,707 KB
参考文献：1. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503鈥?1. blank" title="It opens in new window">CrossRef 2. Shipp MA. A predictive model for aggressive non-Hodgkin鈥檚 lymphoma. The International Non-Hodgkin鈥檚 Lymphoma Prognostic Factors Project N Engl J Med. 1993;329:987鈥?4. 3. Sehn LH, Berry B, Chhanabhai M, Fitzgerald C, Gill K, Hoskins P, et al. The revised International Prognostic Index (R-IPI) is a better predictor of outcome than the standard IPI for patients with diffuse large B-cell lymphoma treated with R-CHOP. Blood. 2007;109:1857鈥?1. blood-2006-08-038257" target="_blank" title="It opens in new window">CrossRef 4. Gascoyne RD, Rosenwald A, Poppema S, Lenz G. Prognostic biomarkers in malignant lymphomas. Leuk Lymphoma. 2010;51:11鈥?. blank" title="It opens in new window">CrossRef 5. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer. 2006;6:857鈥?6. blank" title="It opens in new window">CrossRef 6. Roehle A, Hoefig KP, Repsilber D, Thorns C, Ziepert M, Wesche KO, et al. MicroRNA signatures characterize diffuse large B-cell lymphomas and follicular lymphomas. Br J Haematol. 2008;142:732鈥?4. blank" title="It opens in new window">CrossRef 7. Lawrie CH, Soneji S, Marafioti T, Cooper CDO, Palazzo S, Paterson JC, et al. MicroRNA expression distinguishes between germinal center B cell-like and activated B cell-like subtypes of diffuse large B cell lymphoma. Int J Cancer. 2007;121:1156鈥?1. blank" title="It opens in new window">CrossRef 8. Lawrie CH, Gal S, Dunlop HM, Pushkaran B, Liggins AP, Pulford K, et al. Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol. 2008;141:672鈥?. blank" title="It opens in new window">CrossRef 9. Lawrie CH, Chi J, Taylor S, Tramonti D, Ballabio E, Palazzo S, et al. Expression of microRNAs in diffuse large B cell lymphoma is associated with immunophenotype, survival and transformation from follicular lymphoma. J Cell Mol Med. 2009;13:1248鈥?0. blank" title="It opens in new window">CrossRef 10. Montes-Moreno S, Martinez N, Sanchez-Espiridi贸n B, D铆az Uriarte R, Rodriguez ME, Saez A, et al. miRNA expression in diffuse large B-cell lymphoma treated with chemoimmunotherapy. Blood. 2011;118:1034鈥?0. blood-2010-11-321554" target="_blank" title="It opens in new window">CrossRef 11. Alencar AJ, Malumbres R, Kozloski GA, Advani R, Talreja N, Chinichian S, et al. MicroRNAs are independent predictors of outcome in diffuse large B-cell lymphoma patients treated with R-CHOP. Clin Cancer Res. 2011;17:4125鈥?5. blank" title="It opens in new window">CrossRef 12. Malumbres R, Sarosiek KA, Cubedo E, Ruiz JW, Jiang X, Gascoyne RD, et al. Differentiation stage-specific expression of microRNAs in B lymphocytes and diffuse large B-cell lymphomas. Blood. 2009;113:3754鈥?4. blood-2008-10-184077" target="_blank" title="It opens in new window">CrossRef 13. Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, et al. Identification of the human mature B cell miRNome. Immunity. 2009;30:744鈥?2. blank" title="It opens in new window">CrossRef 14. Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WWL, et al. Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood. 2010;116:e118鈥?7. blood-2010-05-285403" target="_blank" title="It opens in new window">CrossRef 15. Morin RD, O鈥機onnor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu A-L, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008;18:610鈥?1. blank" title="It opens in new window">CrossRef 16. Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42:D68鈥?3. blank" title="It opens in new window">CrossRef 17. Costinean S, Zanesi N, Pekarsky Y, Tili E, Volinia S, Heerema N, et al. Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc Natl Acad Sci U S A. 2006;103:7024鈥?. blank" title="It opens in new window">CrossRef 18. Craig VJ, Tzankov A, Flori M, Schmid CA, Bader AG, M眉ller A. Systemic microRNA-34a delivery induces apoptosis and abrogates growth of diffuse large B-cell lymphoma in vivo. Leukemia. 2012;26:2421鈥?. blank" title="It opens in new window">CrossRef 19. Shaffer 3rd AL, Young RM, Staudt LM. Pathogenesis of human B cell lymphomas. Annu Rev Immunol. 2012;30:565鈥?10. blank" title="It opens in new window">CrossRef 20. Haecker I, Gay LA, Yang Y, Hu J, Morse AM, McIntyre LM, et al. Ago HITS-CLIP expands understanding of Kaposi鈥檚 sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PLoS Pathog. 2012;8:e1002884. blank" title="It opens in new window">CrossRef 21. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, et al. MicroRNA expression profiles classify human cancers. Nature. 2005;435:834鈥?. blank" title="It opens in new window">CrossRef 22. Huang W-T, Kuo S-H, Cheng A-L, Lin C-W. Inhibition of ZEB1 by miR-200 characterizes Helicobacter pylori-positive gastric diffuse large B-cell lymphoma with a less aggressive behavior. Mod Pathol. 2014;27:1116鈥?5. blank" title="It opens in new window">CrossRef 23. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011;476:298鈥?03. blank" title="It opens in new window">CrossRef 24. Camp RL, Dolled-Filhart M, Rimm DL. X-tile: a new bio-informatics tool for biomarker assessment and outcome-based cut-point optimization. Clin Cancer Res. 2004;10:7252鈥?. blank" title="It opens in new window">CrossRef 25. Meng W, McElroy JP, Volinia S, Palatini J, Warner S, Ayers LW, et al. Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues. PLoS One. 2013;8:e64393. blank" title="It opens in new window">CrossRef 26. Allen CDC, Okada T, Cyster JG. Germinal-center organization and cellular dynamics. Immunity. 2007;27:190鈥?02. blank" title="It opens in new window">CrossRef 27. Deutsch AJA, Steinbauer E, Hofmann NA, Strunk D, Gerlza T, Beham-Schmid C, et al. Chemokine receptors in gastric MALT lymphoma: loss of CXCR4 and upregulation of CXCR7 is associated with progression to diffuse large B-cell lymphoma. Mod Pathol. 2013;26:182鈥?4. blank" title="It opens in new window">CrossRef 28. Caramuta S, Lee L, Ozata DM, Ak莽akaya P, Georgii-Hemming P, Xie H, et al. Role of microRNAs and microRNA machinery in the pathogenesis of diffuse large B-cell lymphoma. Blood Cancer J. 2013;3:e152. bcj.2013.49" target="_blank" title="It opens in new window">CrossRef 29. Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, et al. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood. 2010;116:e81鈥?. blood-2010-05-285320" target="_blank" title="It opens in new window">CrossRef 30. Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B, Wang J, et al. Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol. 2008;9:405鈥?4. blank" title="It opens in new window">CrossRef 31. Medina PP, Nolde M, Slack FJ. OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature. 2010;467:86鈥?0. blank" title="It opens in new window">CrossRef 32. Wang M, Li C, Nie H, Lv X, Qu Y, Yu B, et al. Down-regulated miR-625 suppresses invasion and metastasis of gastric cancer by targeting ILK. FEBS Lett. 2012;586:2382鈥?. bslet.2012.05.050" target="_blank" title="It opens in new window">CrossRef 33. Liston A, Papadopoulou AS, Danso-Abeam D, Dooley J. MicroRNA-29 in the adaptive immune system: setting the threshold. Cell Mol Life Sci. 2012;69:3533鈥?1. blank" title="It opens in new window">CrossRef 34. Lin J, Lwin T, Zhao J-J, Tam W, Choi YS, Moscinski LC, et al. Follicular dendritic cell-induced microRNA-mediated upregulation of PRDM1 and downregulation of BCL-6 in non-Hodgkin鈥檚 B-cell lymphomas. Leukemia. 2011;25:145鈥?2. blank" title="It opens in new window">CrossRef 35. Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, et al. MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol. 2008;26:462鈥?. bt1392" target="_blank" title="It opens in new window">CrossRef 36. Fulci V, Colombo T, Chiaretti S, Messina M, Citarella F, Tavolaro S, et al. Characterization of B- and T-lineage acute lymphoblastic leukemia by integrated analysis of MicroRNA and mRNA expression profiles. Genes Chromosomes Cancer. 2009;48:1069鈥?2. blank" title="It opens in new window">CrossRef 37. Xu L, Liang Y-N, Luo X-Q, Liu X-D, Guo H-X. Association of miRNAs expression profiles with prognosis and relapse in childhood acute lymphoblastic leukemia. Zhonghua Xue Ye Xue Za Zhi. 2011;32:178鈥?1. 38. Wang W, Corrigan-Cummins M, Hudson J, Maric I, Simakova O, Neelapu SS, et al. MicroRNA profiling of follicular lymphoma identifies microRNAs related to cell proliferation and tumor response. Haematologica. 2012;97:586鈥?4. blank" title="It opens in new window">CrossRef 39. Teng G, Hakimpour P, Landgraf P, Rice A, Tuschl T, Casellas R, et al. MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase. Immunity. 2008;28:621鈥?. blank" title="It opens in new window">CrossRef 40. Lenze D, Leoncini L, Hummel M, Volinia S, Liu CG, Amato T, et al. The different epidemiologic subtypes of Burkitt lymphoma share a homogenous micro RNA profile distinct from diffuse large B-cell lymphoma. Leukemia. 2011;25:1869鈥?6. blank" title="It opens in new window">CrossRef 41. Ding S, Liang Y, Zhao M, Liang G, Long H, Zhao S, et al. Decreased microRNA-142-3p/5p expression causes CD4+ T cell activation and B cell hyperstimulation in systemic lupus erythematosus. Arthritis Rheum. 2012;64:2953鈥?3. blank" title="It opens in new window">CrossRef 42. Kwanhian W, Lenze D, Alles J, Motsch N, Barth S, D枚ll C, et al. MicroRNA-142 is mutated in about 20% of diffuse large B-cell lymphoma. Cancer Med. 2012;1:141鈥?5. blank" title="It opens in new window">CrossRef 43. Weng L, Wu X, Gao H, Mu B, Li X, Wang J-H, et al. MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens. J Pathol. 2010;222:41鈥?1. 44. Li J, Smyth P, Flavin R, Cahill S, Denning K, Aherne S, et al. Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells. BMC Biotechnol. 2007;7:36. blank" title="It opens in new window">CrossRef 45. Bosch R, Dieguez-Gonzalez R, Moreno MJ, Gallardo A, Novelli S, Espinosa I, et al. Focal adhesion proteins expression in human diffuse large B cell lymphoma. Histopathology. 2014;65:119鈥?1. blank" title="It opens in new window">CrossRef 46. Schneider C, Setty M, Holmes AB, Maute RL, Leslie CS, Mussolin L, et al. microRNA 28 controls cell proliferation and is down-regulated in B-cell lymphomas. Proc Natl Acad Sci U S A. 2014;111:8185鈥?0. 47. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368:2059鈥?4. blank" title="It opens in new window">CrossRef 48. Scott DW, Wright GW, Williams PM, Lih C-J, Walsh W, Jaffe ES, et al. Determining cell-of-origin subtypes of diffuse large B-cell lymphoma using gene expression in formalin-fixed paraffin-embedded tissue. Blood. 2014;123:1214鈥?. blood-2013-11-536433" target="_blank" title="It opens in new window">CrossRef 49. European Genome-phenome Archive. bi.ac.uk/ega/studies/EGAS00001001025" class="a-plus-plus">https://www.ebi.ac.uk/ega/studies/EGAS00001001025. Accessed 25 Dec 2014. 50. Friedl盲nder MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012;40:37鈥?2. 51. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006;22:1036鈥?6. bioinformatics/btl048" target="_blank" title="It opens in new window">CrossRef 52. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562鈥?8. blank" title="It opens in new window">CrossRef 53. Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol. 2011;18:1139鈥?6. b.2115" target="_blank" title="It opens in new window">CrossRef 54. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol. 2004;2:e363. bio.0020363" target="_blank" title="It opens in new window">CrossRef 55. Forman JJ, Legesse-Miller A, Coller HA. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A. 2008;105:14879鈥?4. blank" title="It opens in new window">CrossRef 56. Duursma AM, Kedde M, Schrier M, le Sage C, Agami R. miR-148 targets human DNMT3b protein coding region. RNA. 2008;14:872鈥?. 57. Qin L, Chen Y, Niu Y, Chen W, Wang Q, Xiao S, et al. A deep investigation into the adipogenesis mechanism: profile of microRNAs regulating adipogenesis by modulating the canonical Wnt/beta-catenin signaling pathway. BMC Genomics. 2010;11:320. blank" title="It opens in new window">CrossRef 58. Ott CE, Gr眉nhagen J, J盲ger M, Horbelt D, Schwill S, Kallenbach K, et al. MicroRNAs differentially expressed in postnatal aortic development downregulate elastin via 3鈥?UTR and coding-sequence binding sites. PLoS One. 2011;6:e16250. blank" title="It opens in new window">CrossRef 59. Lytle JR, Yario TA, Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5鈥?UTR as in the 3鈥?UTR. Proc Natl Acad Sci U S A. 2007;104:9667鈥?2. blank" title="It opens in new window">CrossRef 60. Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature. 2009;460:479鈥?6. 61. Hafner M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010;141:129鈥?1. blank" title="It opens in new window">CrossRef 62. Bauer S, Robinson PN, Gagneur J. Model-based gene set analysis for Bioconductor. Bioinformatics. 2011;27:1882鈥?. bioinformatics/btr296" target="_blank" title="It opens in new window">CrossRef 63. Therneau TM, Grambsch PM. Modeling Survival Data: Extending the Cox Model. New York: Springer; 2000. blank" title="It opens in new window">CrossRef
作者单位：Emilia L Lim (1) Diane L Trinh (1) David W Scott (3) Andy Chu (1) Martin Krzywinski (1) Yongjun Zhao (1) A Gordon Robertson (1) Andrew J Mungall (1) Jacqueline Schein (1) Merrill Boyle (3) Anja Mottok (3) (5) Daisuke Ennishi (3) Nathalie A Johnson (3) Christian Steidl (3) Joseph M Connors (3) Ryan D Morin (1) (4) Randy D Gascoyne (3) (5) Marco A Marra (1) (2) 1. Canada鈥檚 Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1 L3, Canada 3. Centre for Lymphoid Cancer, Department of Experimental Therapeutics, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada 5. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada 4. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada 2. Department of Medical Genetics, University of British Columbia, Vancouver, Canada
刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
出版者：BioMed Central
ISSN：1465-6906

文摘

Background Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue samples for validation. Results We identify known and candidate novel miRNAs, 25 of which are associated with survival independently of cell-of-origin and International Prognostic Index scores, which are established indicators of outcome. Of these 25 miRNAs, six miRNAs are significantly associated with survival in our validation cohort. Abundant expression of miR-28-5p, miR-214-5p, miR-339-3p, and miR-5586-5p is associated with superior outcome, while abundant expression of miR-324-5p and NOVELM00203M is associated with inferior outcome. Comparison of DLBCL miRNA-seq expression profiles with those from other cancer types identifies miRNAs that were more abundant in B-cell contexts. Unsupervised clustering of miRNAs identifies two clusters of patients that have distinct differences in their outcomes. Our integrative miRNA and mRNA expression analyses reveal that miRNAs increased in abundance in DLBCL appear to regulate the expression of genes involved in metabolism, cell cycle, and protein modification. Additionally, these miRNAs, including one candidate novel miRNA, miR-10393-3p, appear to target chromatin modification genes that are frequent targets of somatic mutation in non-Hodgkin lymphomas. Conclusions Our comprehensive sequence analysis of the DLBCL miRNome identifies candidate novel miRNAs and miRNAs associated with survival, reinforces results from previous mutational analyses, and reveals regulatory networks of significance for lymphomagenesis.