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

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• 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
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• 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.