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Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia

Leukemia volume 25, pages 1389–1399 (2011)Cite this article

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Abstract

MicroRNAs (miRNAs) relevant to acute lymphoblastic leukemia (ALL) in children are hypothesized to be largely unknown as most miRNAs have been identified in non-leukemic tissues. In order to discover these miRNAs, we applied high-throughput sequencing to pooled fractions of leukemic cells obtained from 89 pediatric cases covering seven well-defined genetic types of ALL and normal hematopoietic cells. This resulted into 78 million small RNA reads representing 554 known, 28 novel and 431 candidate novel miR genes. In all, 153 known, 16 novel and 170 candidate novel mature miRNAs and miRNA-star strands were only expressed in ALL, whereas 140 known, 2 novel and 82 candidate novel mature miRNAs and miRNA-star strands were unique to normal hematopoietic cells. Stem-loop reverse transcriptase (RT)-quantitative PCR analyses confirmed the differential expression of selected mature miRNAs in ALL types and normal cells. Expression of 14 new miRNAs inversely correlated with expression of predicted target genes (−0.49⩽Spearman's correlation coefficients (Rs)⩽−0.27, P⩽0.05); among others, low levels of novel sol-miR-23 associated with high levels of its predicted (antiapoptotic) target BCL2 (B-cell lymphoma 2) in precursor B-ALL (Rs −0.36, P=0.007). The identification of >1000 miR genes expressed in different types of ALL forms a comprehensive repository for further functional studies that address the role of miRNAs in the biology of ALL.

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Acknowledgements

This research was financially supported by The Netherlands Organization for Scientific Research (NWO-Vidi Grant; MLdB), the Quality of Life Foundation (MLdB/RP) and the Pediatric Oncology Foundation Rotterdam, KOCR (MLdB/RP). We thank Christel Kockx and Michael Moorhouse (core-facility high-throughput sequencing, Erasmus Center for Biomics, Rotterdam) for assistance with the Solexa high-throughput sequencing reactions and data extraction, respectively. We are grateful to Dr Eugene Berezikov (InteRNA genomics BV and the Hubrecht Institute, Utrecht) for the bioinformatic analysis of the small RNA sequence reads and helpful discussions. We thank Dr Leila Mohammadi Khankahdani (Department of Pediatric Oncology, Erasmus MC/Sophia Children's Hospital) for her help in the integration of miRNA and mRNA expression data.

Author contributions

DS performed research, analyzed data and wrote manuscript; FAM and EAML-T performed research, analyzed data and revised the manuscript; CC provided custom stem-loop based TaqMan assays for miRNA detection and revised the manuscript; WFJvIJ performed Solexa sequencing and revised the manuscript; RP and MLdB supervised research, analyzed data, wrote and revised the manuscript.

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Author notes

  1. D Schotte and F Akbari Moqadam: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Pediatric Oncology and Hematology, Erasmus MC/Sophia Children's Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands

    D Schotte, F Akbari Moqadam, E A M Lange-Turenhout, R Pieters & M L den Boer

  2. Genomic Assays R&D, Applied Biosystems, Foster City, CA, USA

    C Chen

  3. Erasmus Center for Biomics, Erasmus MC, Rotterdam, The Netherlands

    W F J van IJcken

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  1. D Schotte
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Correspondence to M L den Boer.

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Schotte, D., Moqadam, F., Lange-Turenhout, E. et al. Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia. Leukemia 25, 1389–1399 (2011). https://doi.org/10.1038/leu.2011.105

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