TY - JOUR
T1 - Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia
AU - Schotte, D
AU - Akbari Moqadam, F
AU - Lange-Turenhout, E A M
AU - Chen, C
AU - van Ijcken, W F J
AU - Pieters, R
AU - den Boer, M L
N1 - Funding Information:
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.
PY - 2011/9
Y1 - 2011/9
N2 - 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.
AB - 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.
KW - Child
KW - Computational Biology
KW - Gene Expression Profiling
KW - Gene Library
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - MicroRNAs/genetics
KW - Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
KW - RNA/genetics
KW - Sequence Analysis, DNA
UR - http://www.scopus.com/inward/record.url?scp=80052458509&partnerID=8YFLogxK
U2 - 10.1038/leu.2011.105
DO - 10.1038/leu.2011.105
M3 - Review article
C2 - 21606961
SN - 0887-6924
VL - 25
SP - 1389
EP - 1399
JO - Leukemia
JF - Leukemia
IS - 9
ER -