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Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma

Johannes H Schulte, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh UGent, Stefanie Schlierf, Theresa Thor, Jo Vandesompele UGent, Angelika Eggert, Stefan Schreiber, et al. (2010) NUCLEIC ACIDS RESEARCH. 38(17). p.5919-5928
abstract
Small non-coding RNAs, in particular microRNAs(miRNAs), regulate fine-tuning of gene expression and can act as oncogenes or tumor suppressor genes. Differential miRNA expression has been reported to be of functional relevance for tumor biology. Using next-generation sequencing, the unbiased and absolute quantification of the small RNA transcriptome is now feasible. Neuroblastoma(NB) is an embryonal tumor with highly variable clinical course. We analyzed the small RNA transcriptomes of five favorable and five unfavorable NBs using SOLiD next-generation sequencing, generating a total of > 188 000 000 reads. MiRNA expression profiles obtained by deep sequencing correlated well with real-time PCR data. Cluster analysis differentiated between favorable and unfavorable NBs, and the miRNA transcriptomes of these two groups were significantly different. Oncogenic miRNAs of the miR17-92 cluster and the miR-181 family were overexpressed in unfavorable NBs. In contrast, the putative tumor suppressive microRNAs, miR-542-5p and miR-628, were expressed in favorable NBs and virtually absent in unfavorable NBs. In-depth sequence analysis revealed extensive post-transcriptional miRNA editing. Of 13 identified novel miRNAs, three were further analyzed, and expression could be confirmed in a cohort of 70 NBs.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DISCOVERY, GENE, RNA, CANCER, MIRNA EXPRESSION, STEM-CELLS, TUMOR-SUPPRESSOR, BIOGENESIS, IDENTIFICATION, PATHOGENESIS
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
38
issue
17
pages
5919 - 5928
Web of Science type
Article
Web of Science id
000282173300031
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
7.836 (2010)
JCR rank
30/284 (2010)
JCR quartile
1 (2010)
ISSN
0305-1048
DOI
10.1093/nar/gkq342
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1167513
handle
http://hdl.handle.net/1854/LU-1167513
date created
2011-02-23 15:47:49
date last changed
2017-05-05 11:46:31
@article{1167513,
  abstract     = {Small non-coding RNAs, in particular microRNAs(miRNAs), regulate fine-tuning of gene expression and can act as oncogenes or tumor suppressor genes. Differential miRNA expression has been reported to be of functional relevance for tumor biology. Using next-generation sequencing, the unbiased and absolute quantification of the small RNA transcriptome is now feasible. Neuroblastoma(NB) is an embryonal tumor with highly variable clinical course. We analyzed the small RNA transcriptomes of five favorable and five unfavorable NBs using SOLiD next-generation sequencing, generating a total of {\textrangle} 188 000 000 reads. MiRNA expression profiles obtained by deep sequencing correlated well with real-time PCR data. Cluster analysis differentiated between favorable and unfavorable NBs, and the miRNA transcriptomes of these two groups were significantly different. Oncogenic miRNAs of the miR17-92 cluster and the miR-181 family were overexpressed in unfavorable NBs. In contrast, the putative tumor suppressive microRNAs, miR-542-5p and miR-628, were expressed in favorable NBs and virtually absent in unfavorable NBs. In-depth sequence analysis revealed extensive post-transcriptional miRNA editing. Of 13 identified novel miRNAs, three were further analyzed, and expression could be confirmed in a cohort of 70 NBs.},
  author       = {Schulte, Johannes H and Marschall, Tobias and Martin, Marcel and Rosenstiel, Philipp and Mestdagh, Pieter and Schlierf, Stefanie and Thor, Theresa and Vandesompele, Jo and Eggert, Angelika and Schreiber, Stefan and Rahmann, Sven and Schramm, Alexander},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {DISCOVERY,GENE,RNA,CANCER,MIRNA EXPRESSION,STEM-CELLS,TUMOR-SUPPRESSOR,BIOGENESIS,IDENTIFICATION,PATHOGENESIS},
  language     = {eng},
  number       = {17},
  pages        = {5919--5928},
  title        = {Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma},
  url          = {http://dx.doi.org/10.1093/nar/gkq342},
  volume       = {38},
  year         = {2010},
}

Chicago
Schulte, Johannes H, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh, Stefanie Schlierf, Theresa Thor, et al. 2010. “Deep Sequencing Reveals Differential Expression of microRNAs in Favorable Versus Unfavorable Neuroblastoma.” Nucleic Acids Research 38 (17): 5919–5928.
APA
Schulte, Johannes H, Marschall, T., Martin, M., Rosenstiel, P., Mestdagh, P., Schlierf, S., Thor, T., et al. (2010). Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. NUCLEIC ACIDS RESEARCH, 38(17), 5919–5928.
Vancouver
1.
Schulte JH, Marschall T, Martin M, Rosenstiel P, Mestdagh P, Schlierf S, et al. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. NUCLEIC ACIDS RESEARCH. 2010;38(17):5919–28.
MLA
Schulte, Johannes H, Tobias Marschall, Marcel Martin, et al. “Deep Sequencing Reveals Differential Expression of microRNAs in Favorable Versus Unfavorable Neuroblastoma.” NUCLEIC ACIDS RESEARCH 38.17 (2010): 5919–5928. Print.