Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Johannes H. Schulte,Tobias Marschall,Marcel Martin,Philipp Rosenstiel,Pieter Mestdagh,Stefanie Schlierf,Theresa Thor,Jo Vandesompele,Angelika Eggert,Stefan Schreiber,Sven Rahmann,Alexander Schramm +11 more
TLDR
In this paper, the authors 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.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.read more
Citations
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Book ChapterDOI
Neuroblastoma and Whole Genome Searches
TL;DR: Neuroblastoma is the most frequent solid cancer of early childhood, its incidence is 10.2 cases per million children under 15 years of age and is most frequently in the adrenal medulla and paraspinal ganglia.
Journal ArticleDOI
Current understanding of the role and regulation of miRNAs in Burkitt lymphoma.
TL;DR: The aim of this review was to summarize the current knowledge about BL and to discuss the role of miRNAs in its pathogenesis and their possible use as diagnostic and prognostic indicators.
Book ChapterDOI
MicroRNAs as Novel Targets in Liver Cancer: Facing the Clinical Challenge
Jens U. Marquardt,Peter R. Galle +1 more
TL;DR: The role of microRNAs during liver development and disease is delineated with a particular focus on the development of HCC to indicate their potential as therapeutic targets and potential conceptual and technological challenges that hamper the progress of microRNA-based treatment strategies in liver cancer.
Book ChapterDOI
SVM Based Lung Cancer Prediction Using microRNA Expression Profiling from NGS Data
TL;DR: An algorithm for microRNA expression profiling, its normalization, and a Support Vector based machine learning approach to develop a Cancer Prediction System are discussed.
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