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
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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
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Journal ArticleDOI
Association of microRNA 21 With Biological Features and Prognosis of Neuroblastoma.
Yaodong Zhou,Bo Sheng +1 more
TL;DR: The higher expression of microRNA 21 in NB samples compared with embryonic and normal tissue samples predicted a close correlation between microRNA 20 expression and the biological features of NB, and in patients with NB, higher micro RNA 21 expression correlated with lower rates of overall survival.
Book ChapterDOI
Deep Sequencing of MicroRNAs in Cancer: Expression Profiling and Its Applications
TL;DR: The expression profiles of microRNAs can provide accurate diagnoses, therapy effect predictions and prognoses, and they can act as biomarkers for various types of cancer when characterised by next-generation sequencing technologies.
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Pediatric brain tumor cell lines exhibit miRNA-depleted, Y RNA-enriched extracellular vesicles
Setty M. Magaña,Timothy E. Peterson,Jared M. Evans,Paul A. Decker,Vernadette Simon,Jeanette E. Eckel-Passow,David J. Daniels,Ian F. Parney +7 more
TL;DR: This hypothesis-generating study demonstrated that pediatric brain tumor-derived cell lines secrete EVs comprised of various ncRNA cargoes, which may provide new insights into the pediatric brain tumors microenvironment and identification of novel therapeutic candidates.
Book ChapterDOI
Targeted Methods to Improve Small RNA Profiles Generated by Deep Sequencing
Yoshinari Ando,A. Maxwell Burroughs,Mitsuoki Kawano,Michiel Jan Laurens de Hoon,Yoshihide Hayashizaki +4 more
TL;DR: An array of protocols and tools are focused on with the intention of assisting researchers in improving short RNA profiles constructed with second-generation sequencing, including methods and commentaries on the preparation of sequencing-caliber immunoprecipitation RNA libraries.
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