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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Deregulation of microRNA expression in thyroid neoplasias
TL;DR: The main alterations in miRNA expression that have been identified in thyroid neoplasias are summarized and the mechanisms through which miRNA deregulation might promote thyroid cell transformation are examined.
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The N-myc Oncogene: Maximizing its Targets, Regulation, and Therapeutic Potential.
TL;DR: This review outlines N-myc's contribution to normal development and oncogenic progression and highlights relevant transcriptional targets and mechanisms of regulation.
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Evaluation of normalization methods in mammalian microRNA-Seq data.
TL;DR: Lowess normalization and quantile normalization are recommended for normalizing microRNA-Seq data, whereas the TMM method should be used with caution.
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Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing
Yao-Yin Chang,Wen-Hung Kuo,Jui-Hui Hung,Jui-Hui Hung,Chien-Yueh Lee,Chien-Yueh Lee,Yung-Hua Lee,Ya-Chu Chang,Wen-Chun Lin,Cheng-Ying Shen,Chiun-Sheng Huang,Fon-Jou Hsieh,Liang-Chuan Lai,Mong-Hsun Tsai,King-Jen Chang,Eric Y. Chuang,Eric Y. Chuang +16 more
TL;DR: A novel 25-miRNA expression signature was found to effectively distinguish triple-negative breast cancers from surrounding normal tissues in a hierarchical clustering analysis, and implicate a miR-130b-5p-CCNG2 axis that may be involved in the malignant progression of triple- negative breast cancer.
Journal ArticleDOI
Expression of miR-487b and miR-410 encoded by 14q32.31 locus is a prognostic marker in neuroblastoma.
C-H Gattolliat,L Thomas,Silvia Anna Ciafrè,Guillaume Meurice,G. Le Teuff,Bastien Job,Catherine Richon,Valérie Combaret,Philippe Dessen,Dominique Valteau-Couanet,E May,Philippe Busson,Sétha Douc-Rasy,Jean Bénard +13 more
TL;DR: Expression ofmiR-487b and miR-410 shows predictive value beyond the classical high-/low-risk stratification and is a biomarker of relapse in favourable neuroblastoma.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
MicroRNAs: Genomics, Biogenesis, Mechanism, and Function
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
Journal ArticleDOI
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
Stephen A. Bustin,Vladimir Benes,Jeremy A. Garson,Jan Hellemans,Jim F. Huggett,Mikael Kubista,Reinhold Mueller,Tania Nolan,Michael W. Pfaffl,Gregory L. Shipley,Jo Vandesompele,Carl T. Wittwer,Carl T. Wittwer +12 more
TL;DR: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency.
Journal Article
Oncomirs : microRNAs with a role in cancer
TL;DR: I MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that function as negative gene regulators as discussed by the authors, and have been shown to repress the expression of important cancer-related genes and might prove useful in the diagnosis and treatment of cancer.
Journal ArticleDOI
A direct approach to false discovery rates
TL;DR: The calculation of the q‐value is discussed, the pFDR analogue of the p‐value, which eliminates the need to set the error rate beforehand as is traditionally done, and can yield an increase of over eight times in power compared with the Benjamini–Hochberg FDR method.
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