Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Exiqon]

ABSTRACT: The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line (control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays, Illumina microarray HT12 platform and qRT-PCR verification of targets were performed. 189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates. 3045 target genes in total were detected with 587 common and 2458 unique target genes between up and downregulated miRNAs.The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis. Comparison in triplicates the miRNA expression profile with Exiqon between human JJ012 chondrosarcoma cell line and C28 control chondrocytes

ORGANISM(S): Homo sapiens

SUBMITTER: BIJU ISSAC

PROVIDER: E-GEOD-48396 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Lost miRNA surveillance of Notch, IGFR pathway--road to sarcomagenesis.

Galoian K K Guettouche T T Issac B B Navarro L L Temple H T HT

Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 20140101 1

The goal of this study was to compare and analyze differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C 28 cell lines (control) to elucidate deregulation of major signal transduction pathways involved in sarcomagenesis. Total RNA extraction was followed by analyzing RNA quality and integrity. Exiqon human miRNA panel of 743 unique miRNA assays and Illumina microarray HT-12 platform and quantitative reverse transcriptase–PCR verification of targets were ...[more]

PMID: 23959473

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Project description:The transcription factor cMyb plays a key role in human primary CD34+ hematopoietic progenitor cells (HPCs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. We previously demonstrated that cMyb affects erythroid versus megakaryocyte lineage decision in part by transactivating KLF1 and LMO2 expression. To further unravel the molecular mechanisms through which cmyb affects lineage fate decision, we profiled the miRNA and mRNA changes in myb-silenced CD34+ HPCs. mRNA and miRNA expression for each sample were profiled by Affymetrix GeneAtlas U219 strip array and Exiqon Human miRNome PCR Panel, respectively. miRNA/mRNA data were integrated by Ingenuity Pathway Analysis. The integrative analysis of miRNA/mRNA expression changes upon c-myb silencing in human CD34+ HPCs highlighted a set of 19 miRNA with 150 anticorrelated putative target mRNAs. Among the miRNAs downregulated in myb-silenced progenitors with the highest number of predicted target mRNAs, we selected hsa-miR-486-3p based on the in vitro effects of its overexpression on HPCs commitment. Indeed, morphological and flow cytometric analyses after liquid culture showed that hsa-miR-486-3p overexpression in HPCs enhanced erythroid and granulocyte differentiation while restraining megakaryocyte and macrophage differentiation. Moreover, collagen-based clonogenic assay demonstrated a strong impairement megakaryocyte commitment upon hsa-miR-486-3p overexpression in CD34+ cells. Gene expression profiling of hsa-miR-486-3p overexpressing CD34+ cells enabled us to identify a set of 8 genes downregulated and computationally predicted, putative hsa-miR-486-3p targets. Among them, we selected c-maf transcript as upregulated upon myb silencing. Worth of note, c-maf silencing in CD34+ progenitor cells was able to reverse the affects of myb silencing on erythroid versus megakaryocyte lineage choice. Integrative miRNA/mRNA analysis highlighted a set of miRNAs and anticorrelated putative target mRNAs modulated upon myb silencing, therefore potential players in myb-driven HPCs lineage choice. Among them, we demonstrated the hsa-miR-486-3p/c-maf pair as partially contributing to the effects of myb on HPCs commitment. Therefore, our data collectively identified myb-driven hsa-miR-486-3p upregulation and subsequent c-maf downregulation as a new molecular mechanism through which cMyb favours erythropoiesis while restraining megakaryopoiesis. RNA from CD34+ HPCs transfected with c-myb-targeting/non targeting control (NegCTR) synthetic siRNAs was collected 24 hours post-Nucleofection for a set of 5 independent experiments.

Dataset Information

Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Exiqon]

Publications

Lost miRNA surveillance of Notch, IGFR pathway--road to sarcomagenesis.

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