Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity

ABSTRACT: The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. The product of genomic loci coding for micro RNAs (miRNAs) produce many isoforms (isomiRs). IsomiRs differing at their 5’ end have different seed regions and therefore are expected to target different genes. We used microarrays to study the effect of different isomiRs in the context of breast cancer. Breast cancer MDA-MB-231 cells were cultured and were subject to a negative control treatment or transfected with one of the three selected isomiRs: the archetype miRNA, the miR-183-5p|2|-2| or the miR-183-5p|+2|+2| isomiR. Each treatment was done in triplicate. RNA was extracted and hybridized on Affymetrix microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Isidore Rigoutsos

PROVIDER: E-GEOD-71950 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Hemopoiesis entails a series of hierarchically organized events that proceed throughout cell specification and terminates with cell differentiation. Commitment needs the transcription factors effort that, in concert with microRNAs, drives cell fate specification, answering to promiscuous patterns of gene expression by turning on lineage-specific genes and repressing alternate lineage transcripts. Therefore microRNAs and mRNAs cooperate to direct cell fate decisions. We obtained microRNAs profiles from human CD34+ hemopoietic progenitor cells and in-vitro differentiated erythroblasts, megakaryoblasts, monoblasts and myeloblasts precursors and we analyzed them together with the gene expression profiles of the same populations. We found that for most part of microRNAs specifically up-regulated in one single cell progeny an inverse correlation between microRNAs and down-regulated putative targets expression levels occurs. We chose hsa-mir-299-5p as a model to get further insights into the possible biological relevance of this microRNAs-mRNAs expression integrated analytical approach and we asked if the forced expression of a single lineage-specific microRNA is able to control the cell fate of CD34+ progenitors grown in multilineage culture conditions. Gain and loss of-function experiments established that mir-299-5p regulates hemopoietic progenitors fate modulating reciprocally megakaryocytic-granulocytic versus erythroid-monocytic differentiation and has at least two genuine targets, the transcription factors CTCF and SOX4. CD34+ hematopoietic progenitor cells were transfected with the Amaxa Nucleofector Device, using the Human CD34 Cell Nucleofection Kit, accordingly to the manufacturer’s instructions (Amaxa Biosystem, Cologne, Germany), and 5µg of either the Pre-miR miRNA Precursor Molecule—Negative Control # 1 (NC1) or the hsa-mir-299-5p Pre-miR miRNA Precursor Molecule (299-5p) (Ambion, Austin, TX, USA) and pulsed with the program U-008. The dataset is composed of three independent paired experiment of 299-5p gain of-function (three hsa-299-5p Pre-miR miRNA Precursor Molecule nucleoporated samples and three paired Pre-miR miRNA Precursor Molecule—Negative Control # 1 transfected ones).

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Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity

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