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Small RNA sequencing of murine pancreatic tumors driven by polyoma middle-T antigen with wild-type or single-copy loss of Dicer

ABSTRACT: We report the small RNA sequencing results of mouse pancreatic tumor cell lines driven by polyoma middle-T antigen, which have additionally been engineered to have either wild-type (herein "PDwt") or single-copy loss (herein "PDhet") of the Dicer gene. As expected, PDhet cell lines exhibit lower miRNA levels compared to PDwt cell lines. Principle component analysis, detailed in the published manuscript, reveals PDwt cell lines to be more widely varying in miRNA signature compared to PDhet cell lines. Grouping miRNAs by family reveals several families to be significantly downregulated in PDhet cells lines below 50% of PDwt levels, including miR-10, -148, -17, -28, -299, -30, -34, and -379.

ORGANISM(S): Mus musculus

PROVIDER: GSE99578 | GEO | 2020/06/01

REPOSITORIES: GEO

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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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Small RNA sequencing of murine pancreatic tumors driven by polyoma middle-T antigen with wild-type or single-copy loss of Dicer

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