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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503

ABSTRACT: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503

PROVIDER: PRJNA588174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10416660_1.fastq.gz	Fastqsanger.gz
	SRR10416660_2.fastq.gz	Fastqsanger.gz
	SRR10416661_1.fastq.gz	Fastqsanger.gz
	SRR10416661_2.fastq.gz	Fastqsanger.gz
	SRR10416662_1.fastq.gz	Fastqsanger.gz

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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [miRNA-array]

Project description:The alveolar epithelium is comprised of two cell types, alveolar type 1 (AT1) and type 2 (AT2) cells, the latter being capable of self-renewal and transdifferentiation into AT1 fate to establish alveolar function. Micro-RNAs (miRNAs) re critical regulators of developmental pathways, including branching morphogenesis. To determine if miRNAs also play a crucial role in establishment/maintenance of cellular identity within the alveolar epithelium, we performed genome-wide analysis of miRNAs alongside transcriptomic alterations during transdifferentiation of human AT2 (hAT2) into AT1-like cells in vitro . Our results indicated that miRNAs are tightly correlated to known gene expression pattern changes during AEC differentiation. We were able to define three phases of miRNA expression during the trans differentiation process, “early”, “late” and “consistently” changed, which further sub-classified as up- or downregulated. miRNAs with altered expression at all time points during AT1-like differentiation were the largest subgroup, suggesting the need for consistent regulation of signaling pathways to mediate transdifferentiation . Target prediction analysis and integration with previously published gene expression data identified glucocorticoid signaling as the top pathway regulated by miRNAs. Serum/glucocorticoid kinase 1 (SGK1) emerged as a central regulatory factor with temporally-correlated loss of expression and gain of hsa-miR-424 and hsa-miR-503 expression. Functional validation demonstrated specific targeting of these miRNAs to the 3’UTR of SGK1. Taken together, our data show the time-related contribution of miRNAs to the alveolar transdifferentiation process and suggest the need for inhibition of glucocorticoid pathway signaling to achieve the AT1-like cell phenotype in vitro. The miRNA-mRNA interactions identified herein may help to establish AT2 to AT1 cell differentiation in vivo.

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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [RNA-Seq]

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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [miRNA-array]

Project description:Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [miRNA-array]

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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [RNA-Seq]

Project description:Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [RNA-Seq]

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The miR-424(322)/503 gene cluster regulates pro- vs anti-inflammatory skin DC subset differentiation by modulating TGF-βsignaling

Project description:TGF-β family ligands are key regulators of dendritic cell (DC) differentiation and activation. Epidermal Langerhans cells (LCs) require TGF-β family signaling for their differentiation and canonical TGF-β1 signaling secures a non-activated LC state. LCs reportedly control skin inflammation and are replenished from peripheral blood monocytes, which also give rise to pro-inflammatory monocyte-derived DCs (moDCs). By studying mechanisms in inflammation, we previously screened LCs vs moDCs for differentially expressed miRNAs. miR-424/503 was the most strongly inversely regulated (moDCs > LCs). We found that miR-424/503 is induced during moDC differentiation and promotes moDC differentiation in human and mouse. Inversely, forced repression of miR-424 during moDC differentiation facilitated TGF-β1-dependent LC differentiation. Mechanistically, miR-424/503 deficiency in monocyte/DC precursors leads to the induction of TGF-β1-response genes critical for LC differentiation. Therefore, the miR-424/503 gene cluster plays a decisive role in anti-inflammatory LC vs pro-inflammatory moDC differentiation from monocytes.

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Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503

Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:The discovery of either missense mutations or amplification of ALK (Anaplastic Lymphoma Kinase) gene identified this receptor tyrosine kinase as a therapeutic target in neuroblastoma (NB). Moreover, a high ALK expression has been associated with cases of metastatic NB and with a worse prognosis. In order to identify miRNAs involved in the regulation of ALK expression in NB we therefore analyzed their expression profile in 16 NB cell lines and in 22 patients by qPCR. We then identified miRNAs which were differentially expressed between two groups of samples showing high (ALK+) or low (ALK-) expression levels of ALK by using microarrays containing 866 human miRNA probes (Agilent). Next, the differential expression analysis between the two groups (ALK+ and ALK-) was performed using R. Our analysis showed a higher expression of 30 and 23 miRNAs (p-value <0.05) in NB lines and samples, respectively, both belonging to the ALK- group. Validation analysis and filtering according to in silico suggested miR-424-5p as a potential ALK regulator candidate. Dual luciferase assay indicated a direct binding of this miRNA to ALK-3’UTR. Moreover, we observed a down-regulation of ALK protein expression following transfection of miR-424-5p mimic as well as inhibition of cell viability in ALK+ NB cell lines. In conclusion, our data suggest miR-424-5p as involved in the regulation of ALK expression in NB.

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