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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

ABSTRACT: Functional analysis of transcriptome (mRNA and microRNA) and proteome formation during treatment of cord-blood derived stem cell lines (USSC) with retinoic acid-containing XXL-medium to estimate the impact of microRNAs on final proteome.

OTHER RELATED OMICS DATASETS IN: PXD016915

ORGANISM(S): Homo sapiens

PROVIDER: GSE144464 | GEO | 2020/03/09

REPOSITORIES: GEO

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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

Project description:Functional analysis of transcriptome (mRNA and microRNA) and proteome formation during treatment of cord-blood derived stem cell lines (USSC) with retinoic acid-containing XXL-medium to estimate the impact of microRNAs on final proteome.

2020-03-09 | GSE144465 | GEO

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation.

Project description:The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.

| S-EPMC7040006 | biostudies-literature

Impact of miRNAs on the USSC proteome after XXL-differentiation

2020-01-31 | PXD016915 | Pride

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

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

2020-03-09 | GSE144466 | GEO

A Comparison of the Efficacy of Transplantation of Bone Marrow Derived Mesenchymal Stem Cells and Unrestricted Somatic Stem Cells on Outcome After Acute Myocardial Infarction

Project description:Unrestricted Somatic Stem Cells (USSC) are a cell population derived from umbilical cord blood. They have been shown to have greater plasticity than mesenchymal stem cells, and are being investigated as a therapeutic option for many disease states, including cardiovascular disease. In this study, we aimed to evaluate the efficacy of USSC on treating acute myocardial infarction (MI). We compared the effectiveness of USSC to the more widely studied bone marrow derived mesenchymal stem cell. Finally, we investigated whether pre-conditioning USSC prior to administration enhances their effectiveness. We determined effectiveness primarily using cardiac ultrasound, and supported these findings with histological analyses. We observed that pre-conditioned (guided) USSC had the most significant beneficial effect on cardiac function. (Pre-conditioned cells were grown in serum-free F12 media was supplemented with 50ng/ml Basic Fibroblast Growth Factor (bFGF), 20ng/ml Hepatocyte Growth Factor (HGF) and 20ng/ml Bone Morphogenetic Protein 2 (BMP2)). We performed microarray analysis of guided USSC and unmodified USSC to compare the gene expression profile of both cell populations, in order to evaluate whether any specific genes, or gene groups, were involved in mediating this beneficial effect.

2012-08-24 | E-MEXP-3638 | biostudies-arrayexpress

USSC secretome - Characterization of regenerative phenotype of unrestricted somatic stem cells from human umbilical cord blood by functional secretome analysis

Project description:Stem cell transplantation is a promising therapeutic strategy to enhance axonal regeneration after spinal cord injury. Unrestricted somatic stem cells (USSC) isolated from human umbilical cord blood is an attractive stem cell population available at GMP grade without any ethical concerns. It has been shown that USSC transplantation into acute injured rat spinal cords leads to axonal regrowth and significant locomotor recovery, yet lacking cell replacement. Instead, USSC secrete trophic factors enhancing neurite growth of primary cortical neurons in vitro. Here, we applied a functional secretome approach characterizing proteins secreted by USSC for the first time and validate candidate neurite growth promoting factors using primary cortical neurons in vitro. By mass spectrometric analysis and exhaustive bioinformatic interrogation we identified 1156 proteins representing the secretome of USSC. Using Gene Ontology we revealed that USSC secretome contains proteins involved in a number of relevant biological processes of nerve regeneration such as cell adhesion, cell motion, blood vessel formation, cytoskeleton organization and extracellular matrix organization. We found for instance that 31 well-known neurite growth promoting factors like, e.g., neuronal growth regulator 1, NDNF, SPARC and PEDF spanning the whole abundance range of USSC secretome. By the means of primary cortical neurons in vitro assays we verified SPARC and PEDF as significantly involved in USSC mediated neurite growth and therewith underline their role in improved locomotor recovery after transplantation. From our data we are convinced that USSC are a valuable tool in regenerative medicine as USSC’s secretome contains a comprehensive network of trophic factors supporting nerve regeneration not only by a single process but also maintained its regenerative phenotype by a multitude of relevant biological processes.

2015-07-20 | PXD002241 | Pride

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

Project description:Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

| PRJNA603739 | ENA

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

Project description:Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

| PRJNA603745 | ENA

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

Project description:Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

| PRJNA603740 | ENA

Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process.

Project description:Plant regeneration via somatic embryogenesis is time-consuming and highly genotype-dependent. The plant somatic embryogenesis process provokes many epigenetics changes including DNA methylation and histone modification. Recently, an elite cotton Jin668, with an extremely high regeneration ability, was developed from its maternal inbred Y668 cultivar using a Successive Regeneration Acclimation (SRA) strategy. To reveal the underlying mechanism of SRA, we carried out a genome-wide single-base resolution methylation analysis for nonembryogenic calluses (NECs), ECs, somatic embryos (SEs) during the somatic embryogenesis procedure and the leaves of regenerated offspring plants. Jin668 (R4) regenerated plants were CHH hypomethylated compared with the R0 regenerated plants of SRA process. The increase in CHH methylation from NEC to EC was demonstrated to be associated with the RNA-dependent DNA methylation (RdDM) and the H3K9me2-dependent pathway. Intriguingly, the hypomethylated CHH differentially methylated regions (DMRs) of promoter activated some hormone-related and WUSCHEL-related homeobox genes during the somatic embryogenesis process. Inhibiting DNA methylation using zebularine treatment in NEC increased the number of embryos. Our multi-omics data provide new insights into the dynamics of DNA methylation during the plant tissue culture and regenerated offspring plants. This study also reveals that induced hypomethylation (SRA) may facilitate the higher plant regeneration ability and optimize maternal genetic cultivar.

| S-EPMC6335067 | biostudies-literature

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