Unknown,Transcriptomics,Genomics,Proteomics

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Primary human bone marrow-derived mesenchymal stem cells (MSC) (Chip_9965581030)

ABSTRACT: Mesenchymal stem cells are known to be recruited to the tumor and contribute to a pro-inflammatory environment. The aim of this experiment was to identify potential direct targets of hsa-miR-1246 in human bone marrow derived mesenchymal stem cells in the context of inflammation. For this purpose, miR-1246 mimic or miRIDIAN microRNA Mimic Negative Control #2 both purchased from GE Healthcare Dharmacon Inc. were transiently transfected with LipofectamineÂ® 2000 (Invitrogen AG) at a final concentration of 30nM into primary MSCs. Transfection time was 48h according to manufacturerâs protocol. Transfections were performed in biological triplicates each.

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Bott

PROVIDER: E-MTAB-5033 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to analyse the whole transcriptome of MSCs stimulated with TGFα in order to comprehensively assess the genes regulated by EGFR signalling Methods: Libraries of cDNA were obtained from poly(A)-RNA fractions from not-stimulated or TGFα-stimulated MSCs and sequenced with a SOLiD 5500xl platform. Whole-transcriptome reads were aligned to the version 19 of the human genome (hg19) with the SOLiD LifeScope Genomic Analysis Software version 2.5 (Life Technologies) using the parameters recommended in the user’s manual. The number of observed counts (number of reads/gene) was normalized for the length of the transcript and the number of mapped reads (RPKM) (Reads Per Kilobase per Million of mapped reads). DESeq tool in R package was used to obtain a statistical evaluation of differential gene expression. Results: 1,640 genes resulted highly differentially regulated: 967 genes up-regulated with Fold Induction (FI)≥1.50, and 673 genes down-regulated with FI≤0.50. When highly regulated genes were categorized into enriched categories according to GO molecular function classification and KEGG pathways analysis, a large number of genes coding for potentially secreted proteins or for surface receptors resulted enriched following TGFα treatment. In particular, significant up-regulation of VEGFA, IL6, EREG, HB-EGF, LIF, NGF, NRG1, CCL19, CCL2, CCL25 and CXCL3 was observed. Conclusions: Taken together these findings suggest that EGFR activation in MSCs leads to a significant change in the expression of a wide array of genes coding for secreted proteins that can significantly enhance tumor progression by acting on several mechanisms within the tumor microenvironment mRNA profiles of MSCs starved overnight in serum free medium and treated for 1 hour with recombinant at a concentration of 10 ng/ml by deep sequencing, in quadruplicate, using SOLiD 5500xl.

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Primary human bone marrow-derived mesenchymal stem cells (MSC) (Chip_9965581030)

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