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RNA sequencing and integrative analysis reveal pathways and hub genes associated with TGFβ1 stimulation on prostatic stromal cells (PrSCs)

ABSTRACT: RNA sequencing and integrative analysis reveal pathways and hub genes associated with TGFβ1 stimulation on prostatic stromal cells (PrSCs)

PROVIDER: PRJNA844911 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19523468_1.fastq.gz	Fastqsanger.gz
	SRR19523468_2.fastq.gz	Fastqsanger.gz
	SRR19523469_1.fastq.gz	Fastqsanger.gz
	SRR19523469_2.fastq.gz	Fastqsanger.gz
	SRR19523470_1.fastq.gz	Fastqsanger.gz

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RNA sequencing and integrative analysis reveal pathways and hub genes associated with TGFβ1 stimulation on prostatic stromal cells (PrSCs)

Project description:To examine the effect of TGFβ1 on prostatic stromal cells, we firstly isolated primary prostatic stromal cells from five benign prostatic hyperplasia sample. Then RNA sequencing and bioinformatics analysis were used to reveal important pathways and hub genes associated with TGFβ1 stimulation on PrSCs.

2022-06-29 | GSE205378 | GEO

RNA sequencing and integrative analysis reveal pathways and hub genes associated with TGFβ1 stimulation on prostatic stromal cells.

Project description:Objective: Benign prostatic hyperplasia (BPH) is the most common urological disease in elderly men. The transforming growth factor beta 1 (TGFβ1) plays an important role in the proliferation and differentiation of BPH stroma. However, it is not clear yet which important pathways and key genes are the downstream of TGFβ1 acting on prostatic stromal cells. Methods: GSE132714 is currently the newer, available, and best high-throughput sequencing data set for BPH disease and includes the largest number of BPH cases. We examined the TGFβ1 expression level in BPH and normal prostate (NP) by analyzing the GSE132714 data set as well as carrying out immunohistochemistry of 15 BPH and 15 NP samples. Primary prostatic stromal cells (PrSCs) were isolated from five fresh BPH tissues. RNA sequencing and bioinformatics analysis were used to reveal important pathways and hub genes associated with TGFβ1 stimulation on PrSCs. Results: TGFβ1 was upregulated in BPH stroma compared to NP stroma. A total of 497 genes (244 upregulated and 253 downregulated) were differentially expressed in PrSCs with and without TGFβ1 stimulation. The Gene Ontology revealed that differentially expressed genes (DEGs) were mainly enriched in progesterone secretion, interleukin-7 receptor binding, and CSF1-CSF1R complex. The Wnt signaling pathway, PI3K-Akt signaling pathway, JAK-STAT signaling pathway, and Hippo signaling pathway were screened based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. FN1, SMAD3, CXCL12, VCAM1, and ICAM1 were selected as hub genes according to the degree of connection from the protein-protein interaction (PPI) network. Conclusion: This study sheds some new insights into the role of TGFβ1 in BPH stroma and provides some clues for the identification of potential downstream mechanisms and targets.

| S-EPMC9412917 | biostudies-literature

Prostatic Stromal Cell Gene Expression

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TGFβ1 treatment of A2058 melanoma cells

Project description:4 replicates were prepared from A2058 melanoma cells [transfected with 10ng of empty vector (pcDNA3.1+)] and treated with 5ng/ml TGFβ1 or vehicle control for 24hrs This is the control arm of a larger experiment where cells transfected with a particular expression plasmid were treated with TGFβ1 or control vehicle. The transfection with the expresion plasmid was unsucessful so this empty vector data has been used alone to simply examine the effect of TGFβ1 treatment on A2058 cells.

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ChIP-seq analysis of H3K27ac, GATA1 and TAL1 in MYO1D hub vs non-hub enhancer knockout K562 cells

Project description:Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.

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Project description:To obtain a comprehensive view of the transcriptional programs in prostatic stromal cells of different histological/pathological origin, we profiled 18 adult human stromal cell cultures from normal transition zone (TZ), normal peripheral zone (PZ), benign prostatic hyperplasia (BPH), and prostate cancer (CA) using cDNA microarrays.

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Distinctive gene expression of prostatic stromal cells cultured from diseased versus normal tissues

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Project description:We generated prostatic stromal microarray expression data for functional validation of our LOH/AI hot-/cold-spots in stroma. Stromal cells from normal peripheral zone tissue and from tumors are grown in culture, and were analyed on gene expression platform. Stromal cells cultured from normal peripheral zone tissues (F-PZ-64, F-PZ-79, F-PZ-82, F-PZ-102, F-PZ-105) and from tumors (F-CA-31, F-CA-39, F-CA-52, F-CA-67, F-CA-93) were established and grown as previously described in Peehl et al. (2000). Total RNAs were extracted from semi-confluent cells (passages 4-5) one day after feeding fresh medium using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and treated with TURBO DNA-free kit (Ambion). Hybridizations were performed according to Illumina protocols by the Genomic Core, Lerner Research Institute, Cleveland Clinic. All samples were hybridized to the Illumina Sentrix Human-6_v3 Expression BeadChip (GPL6884) which contains 48,000 distinct oligonucleotide probes. Normalization is done using average normalization algorithm of BeadStudio Gene Expression Module v3.4 (Illumina).

2012-02-27 | E-GEOD-34312 | biostudies-arrayexpress

Different expressed genes in epithelium and stromal of Benign Prostatic Hyperplasia

Project description:To identify the genes differently expressed in the epithelium and the stromal of Benign Prostatic Hyperplasia (BPH), we collect the epithelium and the stromal from the patients with benign prostatic hyperplasia by laser micro-dissection. And then, Affymetrix HG-U133_Plus_2 gene-chip was used to detect and compare the expression level of genes. To find which genes are most abundantly expressed in epithelium and stromal and what is the role of these genes in the pathogenesis of BPH. 8 prostate tissues were collected from patients undergone transurethral resection of the prostate (TURP) with informed consent. Each tissue was embedded in O.C.T and subsequently used for laser micro-dissection. The total RNA was isolated from each sample and equally mixed for gene-chip assay.

2011-08-09 | E-GEOD-31323 | biostudies-arrayexpress

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