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H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA

ABSTRACT: H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA

PROVIDER: PRJNA973979 | ENA |

REPOSITORIES: ENA

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mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with siRNA-mediated knockdown of KMT2E-AS1 or KMT2E

Project description:Purpose: In lung tissue of mice with experimental PH, we identified an upregulated lncRNA 5031425E22 which mapped to a human ortholog KMT2E-AS1. Across mammals, this lncRNA gene sits adjacent (head-to-head) to the chromosomal location of the histone lysine N-methyltransferase 2E gene (KMT2E), a member of a family of regulators controlling histone 3 lysine 4 trimethylation (H3K4Me3) and chromatin remodeling. We found that both mouse lncRNA E22 and human KMT2E-AS1 were increased in multiple in vivo rodent and human instances of PH. This study was designed to compare the RNA profile of human pulmonary arterial endothelial cells (HPAECs) treated with siRNA targeting KMT2E-AS1, KMT2E and negative control respectively. Method: Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza). Experiments were performed at passages 5 to 8. Cultured HPAECs were transfected with siRNAs targeting either negative control, KMT2E-AS1 or KMT2E, then exposed to hypoxic stress (0.2% oxygen) for 24 hours. Cells were harvested for total RNA extraction, and total RNA samples received ribosomal depletion and directional (stranded) RNA library prep. mRNA and lncRNA profiles were generated by deep sequencing, using NextSeq P3 flow cell (2 x 101bp, 40M reads/sample). RNA-Seq reads were mapped against the human genome build hg19 using STAR aligner and the read counts for each gene were calculated using featureCounts. Gene expression was normalized by DESeq2 with variance-stabilizing transformation (VST) and the low expression genes with total counts across all samples less than 10 were excluded. The differential gene expression analysis was performed using DESeq2 with the adjusted p-value cutoff of 0.05. The Benjamini-Hochberg method was used for multiple test correction. GSEA was conducted on differentially expressed genes with the enrichR R package [4] using the "GO_Biological_Process_2021", "Reactome_2022", "KEGG_2021_Human" databases.

2023-11-09 | GSE232797 | GEO

mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with siRNA-mediated knockdown of KMT2E-AS1 or KMT2E

Project description:mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with siRNA-mediated knockdown of KMT2E-AS1 or KMT2E

| PRJNA973984 | ENA

H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA

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

2023-11-09 | GSE232799 | GEO

Gene expression profiles in gastric cancer cells with TM4SF1-AS1 knockdown

Project description:To clarify the function of a long noncoding RNA TM4SF1-AS1 in gastric cancer (GC), we carried out a gene expression microarray analysis using GC cell lines HSC45 transfected with a siRNA targeting TM4SF1-AS1 or a control siRNA. Gene ontology analysis revealed that genes associated with interferon signaling and immune response were significantly enriched among downregulated genes.

2023-07-01 | GSE209814 | GEO

TM4SF1-AS1 inhibits apoptosis by promoting stress granule formation in cancer cells

Project description:Long noncoding RNAs (lncRNAs) play pivotal roles in tumor development, but little is known about their involvement in the early steps of tumorigenesis. To identify lncRNAs dysregulated in precancerous lesions, we analyzed genome-wide trimethylation of histone H3 lysine 4 (H3K4me3) to screen for transcriptionally active lncRNA genes in the nontumorous gastric mucosa of patients with gastric cancer (GC) and healthy individuals. We found that H3K4me3 at TM4SF1-AS1 is specifically upregulated in GC patients and that expression of TM4SF1-AS1 is prevalently elevated in primary and cultured GC cells. TM4SF1-AS1 contributes to GC cell proliferation in vitro and in vivo, and its oncogenic function is mediated, at least in part, through interaction with Pur-α and YB-1. Chromatin isolation by RNA purification (ChIRP)-mass spectrometry demonstrated that TM4SF1‑AS1 associates with several stress granule (SG)-related proteins, including G3BP2, RACK1 and DDX3. Notably, TM4SF1-AS1 promotes SG formation and inhibits apoptosis in GC cells by sequestering RACK1, an activator of the stress-responsive MAPK pathway, within SGs. TM4SF1‑AS1-induced SG formation and apoptosis inhibition are dependent on Pur-α and YB-1. These findings suggest TM4SF1-AS1 contributes to tumorigenesis by enhancing SG-mediated stress adaptation.

2023-09-16 | PXD036766 | JPOST Repository

human pulmonary artery (endothelial and smoorh muscle) cells : control vs ARSB-siRNA transfected

Project description:Transcriptional profiling of human pulmonary artery endothelial (HAPEC) and smooth muscle (PASM) cells comparing control untreated cells with cells transfected with ARSB-siRNA. Goal was to determine the effects of silenced of arylsufatase B on global gene expression in HAPEC and PASM cells.

2018-10-01 | GSE115268 | GEO

Identifying target genes for the long noncoding RNA, GATA2-AS1

Project description:We have identified a set of endothelial-enriched long noncoding RNAs (lncRNAs) in another experiment. In this experiment, we aim to identify genes that are regulated by the GATA2-AS1 lncRNA. We have depleted GATA2-AS1 using two distinct siRNA in human umbilical vein endothelial cells (HUVEC)

2022-02-25 | GSE197376 | GEO

Gene expression data from human breast cancer MCF-7 cells treated with siRNAs targeting long non-coding RNA TMPO-AS1

Project description:To examine the role of long non-coding RNA TMPO-AS1 in breast cancer, MCF-7 cells were treated with siRNAs targeting TMPO-AS1 (siTMPO-AS1) or control siRNA (siControl). TMPO-AS1 was shown to closely associate with estrogen signaling pathway.

2019-09-24 | GSE129004 | GEO

Effects of SOCS2-AS1 inhibition in prostate cancer cells

Project description:Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified a novel androgen-regulated long non-coding (lnc) RNA, SOCS2-AS1. In order to investigate the SOCS2-AS1 function in prostate cancer cells, we performed gene expression in AR-positive prostate cancer cell lines (LNCaP and LTAD) after siSOCS2-AS1 or siSOCS2 treatment. We also treated cells with vehicle or androgen to analyzed the effects of siSOCS2-AS1 on AR function. Observation of androgen dependent gene expression changes after treatmet with siSOCS2-AS1 with microarray.

2016-08-01 | E-GEOD-82224 | biostudies-arrayexpress

Long Noncoding RNA HNF1A-AS1 Regulates Proliferation and Migration in Esophageal Adenocarcinoma Cells

Project description:Objectives: Long non-coding RNAs (lncRNAs) have been shown to play important roles in the development and progression of cancer. However, functional lncRNAs and their downstream mechanisms are largely unknown in the molecular pathogenesis of esophageal adenocarcinoma (EAC) and its progression. Design: lncRNAs that are abnormally upregulated in EACs were identified by RNA-seq analysis, followed by quantitative RT-PCR (qRTPCR) validation using tissues from 31 EAC patients. Cell biological assays in combination with siRNA-mediated knockdown were performed in order to probe the functional relevance of these lncRNAs. Results: We discovered that a lncRNA, HNF1A-AS1, is markedly upregulated in human primary EACs relative to their corresponding normal esophageal tissues (mean fold change 7.2, p<0.01). We further discovered that HNF1A-AS1 knockdown significantly inhibited cell proliferation and anchorage independent growth, suppressed S-phase entry, and inhibited cell migration and invasion in multiple in vitro EAC models (p<0.05). A gene ontological analysis revealed that HNF1A-AS1 knockdown preferentially affected genes that are linked to assembly of chromatin and the nucleosome, a mechanism essential to cell cycle progression. The well-known cancer-related lncRNA, H19, was the gene most markedly inhibited by HNF1A-AS1 knockdown. Consistent to this finding, there was a significant positive correlation between HNF1A-AS1 and H19 expression in primary EACs (p<0.01). In order to identify novel oncogenic lncRNAs in esophageal adenocarcinogenesis, we carried out RNA-seq of a matched NE-BE-EAC tissue pair

2013-10-21 | E-GEOD-48240 | biostudies-arrayexpress

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