Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nc886, a noncoding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer

ABSTRACT: nc886 is a 101 nucleotides long non-coding RNA that is also known as a precursor microRNA or a vault RNA. nc886 has been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s). In order to understand potential roles of nc886 in gastric cancer, we performed the knockdown of nc886 in nonmalignant HFE-145 cells and identified and analyzed genes whose expression is activated by nc886 knockdown in gastric cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51067 | GEO | 2015/09/30

SECONDARY ACCESSION(S): PRJNA220982

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenetic silencing of noncoding RNA nc886 provokes oncogenes during esophageal tumorigenesis

Project description:nc886 is a 101 nucleotides long non-coding RNA that is also known as a precursor microRNA or a vault RNA. nc886 has been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s). Pre-clinical study In order to understand potential roles of nc886 in esophageal squamous cell carcinoma (ESCC), we performed the knockdown of nc886 in nonmalignant HET-1A cells and ESCC cell lines (TE-1 and TE-8) and identified and analyzed genes whose expression is activated by nc886 knockdown in ESCC.

2013-10-31 | E-GEOD-51732 | biostudies-arrayexpress

Epigenetic silencing of noncoding RNA nc886 provokes oncogenes during esophageal tumorigenesis

2013-10-31 | GSE51732 | GEO

Knock down of APE1 suppressed gastric cancer metastasis via improving immune disorders caused by myeloid-derived suppressor cells

Project description:Gastric cancer is a highly immunogenic malignancy. Immune tolerance facilitated by myeloid-derived suppressor cells (MDSCs) has been implicated in gastric cancer resistance mechanisms. The potential role of APE1 in regulating gastric cancer metastasis by targeting MDSCs remains uncertain. In this study, the plasmid Plxpsp-mGM-CSF was used to induce high expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) in GES-1 cells. For tumor transplantation experiments, AGS, AGS+GM-CSF and AGS+GM-CSF-siAPE1 cell lines were established by transfection, followed by subcutaneous implantation of tumor cells. MDSCs, Treg cells, IgG, CD3 and CD8 levels were assessed. Transfection with siAPE1 significantly inhibited tumor growth compared to the AGS+GM-CSF group. APE1 gene knockdown modulated the immune system in gastric cancer mice, characterized by a decrease in MDSCs and an increase in Treg cells, IgG, CD3 and CD8. In addition, APE1 gene knockdown resulted in decreased levels of pro-MDSC cytokines (HGF, CCL5, IL-6, CCL12). Furthermore, APE1 gene knockdown inhibited proliferation, migration and invasion of AGS and MKN45 cells. AGS-GM-CSF cell transplantation increased MDSC levels and accelerated tumor growth, whereas APE1 knockdown reduced MDSC levels, inhibited tumor growth and attenuated inflammatory infiltration in gastric cancer tissues.

2024-06-05 | GSE262050 | GEO

Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Illumina]

Project description:Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge. We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics. We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns. We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC. Pre-clinical study Analysis of Esophageal Squamous Cell Carcinoma cell lines knocked-down for nc886 and vault RNA VTRNA1-1 via antisense oligonucleotide (ASO)-targeting.

2016-06-30 | E-GEOD-55854 | biostudies-arrayexpress

miRNA-seq analysis of YAP5SA overexpressed gastric epithelial cells

Project description:To investigate whether YAP upregulates MYC via miRNA repression, we sequenced miRNAs from gastric epithelial cells (HFE-145) either expressed with vector or YAP-5SA.

2018-04-23 | GSE104822 | GEO

Transcription profiling of Hfe-deficient liver and duodenum in mouse strains with differing susceptibilities to iron loading

Project description:Hfe disruption in the mouse leads to experimental hemochromatosis by a mechanism which remains elusive. Evidence for at least five modifier genes has been obtained. These account for the higher iron load of Hfe-deficient D2 mice compared to B6 mice. Gene expression profling was used to clarify the mechanism of Hfe action and to identify potential modifier genes. Experiment Overall Design: Liver and duodenum were obtained from wild-type and Hfe-deficient B6 and D2 mice (three mice per strain/genotype combination).

2008-04-04 | E-GEOD-7357 | biostudies-arrayexpress

Expression data from Hfe-deficient liver and duodenum in mouse strains with differing susceptibilities to iron loading

2008-03-22 | GSE7357 | GEO

nc886, a TGF-β-induced non-coding RNA, suppresses the microRNA pathway in ovarian cancer

Project description:Transforming growth factor-β (TGF-β) signaling and microRNAs (miRNAs) are important gene regulatory components in cancer. Usually in advanced malignant stages, TGF-β signaling is elevated, but global miRNA expression is suppressed. Such a gene expression signature is well illustrated in a fibrosis/mesenchymal subtype of ovarian cancer (OC) that is of poor prognosis. However, the interplay between the two pathways in the OC subtype has not yet been elucidated. nc886 is a recently identified non-coding RNA implicated in several malignancies. nc886's high expression is associated with the poor prognosis of 285 patients in an OC cohort. Herein we have found in OC that nc886 expression is induced by TGF-β and that nc886 binds to the enzyme Dicer to inhibit the processing of miRNA precursors into mature forms. By preventing the miRNA pathway, nc886 emulates TGF-β in gene expression patterns and potentiates cell adhesion, migration, invasion, and drug resistance. We report nc886 as a novel molecular link between the TGF-β and miRNA pathways.

2017-11-08 | GSE106616 | GEO

Increased FGF8 Signaling Promotes Chondrogenic Rather Than Osteogenic Development in the Embryonic Skull

Project description:RNA-seq of RNA isolated from E14.5 mouse embryos- wildtype cranial base tissue, Msx2-Cre;CAGFgf8 mutant cranial vault, and wildtype cranial vault; 3 replicates of each group.

2018-05-23 | GSE112413 | GEO

Mouse gastric adenocarcinoma

Project description:We have created mice by performing gastric epithelium-specific knockout of common tumor suppressor genes. Mice with transgene were monitored for spontaneous gastric cancer. Gene expression profiles were obtained from fresh frozen mouse primary gastric cancer samples.

2014-04-10 | E-GEOD-45956 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data