Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional characterization of genetic variants associated with upper digestive cancers [ChIP-Seq]

ABSTRACT: Using H3K27ac ChIP-seq assays followed by sequencing to identify regulatory elements in upper digestive cancers

ORGANISM(S): Homo sapiens

PROVIDER: GSE240213 | GEO | 2024/02/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Functional characterization of genetic variants associated with upper digestive cancers [HiChIP]

Project description:Using H3K27ac HiChIP assays to link genetic variants to target genes in upper digestive cancers

2024-02-25 | GSE235431 | GEO

Functional characterization of genetic variants associated with upper digestive cancers

Project description:Functional characterization of genetic variants associated with upper digestive cancers

| PRJNA1002976 | ENA

Functional characterization of genetic variants associated with upper digestive cancers [HiChIP]

Project description:Functional characterization of genetic variants associated with upper digestive cancers [HiChIP]

| PRJNA986062 | ENA

Functional characterization of genetic variants associated with upper digestive cancers [ChIP-Seq]

Project description:Functional characterization of genetic variants associated with upper digestive cancers [ChIP-Seq]

| PRJNA1002983 | ENA

Functional characterization of genetic variants associated with upper digestive cancers

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

2024-02-24 | GSE240214 | GEO

Translocation driven high expression of NOTCH2 in glomus tumors of the upper digestive tract

Project description:Glomus tumors (GT) are perivascular tumors mostly occurring in the distal extremities. Rare cases occur in the digestive tract and may be misdiagnosed with neuroendocrine or gastrointestinal stromal tumors. We aimed to specify the features of GT of the upper digestive tract. We investigated two cases using whole exome sequencing (WES) and RNA-sequencing, and present clinical, histological, phenotypic and molecular features of 16 cases. WES did not reveal any commonly involved cellular pathway. By contrast, RNA-sequencing disclosed a t(1:5)(p13;q32) translocation between MIR143HG and NOTCH2 in both cases. The deducted fusion protein sequence corresponded to the NOTCH2 intracellular domain known as NICD2, which acts as transcription factor. These data were confirmed by high expression of the transcripts of genes targeted by NOTCH cellular pathway (HES and HEY gene families). In our retrospective multicentric series of 16 GT of upper digestive tract MIR143HG-NOTCH2 translocation was detected in 14 (88%) cases. By contrast, it was present in only 2/6 (33%) GT of the distal extremities. Most digestive GT raised from the stomach (n=13), and the others from duodenal (2) or oesophagous (1). All digestive GT were positive for α-smooth muscle actin and transgelin, and negative for cytokeratin AE1/AE3, chromogranine, DOG1, KIT and S100. Most cases were positive for H-caldesmon (n=14) and/or for synaptophysin (n=10). Desmin, CD34 or CD56 were positive in only one case each. Nuclear expression of NOTCH2 was detected in the 14 cases containing the fusion transcripts. The present study shows that MIR143HG-NOTCH2 translocation is present in most digestive GT. This fusion transcript is associated with activation of the NOTCH2 pathway and may drive tumor development. Detection of nuclear NOTCH2 expression may be helpful for diagnosis.

2019-08-31 | GSE118896 | GEO

Translocation driven high expression of NOTCH2 in glomus tumors of the upper digestive tract

Project description:Translocation driven high expression of NOTCH2 in glomus tumors of the upper digestive tract

| PRJNA487177 | ENA

Common genetic variants in epigenetic machinery genes and risk of upper gastrointestinal cancers.

Project description:BackgroundPopulations in north central China are at high risk for oesophageal squamous cell carcinoma (ESCC) and gastric cancer (GC), and genetic variation in epigenetic machinery genes and pathways may contribute to this risk.MethodsWe used the adaptive multilocus joint test to analyse 192 epigenetic genes involved in chromatin remodelling, DNA methylation and microRNA biosynthesis in 1942 ESCC and 1758 GC cases [1126 cardia (GCA) and 632 non-cardia adenocarcinoma (GNCA)] and 2111 controls with Chinese ancestry. We examined potential function of risk alleles using in silico and expression quantitative trait loci (eQTLs) analyses.ResultsSuggestive pathway-based associations were observed for the overall epigenetic (P-value(PATH) = 0.034) and chromatin remodelling (P-value(PATH) = 0.039) pathways with risk of GCA, but not GC, GNCA or ESCC. Overall, 37 different epigenetic machinery genes were associated with risk of one or more upper gastrointestinal (UGI) cancer sites (P-value(GENE )< 0.05), including 14 chromatin remodelling genes whose products are involved in the regulation of HOX genes. We identified a gastric eQTL (rs12724079; rho = 0.37; P = 0.0006) which regulates mRNA expression of ASH1L. Several suggestive eQTLs were also found in oesophageal (rs10898459 in EED), gastric cardia (rs7157322 in DICER1; rs8179271 in ASH1L), and gastric non-cardia (rs1790733 in PPP1CA) tissues.ConclusionsResults of our analyses provide limited but suggestive evidence for a role of epigenetic gene variation in the aetiology of UGI cancer.

| S-EPMC4598798 | biostudies-literature

Matching variants for functional characterization of genetic variants.

Project description:Rapid and low-cost sequencing, as well as computer analysis, have facilitated the diagnosis of many genetic diseases, resulting in a substantial rise in the number of disease-associated genes. However, genetic diagnosis of many disorders remains problematic due to the lack of interpretation for many genetic variants, especially missenses, the infeasibility of high-throughput experiments on mammals, and the shortcomings of computational prediction technologies. Additionally, the available mutant databases are not well-utilized. Toward this end, we used Caenorhabditis elegans mutant resources to delineate the functions of eight missense variants (V444I, V517D, E610K, L732F, E817K, H873P, R1105K, and G1205E) and two stop codons (W937stop and Q1434stop), including several matching variants (MatchVar) with human in ciliopathy associated IFT-140 (also called CHE-11)//IFT140 (intraflagellar transport protein 140). Moreover, MatchVars carrying C. elegans mutants, including IFT-140(G680S) and IFT-140(P702A) for the human (G704S) (dbSNP: rs150745099) and P726A (dbSNP: rs1057518064 and a conflicting variation) were created using CRISPR/Cas9. IFT140 is a key component of IFT complex A (IFT-A), which is involved in the retrograde transport of IFT along cilia and the entrance of G protein-coupled receptors into cilia. Functional analysis of all 10 variants revealed that P702A and W937stop, but not others phenocopied the ciliary phenotypes (short cilia, IFT accumulations, mislocalization of membrane proteins, and cilia entry of nonciliary proteins) of the IFT-140 null mutant, indicating that both P702A and W937stop are phenotypic in C. elegans. Our functional data offered experimental support for interpreting human variants, by using ready-to-use mutants carrying MatchVars and generating MatchVars with CRISPR/Cas9.

| S-EPMC10700107 | biostudies-literature

Genetic and Molecular Characterization Revealed the Prognosis Efficiency of Histone Acetylation in Pan-Digestive Cancers.

Project description:The imbalance between acetylation and deacetylation of histone proteins, important for epigenetic modifications, is closely associated with various diseases, including cancer. However, knowledge regarding the modification of histones across the different types of digestive cancers is still lacking. The purpose of this research was to analyze the role of histone acetylation and deacetylation in pan-digestive cancers. We systematically characterized the molecular alterations and clinical relevance of 13 histone acetyltransferase (HAT) and 18 histone deacetylase (HDAC) genes in five types of digestive cancers, including esophageal carcinoma, gastric cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer. Recurrent mutations and copy number variation (CNV) were extensively found in acetylation-associated genes across pan-digestive cancers. HDAC9 and KAT6A showed widespread copy number amplification across five pan-digestive cancers, while ESCO2, EP300, and HDAC10 had prevalent copy number deletions. Accordingly, we found that HAT and HDAC genes correlated with multiple cancer hallmark-related pathways, especially the histone modification-related pathway, PRC2 complex pathway. Furthermore, the expression pattern of HAT and HDAC genes stratified patients with clinical benefit in hepatocellular carcinoma and pancreatic cancer. These results indicated that acetylation acts as a key molecular regulation of pan-digestive tumor progression.

| S-EPMC9005301 | biostudies-literature

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