Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenomic profiles of African American Transthyretin Val122Ile carriers reveals putatively dysregulated amyloid mechanisms

ABSTRACT: The Val122Ile mutation in Transthyretin (TTR) gene causes a rare, difficult to diagnose hereditary form of cardiac amyloidosis. This mutation is most common in the United States and mainly present in people of African descent. The carriers have an increased risk of congestive heart failure, peripheral edema, and several other non-cardiac phenotypes such as carpal tunnel syndrome, and arthroplasty which are top reasons for ambulatory/outpatient surgeries in the country. We conducted first-ever epigenome-wide association study in Val122Ile carriers of African descent for heart disease (HD) and multiple outpatient surgeries (OS) - an early disease indicator. DNA was extracted from whole blood of Yale-Penn participants using the EZ-96 DNA methylation kit (Zymo Research, CA, USA). DNA methylation was assayed using the Illumina Infinium MethylationEPIC chip quantifying >850,000 CpG sites and imaged on the Illumina iScan system at YCGA. The methylation intensity data (*.idat files) was exported for analysis using the manufacturer's recommended protocol using the GenomeStudio methylation module.

ORGANISM(S): Homo sapiens

PROVIDER: GSE154683 | GEO | 2020/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of obesity-induced DNA methylation in visceral adipose tissue

Project description:The purpose of this study was to use global gen expression to identify obesity-induced changes in gene expression profiles of lean and obese adolescent females. Visceral adipose tissue was extracted during abdominal surgeries on Lean and Obese adolescent females of african-americam, caucasian, and hispanic descent.

2017-10-08 | GSE88940 | GEO

Analysis of obesity-induced gene expression changes in visceral adipose tisssue

Project description:The purpose of this study was to use global gene expression to identify obesity-induced changes in gene expression profiles of lean and obese adolescent females. Visceral adipose tissue was extracted during abdominal surgeries on Lean and Obese adolescent females of african-americam, caucasian, and hispanic descent.

2017-10-08 | GSE88837 | GEO

Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity

Project description:Background: Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more common and more severe in people of African descent. To investigate inherent epigenetic differences in T cells between ethnicities, we characterized genome-wide DNA methylation patterns in naïve CD4+ T cells in healthy African-Americans and European-Americans, and then confirmed our findings in lupus patients. Results: Impressive ethnicity-specific clustering of DNA methylation profiling in naïve CD4+ T cells was revealed. Hypomethylated loci in healthy African-Americans were significantly enriched in pro-apoptotic and pro-inflammatory genes. We also found hypomethylated genes in African-Americans to be disproportionately related to autoimmune diseases including lupus. We then confirmed that these genes, such as IL32, CD226, CDKN1A, and PTPRN2 were simi‑ larly hypomethylated in lupus patients of African-American compared to European-American descent. Using patch DNA methylation and luciferase reporter constructs, we showed that methylation of the IL32 promoter region reduces gene expression in vitro. Importantly, bisulfite DNA sequencing demonstrated that cis-acting genetic variants within and directly disrupting CpG sites account for some ethnicity-specific variability in DNA methylation.

2016-10-01 | GSE79237 | GEO

African Ancestry Associated Gene Expression Profiles in Triple Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent

Project description:Women of sub-Saharan African descent have disproportionately higher incidence of Triple Negative Breast Cancer (TNBC), and TNBC-specific mortality. Population comparative studies show racial differences in TNBC biology, including higher prevalence of basal-like and Quadruple-Negative subtypes in African Americans (AA). However, previous investigations relied on self-reported race (SRR) of primarily United States (US) populations. Due to heterogenous genetic admixture, and biological consequences of social determinants, the true association of African ancestry with TNBC biology is unclear. To address this, we conducted RNAseq on an international cohort of AAs, west and east Africans with TNBC. Using comprehensive genetic ancestry estimation in this African-enriched cohort, we found expression of 613 genes associated with African ancestry and 2000+ associated with regional African ancestry. A subset of African-associated genes also showed differences in normal breast tissue. Pathway enrichment and deconvolution of tumor cellular composition revealed tumor-associated immunological profiles are distinct in patients of African descent.

2022-11-09 | GSE211167 | GEO

Epigenomic profiles of African American Transthyretin Val122Ile carriers reveals putatively dysregulated amyloid mechanisms

Project description:Epigenomic profiles of African American Transthyretin Val122Ile carriers reveals putatively dysregulated amyloid mechanisms

| PRJNA647190 | ENA

Epigenetic methylation chip analysis of childhood ependymoma PFA subgroup patient samples [Infinium 450K Methylation Beadchip]

Project description:DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

2023-06-01 | GSE226960 | GEO

Epigenetic methylation chip analysis of childhood PFA ependymoma patient samples [EPIC Methylation]

Project description:DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 65 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

2023-06-01 | GSE226895 | GEO

Circulating microRNAs profile in patients with transthyretin variant amyloidosis

Project description:Transthyretin variant amyloidosis (ATTRv) is a rare autosomal dominant disease characterized by the accumulation of amyloid in many organs, mostly causing a sensory-motor neuropathy, cardiomyopathy, and dysautonomia. The aim of the study was to report microRNAs (miRNAs) expression profile identified in the blood of ATTRv patients. 10 symptomatic ATTRv patients, 10 asymptomatic carriers of transthyretin variant (TTRv), 10 patients with Charcot-Marie-Tooth (CMT) disease, and 10 healthy controls were studied. Human Schwann cells cultures were used to study the regulatory effects of miR-150-5p on the expression of cAMP response element-binding protein (CREB), brain-derived neurotrophic factor (BDNF), and nerve growth factor (NGF). ATTRv patients had 33 miRNAs up-regulated and 48 down-regulated versus healthy controls; 9 miRNAs were up-regulated and 30 down-regulated versus CMT patients; 19 miRNAs were up-regulated and 38 down-regulated versus asymptomatic TTRv carriers. Twelve out of the 19 upregulated miRNAs had a fold increase higher than 100. The validation experiment indicated miR-150-5p as a valuable biomarker to differentiate ATTRv patients from asymptomatic TTRv carriers (AUC: 0.9728; p<0.0001). Schwann cells culture model demonstrated that miR-150-5p is a powerful negative regulator of CREB, BDNF and NGF genes. Identification of deregulated miRNAs can help in understanding the complex pathomechamism underlying the development of ATTRv and related multisystemic pathology. Further investigations are needed on the role of circulating miR-150-5p to predict the shift of TTRv carriers from an asymptomatic status to symptoms appearance.

2020-05-31 | GSE149665 | GEO

Breast tissue methylation analysis

Project description:We aimed to assess breast tissue methylation in breast cancers (triple negative breast cancer) as well as control breast tissue and breast tissue from women with increased breast cancer risk. The dataset includes methylation data from triple negative breast cancer tissue, breast tissue from risk-reducing surgeries (BRCA1/2 mutation carriers), normal breast tissue (cosmetic surgeries) as well as normal tissue adjacent to breast cancers. This dataset also comprises methylation data from controls or BRCA1/2 mutation carriers before and after mifepristone or placebo treatment.

| EGAS00001005070 | EGA

Papillary Tumor of the Pineal Region: analysis of DNA methylation profiles and clinical outcomes in 76 cases

Project description:Genomewide DNA methylation array profiling and analysis of 76 new and public published Papillary Tumor of the Pineal Region (PTPR). The methylation idat profiles of 39 newly profiled tumors were provided here.

2024-07-19 | GSE254031 | GEO

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