Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome DNA methylation and expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE78942 | GEO | 2016/12/15

SECONDARY ACCESSION(S): PRJNA314472

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome DNA methylation profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes.

Project description:The loss of the CD28 co-stimulatory molecule by CD4+ lymphocytes (CD28null T cells) is accompanied by the acquisition of new biological and functional properties that lead to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset in several inflammatory disorders and in healthy individuals, mainly in aging, are yet a controversial point. Here, we provide the whole-genome DNA methylation profile of CD28null T cells and its CD28+ counterpart. A comparative analysis reveals that 296 genes are differentially methylated between both cell subsets. One hundred sixty (160 genes) associated with the cytotoxicy ability (e.g., GRZB, TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g., CX3CR1, CD27, and IL1R) are demetylated in CD28null T cells, whilst 136 de-novo methylated genes matched with defects in the TCR signaling pathway (e.g., ITK, TXK, CD3G, and LCK). Overall, our results reveal that CD28null T cells have a unique DNA methylation landscape, which is associated with alteration in gene expression and contributes to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could provide novel therapeutic strategies to prevent the accumulation and activation of these cells in aging and inflammatory disorders.

2016-12-15 | GSE78940 | GEO

Phenotypic characteristics of aged CD4<sup>+</sup> CD28<sup>null</sup> T lymphocytes are determined by changes in the whole-genome DNA methylation pattern.

Project description: Not available

| S-EPMC5334526 | biostudies-literature

Whole-genome expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes.

Project description:The loss of the CD28 co-stimulatory molecule by CD4+ lymphocytes (CD28null T cells) is accompanied by the acquisition of new biological and functional properties that lead to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset in several inflammatory disorders and in healthy individuals, mainly in aging, are yet a controversial point. Here, we provide the whole-genome DNA methylation and gene expression profiles of CD28null T cells and its CD28+ counterpart. A comparative analysis reveals that 296 genes are differentially methylated between both cell subsets. One hundred sixty (160 genes) associated with the cytotoxicy ability (e.g., GRZB, TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g., CX3CR1, CD27, and IL1R) are demetylated in CD28null T cells, whilst 136 de-novo methylated genes matched with defects in the TCR signaling pathway (e.g., ITK, TXK, CD3G, and LCK). Moreover, we show that genes related inflammasome activation are differentially expressed between CD28null and CD28+ T cells, highlight the contribution of this pathways to the pro-inflammatory profile of CD28null T cells. Overall, our results reveal that CD28null T cells have a unique DNA methylation landscape, which is associated with alteration in gene expression and contributes to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could provide novel therapeutic strategies to prevent the accumulation and activation of these cells in aging and inflammatory disorders.

2016-12-15 | GSE78941 | GEO

Whole-genome DNA methylation and expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes

Project description:Whole-genome DNA methylation and expression profiles of CD4+ CD28+ and CD4+ CD28null T lymphocytes

| PRJNA314472 | ENA

MethylSig: a whole genome DNA methylation analysis pipeline.

Project description: Not available

| S-EPMC4147891 | biostudies-other

Optical mapping discerns genome wide DNA methylation profiles.

Project description: Not available

| S-EPMC2516518 | biostudies-other

Genome-wide DNA methylation profiles of human hepatocellular carcinoma

Project description: Not available

| S-DIXA-D-1150 | biostudies-other

Differential DNA methylation profiles of human B lymphocytes and Epstein-Barr virus-immortalized B lymphocytes.

Project description: Not available

| S-EPMC5842224 | biostudies-literature

Whole-genome profiling of DNA methylation and hydroxymethylation identify distinct regulatory programs among innate lymphocytes

Project description:Innate lymphocytes encompass a diverse array of phenotypic identities with specialized effector functions. DNA methylation and hydroxymethylation are essential mechanisms for epigenetic fidelity and fate commitment. The landscapes of these modifications are unknown in innate lymphocytes. Here, we characterized the whole-genome distribution of methyl-CpG and 5-hydroxymethylcytosine (5hmC) in mouse ILC3, ILC2, and NK cells. We identified differentially methylated and hydroxymethylated DNA regions between ILC-NK subsets and correlated them with signature transcriptional modules. We associated lineage-determining transcription factors with demethylation and demonstrated unique patterns of DNA methylation/hydroxymethylation in relationship to open chromatin regions, histone modifications, and transcription factor binding sites. We also discover a novel association between 5hmC and NK cell super-enhancers. Using Tet2-deficient mice, we showed that the DNA hydroxymethylase Tet2 is required for optimal production of hallmark cytokines by ILC3 and production of IL-17A by inflammatory ILC2. These findings provide a powerful resource for studying immune epigenetic regulation and further decode the regulatory logic governing innate lymphocyte identity.

2022-02-16 | GSE190944 | GEO

Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology.

Project description: Not available

| S-EPMC5014706 | biostudies-literature