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DNA Methylation Analysis of Systemic Lupus Erythematosus

ABSTRACT: This study performed Illumina Methylation450 analysis of CD4+ T-cells, CD19+ B-cells and CD14+ Monocytes from lupus patients and controls. A validation cohort was further analyzed with the same platform using CD4+ T-cells, CD45RO-CD45RA+ naive T-cells, CD45RO+CD45RA- memory T-cells, and CD25+CD127- regulatory T-cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE59250 | GEO | 2014/07/10

SECONDARY ACCESSION(S): PRJNA254821

REPOSITORIES: GEO

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DNA Methylation Analysis of Systemic Lupus Erythematosus

Project description:This study performed Illumina Methylation450 analysis of CD4+ T-cells, CD19+ B-cells and CD14+ Monocytes from lupus patients and controls. A validation cohort was further analyzed with the same platform using CD4+ T-cells, CD45RO-CD45RA+ naive T-cells, CD45RO+CD45RA- memory T-cells, and CD25+CD127- regulatory T-cells. SLE v Control comparisions were made within each cell type. The SLE patient samples are labeled SLEnnnn and the controls Xnnnn. The cell type CD4, CD14, CD19, Tmem, Treg, Tnaive is appended to each sample ID.

2014-07-10 | E-GEOD-59250 | biostudies-arrayexpress

Expression data from human effector CD4 T cells co-cultured with various Treg subsets sorted from human peripheral blood.

Project description:Teff cells (CD4+CD25-CD127+CD45RO+) were co-cultured with and without sorted Treg subsets plus dendritic cells for 18h. All the sorted Teff cells are gated on CD4+CD25-CD127(hi), and further sorted for CD45RO- and CD45RO+ phenotype.

2015-10-01 | GSE64180 | GEO

Expression data from Treg subsets sorted from healthy human peripheral blood

Project description:All the sorted Treg cells are gated on CD4+CD25+CD127(low), followed by gating on various subsets using markers indicated in the sample names. All the sorted Teff cells are gated on CD4+CD25-CD127(hi), and further sorted for CD45RO- and CD45RO+ phenotype.

2015-10-01 | GSE64176 | GEO

Transcription profiling of human CD4 positive T cell subsets

Project description:Peripheral Blood Mononuclear Cells (PBMCs) were isolated from a buffy coat (Australian Blood Bank) using Ficoll methodology. CD4+ T cells were isolated using Dynal Beads kit. Pure CD4+ T cells were then stained using a cocktail of monoclonal antobodies (mAbs), including: anti-CD4PE, CD45RO ECD, CD62L APC-Cy7, CD25 APC, CD127 Pacific Blue. After incubation, cells were washed twice in PBS/FCS (0.2%), and sorted into five different cell subsets: CD4+CD25+CD127low CD62L+CD45RO- (naive regulatory T cells), CD4+CD25+CD127low CD62L+/- CD45RO+ (activated regulatory T cells), CD4+CD25+CD127hi CD62L+/- CD45RO+ (memory T cells), CD4+CD25-CD127low CD62L+/- CD45RO+ (effector T cells) and CD4+CD25-CD127hi CD62L+ CD45RO- (naive T cells).

2011-02-10 | E-MEXP-2578 | biostudies-arrayexpress

The GEP of Treg subpopulations A and B and matchd T conventional

Project description:Transcriptom analysis of Treg subpopulations based on CD4,CD25,CD127,CCR4,CD45RO and CD95 expression

2016-11-22 | GSE78004 | GEO

Naive CD4+ T cell expansion defined by CD25 and CD31 expression

Project description:Naive CD4 T cells defined as (TCRab+ CD4+ CD45RA+ CD62L+ CD127+) were further divided by CD25 and CD31 expression with FACS-based flow sorting. Subsequently, gene expression levels of each subset were assessed by using transcription arrays.

2017-08-15 | E-MTAB-4853 | biostudies-arrayexpress

CD4+ cell transcriptional profiling by RNA sequencing

Project description:We use next generation sequencing to investigate the different transcriptomes of closely related CD4+ T-cells from healthy human donors to elucidate the genetic programs that underlie their specialized immune functions. Six cell types were included: Regulatory T-cells (CD25hiCD127low/neg with >95% FOXP3+ purity), regulatory T-cells activated using PMA/ionomycin, CD25-CD45RA+ ('naive' helper T-cells), CD25-CD45RO+ ('memory' helper T-cells), activated Th17 cells (>98% IL17A+ purity) and activated IL17-CD4+ T-cells (called 'ThPI'). Poly-T capture beads were used to isolate mRNA from total RNA, and fragment sizes of ~200 were sequenced from both ends on Illumina's genome analyzer. We confirm many of the canonical signature genes of T-cell populations, but also discover new genes whose expression is limited to specific CD4 T-cell lineages, including long non-coding RNAs. Additionally, we find that genes encoded at loci linked to multiple human autoimmune diseases are enriched for preferential expression upon T-cell activation, suggesting that an aberrant response to T-cell activation is fundamental to pathogenesis.

| phs000626 | dbGaP

Gene expression profiling of effector and regulatory T-cells from peripheral blood of rheumatoid arthritis (RA) patients and healthy volunteers.

Project description:Objective: Conflicting evidence exists regarding the suppressive capacity of Tregs from the peripheral blood (PB) of patients with rheumatoid arthritis (RA). Our aim was to determine whether Tregs are intrinsically defective in RA using a wide range of read-out assays. Methods: CD3+CD4+CD25+CD127low Tregs from CD45RO+ and CD45RA+ compartments of PB from patients with RA and healthy controls (HC) were analysed for phenotype, cytokine expression profile (ex vivo and after in vitro stimulation), suppression of effector T-cell proliferation and cytokine production, suppression of monocyte-derived cytokine/chemokine production, and gene expression profiling. Results: No differences were observed between patients with RA and HC regarding Treg frequency, ex vivo phenotype (CD4, CD25, CD127, CD39, CD161) or pro-inflammatory cytokine profile (IL-17, IFN-gamma, TNF-alpha). FOXP3 expression was increased in Tregs from RA blood. The ability of Tregs to suppress T-cell proliferation or cytokine (IFN-gamma, TNF-alpha) production upon co-culture with autologous CD45RO+ effector T-cells and monocytes was not significantly different between patients with RA and HC. CD45RO+ Tregs from RA blood showed a slightly impaired ability to suppress production of some cytokines/chemokines by autologous LPS-activated monocytes (IL-1-beta, IL-1Ra, IL-7, CCL3, CCL4), but this was not true for all patients and other cytokines/chemokines (TNF-alpha, IL-6, IL-8, IL-12, IL-15, CCL5) were suppressed in the majority of patients similarly to HC. Finally, gene expression profiling of CD45RA+ or CD45RO+ Tregs from PB revealed no statistically significant differences between patients with RA and HC. Conclusions: Our findings suggest that Tregs isolated from PB of patients with RA are not intrinsically defective.

2015-09-05 | GSE65010 | GEO

Transcription profiling of human CD4 regulatory T cells that express either CD45RA or CD45RO

Project description:CD4 T cells taken from 6 donors were sorted into CD25hi CD45RA+ (naï¿½ve Treg), CD25hi CD45RO+ (memory Treg), CD25- CD45RA+ (naï¿½ve responder) and CD25- CD45RO+ (memory responder) populations. RNA was extracted (Ambion RNAqueous), amplified (SMART), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. One sample was deemed to be of too low hybridisation quality, and was hence removed at this point. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 10% FDR. HCL and PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment

2009-10-05 | E-MEXP-2372 | biostudies-arrayexpress

Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood

Project description:Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood from two different donors

2018-03-15 | GSE111901 | GEO

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