Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome comparison between TCR γδ T subsets reveals their exclusive and shared markers

ABSTRACT: Intestinal intraepithelial gamma-delta T cells (iIEL gd T cells) constitute a peculiar subset of T lymphocytes located in the gut epithelial barrier involved in intestinal homeostasis. To date, type 1 and type 17 TCR gamma-delta T cells have been well characterized into two functional categories based on phenotypic and functional markers e.g. CD44 and CD27. However, It remains to be determined how to classify iIEL gamma T cells based on commonly used markers. We addressed this question by comparing the transcriptomes of mouse iIEL gamma-delta T cells with distinct functionally well-described gamma-delta T cells present in the periphery.

ORGANISM(S): Mus musculus

PROVIDER: GSE198703 | GEO | 2022/06/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq of sorted mouse gdT cell populations based on TCR Vg chain and Ly6C status

Project description:Gamma-delta (gd) T cells from pooled mouse lymph nodes and spleens were isolated and FACS-sorted for Vg1+Ly6C-, Vg1+Ly6C+, Vg4+Ly6C- and Vg4+Ly6C+ subsets of bulk CD27+ gdT cells.

2024-04-16 | E-MTAB-13897 | biostudies-arrayexpress

Single-cell RNA sequencing comparison of CD4+, CD8+ and T-cell receptor γδ+ cutaneous T-cell lymphomas reveals subset-specific molecular phenotypes

Project description:Background: Malignant clones of primary cutaneous T-cell lymphomas (CTCL) can show a CD4+, CD8+ or T-cell receptor γδ+ phenotype, but their individual impact on tumor biology and skin lesion formation remains ill-defined. We perform a comprehensive molecular characterization of CD4+ vs. CD8+ and TCR-γ/δ+ CTCL lesions. Methods: We performed scRNA-seq of 18 CTCL skin biopsies to compare classic CD4+ advanced-stage mycosis fungoides (MF) with TCR-γ/δ+ MF and primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (Berti’s lymphoma). Results: Malignant clones of TCR-γ/δ+ MF and Berti’s lymphoma showed similar clustering patterns distinct from CD4+ MF, along with increased expression of cytotoxic markers such as NKG7, CTSW, GZMA, and GZMM. Only advanced-stage CD4+MF clones expressed central memory T-cell markers (SELL, CCR7, LEF1), alongside B1/B2 blood involvement, whereas TCR-γ/δ+ MF and Berti’s lymphoma harbored a more tissue-resident phenotype (CD69, CXCR4, NR4A1) without detectable cells in the blood. CD4+ MF and TCR-γ/δ+ MF skin lesions harbored strong type 2 immune activation across myeloid cells, while Berti’s lymphoma was more skewed towards type 1 immune responses. Both CD4+ MF and TCR-γ/δ+ MF lesions showed upregulation of keratinocyte hyperactivation markers such as S100As and KRT16 genes. This increase was entirely absent in Berti’s lymphoma, possibly reflecting an aberrant keratinocyte response to invading tumor cells, that could contribute to the formation of the typical ulcero-necrotic lesions within this entity. Conclusions: Our scRNAseq profiling study reveals specific molecular patterns associated with distinct CTCL subtypes.

2024-10-24 | GSE266862 | GEO

Integration of epigenetic and transcriptional mechanisms governs functional commitment versus plasticity of gd T cell subsets

2013-09-01 | GSE42098 | GEO

Integration of epigenetic and transcriptional mechanisms governs functional commitment versus plasticity of gd T cell subsets

Project description:gd T cells are major innate sources of interleukin-17 (IL-17) and interferon-g (IFN-g), which are differentially produced by two thymically-derived subsets segregated on CD27 expression. However, the molecular mechanisms that program the functional differentiation of gd cells remain incompletely understood. Here we show that CD27+ gd cells are epigenetically committed to express Ifng but not Il17, whereas CD27- gd cells spontaneously make IL-17 but can be induced to produce IFN-g under specific inflammatory conditions. This M-bM-^@M-^\plasticM-bM-^@M-^] behavior of CD27- gd cells associates with permissive histone H3 marks at loci encoding Ifng and upstream M-bM-^@M-^\type 1M-bM-^@M-^] transcription factors. By contrast, Il17 and related M-bM-^@M-^\type 17M-bM-^@M-^] factors are epigenetically and transcriptionally active in CD27- but silenced in CD27+ gd cells. Hence, stable versus plastic behaviors of gd cell subsets are controlled by integrated epigenetic and transcriptional mechanisms that regulate the expression of M-bM-^@M-^\masterM-bM-^@M-^] transcription factors and effector cytokine genes. ChIP was carried out on FACS-sorted cells from pooled spleen/ lymph nodes. The following antibodies were used: anti-histone H3K4me2 (07-030, Millipore) and anti-histone H3k27me3 (07-449, Millipore). Between 105 - 106 cells were crosslinked with formaldehyde and nuclei were isolated and sonicated with a Sanyo Soniprep 150 at an amplitude of 10 microns with 17 times 10s bursts, resulting in 200M-bM-^@M-^S400bp chromatin fragments. IP was carried out as previously described 49. The Immunoprecipitated DNA released from crosslinked proteins was extracted with the QiaQuick kit (Qiagen) in accordance with the manufacturerM-BM-4s instructions. Deep sequencing was performed at the GeneCore facility of EMBL (http://www.genecore.embl.de/). At least 1 ng of immunoprecipitated DNA was used for library preparation according to the Illumina protocol.

2013-09-01 | E-GEOD-42098 | biostudies-arrayexpress

Haplo / Allogeneic NKG2DL-targeting Chimeric Antigen Receptor-grafted γδ T Cells for Relapsed or Refractory Solid Tumour

Project description:This clinical trial is an open-label, single-centre, dose escalation, phase I study designed to investigate the safety and tolerability of Haploidentical / Allogeneic NKG2DL-targeting Chimeric Antigen Receptor-grafted Gamma Delta (γδ) T Cells (CTM-N2D) in Subjects with Relapsed or Refractory Solid Tumour. The study objectives of this phase I study are to determine the safety, activity and the safe dose of haploidentical or allogeneic NKG2DL-targeting chimeric antigen receptor-grafted γδ T cells given four times weekly in patients with relapsed or refractory solid tumors of different types.

| 2317628 | ecrin-mdr-crc

Identification of Ligands for the human gamma-delta TCR

Project description:T cells bearing gamma delta T cell antigen receptors (TCRs) function in lymphoid stress surveillance. However, the contribution of gamma delta TCRs to such responses is unclear. Here we found that the TCR of a human V gamma4Vdelta5 clone directly bound endothelial protein C receptor (EPCR), which allowed gamma delta T cells to recognize both endothelial cells targeted by cytomegalovirus and epithelial tumors. EPCR is a major histocompatibility complex–like molecule that binds lipids analogously to the antigen-presenting molecule CD1d. However, the V gamma4Vdelta5 TCR bound EPCR independently of lipids, in an antibody-like way. Moreover, the recognition of target cells by gamma delta T cells required a multimolecular stress signature composed of EPCR and costimulatory ligand(s). Our results demonstrate how a gamma delta TCR mediates recognition of broadly stressed human cells by engaging a stress-regulated self antigen. 2E9 is an antibody that blocks gd-TCR recognition of human cells that are the targets of the clone LES. 2E9 also stains cells that are targeted by LES. Therefore, to identify the TCR ligand expressed by 2E9-positive cells, Gene Expression was compared in two cell lines that stain with 2E9 (K562 and U937) versus two cell lines that do not (Hutu80 and Huh7).

2012-07-27 | E-GEOD-39709 | biostudies-arrayexpress

Murine gamma delta intraepithelial lymphocyte response to type I IFN and TCR blockade

Project description:Interferon alpha (IFNa) is a pro-inflammatory cytokine that is rapidly upregulated as part of an innate immune response. Gamma delta intraepithelial lymphocytes (gd IEL) mount a rapid antimicrobial response to luminal microorganisms and previous report indicate that the T cell receptor (TCR) of these cells is constantly triggered at steady-state. We assessed the contribution of tonic TCR activation in response to acute, systemic IFNa administration among murine gd IELs. Our data demonstrate that inhibiting basal TCR signaling has a minimal effect on the transcriptional profile of gd IELs and acute IFNa exposure induces antiviral gene programs independent of TCR signaling.

2024-10-01 | GSE262121 | GEO

Antigen-expanded CD8+ gd T cells with NK-like phenotype and function respond in persistent infection [Bulk RNA-seq]

Project description:Gamma Delta (gd) T cells play unique protective roles in different settings of acute and chronic infections. However, what they respond to and how they function in the acute versus chronic phases of the same infection remains unclear. It is well documented that cytolytic gd T cells that express Vg9Vd2 TCRs and respond to phosphoantigens (pAgs) expand in acute Mycobacterium tuberculosis (Mtb) infection in humans. However, most infections with Mtb manifest as a chronic, clinically asymptomatic state. While past work indicates that gd T cells contribute to Mtb infection control, their response during this phase of Mtb infection is not well understood. Here, we analyze peripheral blood gd T cells from a South African adolescent cohort and show that a unique CD8+ gd T cell subset with features of “memory inflation” expand in chronic Mtb infection.

2022-10-31 | GSE216652 | GEO

Antigen-expanded CD8+ gd T cells with NK-like phenotype and function respond in persistent infection [scRNA-seq]

2022-10-31 | GSE216654 | GEO

Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span

Project description:Early in ontogeny, gd T cells emerge from the thymus and directly seed peripheral tissues for in situ immunity, though their function in human tissues is not clear. Through analysis of gd T cells in mucosal and lymphoid tissues across the human lifespan, we reveal age- and site-specific differentiation states, functions, and dynamics. Pediatric tissues uniquely contain newly generated gd T cells with diverse repertoires, exhibiting tissue repair and effector functions. In adult tissues, gd T cells persist in lower frequencies, exhibiting highly expanded repertoires and cytolytic profiles. Over childhood, gd T cells convert to adult-like differentiation profiles in mucosal sites, revealing that gd T cells provide diverse recognition and functions for numerous antigenic challenges during early life but persist as terminally differentiated, innate-like cells thereafter.

2024-04-01 | GSE240858 | 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