Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Follicular T Cells are Clonally and Transcriptionally Distinct in B Cell-Driven Autoimmune Disease

ABSTRACT: Follicular T Cells are Clonally and Transcriptionally Distinct in B Cell-Driven Autoimmune Disease

PROVIDER: PRJNA662326 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12607500.fastq.gz	Fastqsanger.gz
	SRR12607600.fastq.gz	Fastqsanger.gz
	SRR12607501.fastq.gz	Fastqsanger.gz
	SRR12607601.fastq.gz	Fastqsanger.gz
	SRR12607502.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 128

Similar Datasets

Follicular T Cells are Clonally and Transcriptionally Distinct in B Cell-Driven Autoimmune Disease

Project description:To better understand the role of follicular T cells in autoantibody-mediated disease, we performed single cell RNA and T cell receptor (TCR) sequencing of follicular T cells in a mouse model of autoantibody-mediated disease. This repository provides paired transcriptomes and unbiased TCRab repertoires from sorted CD4+CXCR5+PD1+ follicular T cells at single cell resolution. Our analysis revealed that a minority of clonotypes are preferentially shared amongst autoimmune follicular T cells, and clonotypic expansion is associated with differential gene signatures in autoimmune disease. These data provide insight into the phenotypic differences of follicular T cells in B cell-driven autoimmune disease versus foreign immunization.

2021-09-20 | GSE157649 | GEO

Follicular T cells are clonally and transcriptionally distinct in B cell-driven mouse autoimmune disease.

Project description:Pathogenic autoantibodies contribute to tissue damage and clinical decline in autoimmune disease. Follicular T cells are central regulators of germinal centers, although their contribution to autoantibody-mediated disease remains unclear. Here we perform single cell RNA and T cell receptor (TCR) sequencing of follicular T cells in a mouse model of autoantibody-mediated disease, allowing for analyses of paired transcriptomes and unbiased TCRαβ repertoires at single cell resolution. A minority of clonotypes are preferentially shared amongst autoimmune follicular T cells and clonotypic expansion is associated with differential gene signatures in autoimmune disease. Antigen prediction using algorithmic and machine learning approaches indicates convergence towards shared specificities between non-autoimmune and autoimmune follicular T cells. However, differential autoimmune transcriptional signatures are preserved even amongst follicular T cells with shared predicted specificities. These results demonstrate that follicular T cells are phenotypically distinct in B cell-driven autoimmune disease, providing potential therapeutic targets to modulate autoantibody development.

| S-EPMC8602266 | biostudies-literature

Innate immunity-driven cell recruitment in rat autoimmune diabetes

Project description:Innate immunity-driven cell recruitment in rat autoimmune diabetes

| PRJNA734852 | ENA

Genetically-driven target tissue over-expression of CD40: A novel mechanism in autoimmune disease

Project description:The CD40 gene, an important immune regulatory gene, is also expressed and functional on non-myeloid derived cells, many of which are targets for tissue specific autoimmune diseases, including d thyroid follicular cells in Graves’ disease (GD). Whether target tissue CD40 expression plays a role in autoimmune disease etiology has yet to be determined. Here we show for the first time, that target-tissue over-expression of CD40 plays a key role in the etiology of autoimmunity. Using a murine model of GD, we demonstrated that thyroidal CD40 over-expression augmented the production of thyroid specific antibodies, resulting in more severe experimental autoimmune Graves’ disease (EAGD), whereas deletion of thyroidal CD40 suppressed disease. Using transcriptome and immune-pathway analyses we showed that in both EAGD mouse thyroids and human primary thyrocytes, CD40 mediates this effect by activating downstream cytokines and chemokines, most notably IL-6. To translate these findings into therapy, we blocked IL-6 during EAGD induction in the setting of thyroidal CD40 over-expression, and showed decreased levels of TSHR stimulating antibodies and frequency of disease. We conclude that target tissue over-expression of CD40 plays a key role in the etiology of organ specific autoimmune disease. CD40 in Thyroid Autoimmunity: 1) Incubation of human thyroid cells with G28.5, a CD40 stimulating antibody, and purification of RNA, conversion to cDNA, measurement of mRNA expression using RNAseq. 2) Removal of thyroid tissues from CD40 over-expressing transgenic mice and wild type mice, purification of RNA, conversion to cDNA measurement of mRNA expression using RNAseq.

2012-10-03 | E-GEOD-39081 | biostudies-arrayexpress

Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis

Project description:Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis

| PRJNA330859 | ENA

RNA-Seq of IL-2-KO follicular CD8 T cells and IL-2-KO follicular CD4 T cells

Project description:Follicular CXCR5+ PD-1+ CD8 T cells (CD8 Tfc) arise in multiple models of systemic autoimmunity yet their functional contribution to disease remains in debate. Here we define the follicular localization and functional interactions of CD8 Tfc with B cells during autoimmune disease. The absence of functional T regulatory cells in autoimmunity allows for CD8 Tfc development that then expands with lymphoproliferation. CD8 Tfc are identifiable within the lymph nodes and spleen during systemic autoimmunity, but not during tissue-restricted autoimmune disease. Autoimmune CD8 Tfc cells are polyfunctional, producing helper cytokines IL-21, IL-4, and IFNγ while maintaining cytolytic proteins CD107a, granzyme B, and TNF. During autoimmune disease, IL-2-KO CD8 T cells infiltrate the B cell follicle and germinal center, including the dark zone, to induce AID in vitro in naïve B cells via IL-4 secretion. CD8 Tfc represent a unique CD8 T cell population with a diverse effector cytokine repertoire that can contribute to pathogenic autoimmune B cell response.

2022-01-22 | GSE177911 | GEO

Genetically-driven target tissue over-expression of CD40: A novel mechanism in autoimmune disease

2012-10-03 | GSE39081 | GEO

Amyloid driven clonally expanded CD8+ effector memory T cells infiltrate Alzheimer’s disease bigenic mouse models

Project description:Amyloid driven clonally expanded CD8+ effector memory T cells infiltrate Alzheimer’s disease bigenic mouse models

| PRJNA876731 | ENA

Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes

Project description:Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed an unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the nonobese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets, accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal proinflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions.

2020-03-27 | GSE141786 | GEO

Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes

Project description:Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of the immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the non-obese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal pro-inflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions.

2020-03-27 | GSE141784 | 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