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ScRNA-seq and scTCR-seq of autoreactive CD8 T cells from NOD mice

ABSTRACT: scRNA-seq and scTCR-seq of autoreactive CD8 T cells from NOD mice

PROVIDER: PRJNA825521 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18715649_1.fastq.gz	Fastqsanger.gz
	SRR18715649_2.fastq.gz	Fastqsanger.gz
	SRR18715650_1.fastq.gz	Fastqsanger.gz
	SRR18715650_2.fastq.gz	Fastqsanger.gz
	SRR18715651_1.fastq.gz	Fastqsanger.gz

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scRNA-seq and scTCR-seq of autoreactive CD8 T cells from NOD mice

Project description:Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell-mediated destruction of pancreatic β cells. Our previous work has shown that diabetogenic CD8 T cells in the islets of the non-obese diabetic (NOD) mouse model of T1D are phenotypically heterogenous, but CD8 T cell clonal heterogeneity in this model remains relatively unexplored. Here, we use paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of NOD mice. Clonal analysis of scTCR-seq data demonstrates that CD8 T cells targeting the immunodominant β cell epitope IGRP206-214 exhibit highly restricted TCR gene usage, with over 70% of IGRP206-214-reactive cells utilizing the same TCR V alpha, J alpha, and V beta genes. Despite this, we observe only 5% overlap of IGRP206-214-reactive CD8 T cell clones between two groups of 10 NOD mice, demonstrating the immense TCR heterogeneity generated by junctional diversity during V(D)J recombination. scRNA-seq identifies two new clusters of autoreactive CD8 T cells in the islets and six clusters of diabetogenic CD8 T cells in the spleen, including multiple memory-like clusters and a population of exhausted cells. Strong clonal overlap between IGRP206-214-reactive CD8 T cells in the islets and spleen suggests that these cells may exit the islets and enter the peripheral circulation. Finally, we identify correlations between TCR J beta gene usage, which is less restricted than that of other TCR genes, and CD8 T cell clonal expansion as well as effector fate. Collectively, our work demonstrates that IGRP206-214-specific CD8 T cells are phenotypically heterogeneous but clonally similar, raising the possibility of selectively targeting either conserved or divergent TCR structures of these cells for therapeutic benefit.

2022-06-02 | GSE200608 | GEO

Paired scRNA-seq and scTCR-seq of GP33-specific CD8 T cells in chronic LCMV infection

Project description:Chronic viral infection results in CD8 T cell exhaustion. Here, we use paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) to investigate CD8 T cell phenotypic and clonal heterogeneity in multiple mice during the late stage of LCMV Clone 13 infection.

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Paired scRNA-seq and scTCR-seq of GP33-specific CD8 T cells in chronic LCMV infection

Project description:Paired scRNA-seq and scTCR-seq of GP33-specific CD8 T cells in chronic LCMV infection

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Murine bone marrow immature B cells: autoreactive versus non-autoreactive

Project description:Transcriptional profiling of mouse bone marrow B220+CD23–CD43–IgD– autoreactive immature B cells from 3-83Igi,Rag1-/-,H-2b mice relative to non-autoreactive immature B cells from 3-83Igi,H-2d mice. Goal was to determine genes that potentially mediate negative and positive selection of immature B cells. Biological replicates: 2 autoreactive replicate against, 2 non-autoreactive replicates

2010-08-31 | E-GEOD-22802 | biostudies-arrayexpress

Ubiquitin Thioesterase OTUB2 is An Endoplasmic Reticulum Stress-associated β Cell Autoantigen Targeted by CD8+ T cells in Type 1 Diabetes

Project description:Autoreactive CD8+ T cell plays a key role in the pathogenesis of Type 1 diabetes (T1D), but the antigen spectrum that activate autoreactive CD8+ T cells is still not completely clear. Endoplasmic reticulum stress（ERS）has been implicated in the generation of β cell autoantigens and the enhanced immune visibility of β cells to autoreactive T cells. Here, we in-depth analyzed the major histocompatibility complex class I (MHC-I) associated immunopeptidome (MIP) of islets β cell under steady-state and ERS-state, and found couples of peptides exclusively present in the MIP of β cell line under ERS state. Among them, peptide OTUB258-66 derived from ubiquitin thioesterase OTUB2 showed immunodominance in NOD mice, and autoreactive CD8+ T cells targeting OTUB258-66 were diabetogenic in NOD mice. High glucose intake upregulated the expression of OTUB2 in the pancreas and amplified the OTUB258-66-specific CD8+ T cell response in NOD mice. Repeated administration with OTUB258-66 significantly reduced the incidence of T1D in NOD mice. This study not only provides an explanation for the role of ERS induced by environmental factors such as high glucose intake in promoting β cell autoimmune injury, but also provides a novel ERS-associated β cell autoantigens for developing specific immune intervention in prevention and treatment of T1D.

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Nfkbid-overexpression and -ablation enhances thymic deletion of autoreactive AI4 CD8 T-cells

Project description:Purpose: Analyze genes involved in the negative selection of CD4CD8 double positive thymocytes from NOD-AI4 control mice, NOD-AI4-Nfkbid-/- (KO) and NOD-AI4-60A undergoing negative selection. Methods: RNA-Seq based gene expression analyses were used to identify differentially expressed genes in CD4CD8 double positive thymocytes from NOD-AI4 (control), NOD-AI4-Nfkbid-/- (KO) and NOD-AI4-60A undergoing negative selection.

2022-05-16 | GSE176566 | GEO

PD-1-PD-L1 Axis Activation Suppresses CD8+ T Cells and Improves Nephritis [scRNA-seq, scTCR-seq]

Project description:PD-1-PD-L1 Axis Activation Suppresses CD8+ T Cells and Improves Nephritis [scRNA-seq, scTCR-seq]

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Nfkbid represents an Idd7 locus gene contributing to impaired thymic deletion of CD8 T-cells in NOD mice

Project description:In both NOD mice and humans, the development of type 1 diabetes (T1D) is dependent in part on autoreactive CD8+ T-cells recognizing pancreatic ß-cell peptides presented by often quite common MHC class I variants. Studies in NOD mice previously revealed the common H2-Kd and/or H2-Db class I molecules expressed by this strain acquire an aberrant ability to mediate pathogenic CD8 T-cell responses through interactions with T1D susceptibility (Idd) genes outside the MHC. A gene(s) mapping to the Idd7 locus on proximal Chromosome 7 was previously shown to be an important contributor to the failure of the common class I molecules expressed by NOD mice to mediate the normal thymic negative selection of diabetogenic CD8+ T-cells. Using an inducible model of thymic negative selection and mRNA transcript analyses we initially identified an elevated Nfkbid expression variant as a strong candidate for an NOD Idd7 region gene contributing to impaired thymic deletion of diabetogenic CD8+ T-cells. CRISPR/Cas9-mediated genetic attenuation of Nfkbid expression in NOD mice resulted in improved negative selection of autoreactive diabetogenic AI4 and NY8.3 CD8+ T-cells. These results indicated allelic variants of Nfkbid represent an Idd7 gene contributing to the efficiency of intrathymic deletion of diabetogenic CD8+ T-cells. However, while enhancing thymic deletion of pathogenic CD8+ T-cells, ablation of Nfkbid expression surprisingly accelerated T1D onset in NOD mice likely by numerically decreasing regulatory T- and B-lymphocytes (Tregs/Bregs), thereby reducing their peripheral immunosuppressive effects. We used microarray analysis to identify differentialy expressed genes in thymus under conditions of induced thymic negative selection. We compare two mice strains, NOD-LCMV vs NOD.Ln82-LCMV (a congenic stock for a C57BL/6 derived segment delimited by markers D7Mit117–D7Mit247).

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Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer [scTCR-seq]

Project description:Purpose: The goal of this study is to delineate the processes of CD8+ T cell differentiation in primary NSCLC by integrating transcriptomic and tcr profiles. Methods: A combination of single cell RNA and TCR sequencing (scRNA-seq and scTCR- seq) was used, in tumors, normal tissues adjacent to the tumor (juxta-tumor), and circulating blood derived from 11 patients with untreated, primary NSCLC. Results: We show that precursor, memory-like CD8+ TILs include 2 main populations: one is also present in the blood (circulating precursors); the other is also present in juxta-tumor tissue and bears markers of memory resident T cells (resident precursors). Both precursor subtypes differentiate into a main population of terminal effectors through a similar “transitional” stage. Terminal effectors are not observed in blood or juxta-tumor tissue, are more clonally expanded, and express signatures of exhaustion. A significant proportion of transitional and terminal effectors also express cell cycle signatures and Ki67, suggesting that clonal expansion occurs in situ is part of the terminal differentiation process.

2021-01-29 | GSE162499 | GEO

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