Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA379013: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of T-cell clone)

Source: NCBI / GSE96562
Submission Date: Mar 13 2017
Release Date: Jun 08 2017
Update Date: May 15 2019

Summary: Islet-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects are thought to be involved in disease pathogenesis, but full understanding of their role is complicated by their presence also in blood of in healthy subjects. To elucidate their role in T1D, we have combined flow cytometry and single cell RNA sequencing (RNA-seq) techniques to link prior antigen exposure, inferred from expanded TCR clonotypes, and functional capacities of islet antigen-reactive CD4+ memory T cells. We find that cells activated by pooled peptides from immunodominant islet antigens showed significantly higher clonotype sharing within recent onset T1D subjects than in healthy individuals, consistent with in vivo T cell expansion during disease progression. There was no clonotype sharing between donors, indicating a predominance of TCRs with distinct or “private” specificities. Expanded clonotypes could be stable, as one was detected at repeat visits by spanning more than a year by one subject. We identified distinct IGRP peptides as the targets of expanded TCR clonotypes from two T1D subjects, thereby implicating this molecule as a trigger for CD4+ T cell expansion during T1D. Transcriptome profiles of cells from T1D and healthy subjects differed, particularly in cells having the most highly expanded TCR clonotypes. As a group, cells with the most highly expanded TCR clonotypes showed Th2-like phenotypes, but at the single cell level there was phenotypic heterogeneity within and between donors. Our findings demonstrate unique specificities and phenotypes of individual islet-reactive CD4+ memory T cells that have expanded during disease progression.

Overall Design: This project contains RNA-seq files from four cell types: 1) T cell clone (N=149 single cell profiles); 2) T cell clone (N=9 bulk cell profiles); 3) CD8+ influenza-reactive T cells (N=45 single cell profiles); and 4) CD4+ pooled islet antigen-reactive T cells (N=246 single cell profiles).

GEN Datasets:
GEND000221
Strategy:
Species:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Single cells were captured on a C1 system, using a 5-10 um mRNA Seq IFC according to manufacturer^ instructions (Fluidigm, South San Francisco, CA). Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA).
Library Construction Protocol: Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer^ instructions (Illumina, San Diego, CA).
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiScanSQ
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.
Journal of immunology (Baltimore, Md. : 1950) . 2017-05-31 [PMID: 28566371]