GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE228233 Query DataSets for GSE228233
Status Public on Jul 05, 2023
Title 10X single-cell RNA-seq profiling of T cells from the pancreas, pancreatic lymph nodes, and blood of NOD mice with spontaneous or anti-PD-1-induced Type 1 Diabetes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Immune-related adverse events (irAEs) are a notable complication of PD-1 cancer immunotherapy. A better understanding of how these iatrogenic diseases compare to naturally arising autoimmune diseases is needed for treatment and monitoring of irAEs. We identified differences in anti-PD-1-induced Type 1 Diabetes (T1D) and spontaneous T1D in non-obese diabetic (NOD) mice by performing single-cell RNA-seq and TCR-seq on T cells from the pancreas, pancreas-draining lymph node (pLN), and blood of mice with PD-1-induced T1D or spontaneous T1D. In the pancreas, anti-PD-1 resulted in expansion of terminally-exhausted/effector-like CD8+ T cells, an increase in T-bethi CD4+FoxP3- T cells, and a decrease in memory CD4+FoxP3- and CD8+ T cells in contrast to spontaneous T1D. Notably, anti-PD-1 caused increased TCR sharing between the pancreas and the periphery. Moreover, T cells in the blood of anti-PD-1-treated mice expressed markers that differed from spontaneous T1D, suggesting that the blood may provide a window to monitor irAEs rather than relying exclusively on the autoimmune target organ.
Overall design 10X 5' single cell RNASeq and paired TCR sequencing was performed on sorted TCR-beta+CD11A+ T cells from the pancreas, pancreatic lymph nodes, and peripheral blood of NOD mice. Samples from individual mice were labeled using hashtag antibodies and detected using CITE-seq. Using the TCR sequence as a molecular barcode, we identified matching T cell clones between the pancreatic lymph node, blood and pancreas, and characterized the matching versus non-matching T cell populations within a tissue compartment and between tissue compartments.
Please note that processed data files generated from both *FB* and *GEX* raw data are linked to the corresponding *GEX* sample records.
Web link http://10.1084/jem.20221920
Contributor(s) Collier JL, Pauken KE, Sharpe AH
Citation(s) 37432393
Submission date Mar 26, 2023
Last update date Jul 28, 2023
Contact name Jenna Lynn Collier
Organization name Harvard University
Department Immunology
Street address 77 Avenue Louis Pasteur
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (27)
GSM7117468 pan_FB_IgG
GSM7117469 pan_FB_PD1
GSM7117470 pan_FB_Spt
BioProject PRJNA948872

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE228233_RAW.tar 337.6 Mb (http)(custom) TAR (of CSV, MTX, TSV)
GSE228233_all_cells_integrated.rds.gz 1.0 Gb (ftp)(http) RDS
GSE228233_cd4_pancreas_only.rds.gz 249.9 Mb (ftp)(http) RDS
GSE228233_cd8_pancreas_only.rds.gz 197.9 Mb (ftp)(http) RDS
GSE228233_feature_barcoding_antibody_reference.csv.gz 250 b (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap