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Series GSE178991 Query DataSets for GSE178991
Status Public on Sep 25, 2021
Title 10X genomics single cell GEX and VDJ 5' sequencing of PBMC from Type 1 Diabetes patients treated with Treg therapy alone or plus low dose IL-2
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Background: A previous Phase I study showed that the infusion of autologous Treg cells expanded ex-vivo into recent onset Type 1 Diabetes (T1D) patients had an excellent safety profile, however, the majority of the infused Tregs could no longer be detected in the peripheral blood three months post-infusion (NCT01210664-Treg-T1D Trial). Interleukin-2 (IL-2) is a well-characterized cytokine that has been shown to enhance human Treg cell survival and expansion at low doses in vivo. Therefore, a Phase 1 study (NCT02772679-TILT trial) was conducted combining a single infusion of autologous polyclonal Tregs, expanded ex vivo, followed by one or two 5-day courses of recombinant human low dose IL-2 (ld-IL-2) at 0.3 x 10^6 to 1 x 10^6 units/dose. The infusions had an acceptable safety profile, but all 9 patients failed to maintain C-peptide production at pre-treatment levels.
Results: Single cell gene expression analysis revealed that the combination therapy led to a transient increase in the number of infused and endogenous Tregs but also resulted in a significant increase from baseline in a subset of activated NK, Mucosal-associated invariant T (MAIT) and clonal CD8+ T populations from populations
 
Overall design CD45+ cells were isolated by FACS, combined into 30 pools and sequenced into three distinct batches. The data from each time point of each patient’s sample was then deconvoluted using the Demuxlet computational package. The gene expression profile and TCR sequencing of more than 400,000 cells was analyzed
Each sequenced sample is a mix of several patients and timepoints.
 
Contributor(s) Dong S, Bluestone JA
Citation(s) 34324441
Submission date Jun 27, 2021
Last update date Jun 29, 2022
Contact name Jeffrey A Bluestone
E-mail(s) Jeff.Bluestone@ucsf.edu
Phone 415-514-0417
Organization name UCSF
Lab Bluestone Lab, HSW 1112
Street address 513 Parnassus Ave
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (84)
GSM5402855 sorted CD45+ gene expression batch1 (V0)
GSM5402856 sorted CD45+ gene expression batch1 (V6)
GSM5402857 sorted CD45+ gene expression batch1 (V8)
Relations
BioProject PRJNA741804
SRA SRP325792

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
GSE178991_20201228_adata.h5ad.gz 2.5 Gb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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