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Series GSE185854 Query DataSets for GSE185854
Status Public on Oct 15, 2021
Title Epigenetic signature induced by prolonged culture may impact therapeutic function of Tregs used in adoptive cell therapy
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Adoptive transfer of regulatory T cells (Treg) is a promising new therapeutic option to treat detrimental inflammatory conditions. To reach sufficient cell yield for treatment, ex vivo isolated autologous or allogenic Tregs need to be expanded extensively in vitro during manufacturing of the Treg product. However, repetitive cycles of restimulation and prolonged culture have been shown to impact T cell phenotypes, functionality and fitness. We performed genome-wide DNA methylation profiling of cells throughout the manufacturing process of a polyclonal Treg product, which may be informative for predicting the cellular state and function of the final Treg product.
 
Overall design First generation (1st gen.) Treg products were generated from peripheral blood-derived starting material which is depleted of CD8+ cells and enriched for CD25-expressing cells using the CliniMACS system. The cells were expanded for 23 days with repetitive TCR stimulation (using antiCD3/CD28 microbeads, 8 stimulations in total) in the presence of IL2 and Rapamycin. Cells were harvested at multiple timepoints throughout expansion, and subjected to DNA methylation analysis with the Illumina MethylationEPIC Array.
 
Contributor(s) Ou K, Schulze A, Gasparoni G, Salhab A, Walter J, Polansky JK
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Submission date Oct 13, 2021
Last update date Oct 19, 2021
Contact name Julia Polansky
E-mail(s) julia.polansky-biskup@charite.de
Organization name Charité - Universitätsmedizin Berlin
Street address Augustenburger Platz 1
City Berlin
ZIP/Postal code 13353
Country Germany
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (83)
GSM5624661 1stgen.Treg.product_Run1_day0_rep1
GSM5624662 1stgen.Treg.product_Run1_day0_rep2
GSM5624663 1stgen.Treg.product_Run1_day0_rep3
Relations
BioProject PRJNA771074

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
GSE185854_RAW.tar 1.3 Gb (http)(custom) TAR (of IDAT)
Raw data provided as supplementary file
Processed data included within Sample table

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