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Series GSE234778 Query DataSets for GSE234778
Status Public on Jun 17, 2023
Title A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track them in vivo. While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells. Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against EBV-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This approach has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens.
Overall design PBMCs from two EBV reactive healthy donors were pulsed with Peptivator EBV Consensus peptide pool in presence of IL4 and IL7. After three days of culture, T cells were engineered using CRISPR/Cas9 genome editing to integrate a GFP barcoded reporter gene with a library diversity of 3x10e4 into the CCR5 locus. After 7 additional days of expansion, single cell RNA sequencing data of GFP+ and GFP- sorted samples was generated.
Contributor(s) Palianina D, Di Roberto RB, Castellanos-Rueda R, Reddy ST, Khanna N
Citation(s) 37448595
Submission date Jun 12, 2023
Last update date Sep 12, 2023
Contact name Rocio Castellanos Rueda
Organization name ETH
Department D-BSSE
Lab Reddy LAB
Street address Mattenstrasse 26
City Basel
State/province --None--
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM7474568 D1_1_GFP+_GEX
GSM7474569 D1_2_GFP+_GEX
GSM7474570 D1_1_GFP-_GEX
BioProject PRJNA982888

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Supplementary file Size Download File type/resource
GSE234778_RAW.tar 394.8 Mb (http)(custom) TAR (of CSV, TAR)
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Raw data are available in SRA
Processed data provided as supplementary file

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