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Series GSE192828 Query DataSets for GSE192828
Status Public on May 05, 2023
Title Genome-wide CRISPR screens decode cancer cell pathways that trigger gamma-delta T cell detection and killing
Organism synthetic construct
Experiment type Other
Summary Gamma-delta T cells are potent anti-cancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or HLA background. Gamma-delta T cells can sense conserved cell stress signals prevalent in transformed cells, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vg9Vd2 T cells – the most abundant subset of human gamma-delta T cells – recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1, a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here, we layered genome-wide CRISPR screens in target cancer cells to identify pathways that regulate: (1) killing by gamma-delta T cells during co-culture, and (2) BTN3A cell surface expression. In addition to confirming the importance of the phosphoantigen-producing mevalonate pathway, the screens revealed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of gamma-delta T cells through transcription, post-translational modifications, membrane trafficking. Notably, IRF1 and ZNF217 were discovered to be positive and negative transcriptional regulators that directly occupy the promoters of BTN3A1/2/3 genes. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of BTN3A, as well as BTN2A1, during metabolic crises was dependent on AMP-activated protein kinase (AMPK). Finally, small molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vg9Vd2 TCR-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of gamma-delta T cell stress surveillance and suggests new avenues to enhance gamma-delta T cell anti-cancer activity.
 
Overall design Genome-wide CRISPR KO in Daudi-Cas9 cells, followed by co-culturing with primaryhuman Vg9Vd2 T cells
 
Contributor(s) Mamedov M, Vedova S, Freimer JW, Sahu AD, Ramesh A, Arce MM, Meringa AD, Ota M, Chen PA, Hanspers K, Nguyen VQ, Takeshima KA, Pritchard JK, Kuball J, Sebestyen Z, Adams EJ, Marson A
Citation(s) 37648854
Submission date Dec 30, 2021
Last update date Sep 08, 2023
Contact name Alexander Marson
E-mail(s) alexander.marson@ucsf.edu
Organization name Gladstone-UCSF Institute of Genomic Immunology
Street address 1650 Owens St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (1)
GPL26526 Illumina NovaSeq 6000 (synthetic construct)
Samples (4)
GSM5766301 CRISPR_Donor1_E:T_1:4
GSM5766302 CRISPR_Donor2_E:T_1:4
GSM5766303 CRISPR_Donor3_E:T_1:2
Relations
BioProject PRJNA793279

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
GSE192828_Killing_screen_counts.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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