CRISPR screens decode cancer cell pathways that trigger γδ T cell detection

  • Nature. 2023 Aug 30. doi: 10.1038/s41586-023-06482-x.
Murad R Mamedov  1  2 ,  Shane Vedova  #  3  4 ,  Jacob W Freimer  #  3  4  5 ,  Avinash Das Sahu  6  7  8 ,  Amrita Ramesh  9 ,  Maya M Arce  3  4 ,  Angelo D Meringa  10 ,  Mineto Ota  3  4  5 ,  Peixin Amy Chen  3  4 ,  Kristina Hanspers  11 ,  Vinh Q Nguyen  3  12  13  14 ,  Kirsten A Takeshima  3 ,  Anne C Rios  15  16 ,  Jonathan K Pritchard  5  17 ,  Jürgen Kuball  10  18 ,  Zsolt Sebestyen  10 ,  Erin J Adams  9  19 ,  Alexander Marson  20  21  22  23  24  25  26  27
Affiliations
  • 1. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. [email protected].
  • 2. Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 3. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
  • 4. Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
  • 5. Department of Genetics, Stanford University, Stanford, CA, USA.
  • 6. Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
  • 7. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • 8. UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA.
  • 9. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
  • 10. Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
  • 11. Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
  • 12. Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.
  • 13. Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
  • 14. UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA.
  • 15. Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
  • 16. Oncode Institute, Utrecht, the Netherlands.
  • 17. Department of Biology, Stanford University, Stanford, CA, USA.
  • 18. Department of Hematology, University Medical Center Utrecht, Utrecht, the Netherlands.
  • 19. Committee on Immunology, University of Chicago, Chicago, IL, USA.
  • 20. Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. [email protected].
  • 21. Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 22. Diabetes Center, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 23. Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 24. Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA. [email protected].
  • 25. UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 26. Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • 27. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA. [email protected].
  • # Contributed equally.
PMID: 37648854 DOI: 10.1038/s41586-023-06482-x
Abstract

γδ T cells are potent Anticancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or human leukocyte antigen background1-5. γδ T cells can sense conserved cell stress signals prevalent in transformed cells2,3, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vγ9Vδ2 T cells-the most abundant subset of human γδ T cells4-recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1 (refs. 6-8), a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here we combined genome-wide CRISPR screens in target Cancer cells to identify pathways that regulate γδ T cell killing and BTN3A cell surface expression. The screens showed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of γδ T cells through transcription, post-translational modifications and membrane trafficking. 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 both BTN3A and BTN2A1 during metabolic crises is 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 Vγ9Vδ2 T cell receptor-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of γδ T cell stress surveillance and suggests new avenues available to enhance γδ T cell Anticancer activity.

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