In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma

CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of...

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Bibliographic Details
Published in:Immunity (Cambridge, Mass.) Mass.), 2021-03, Vol.54 (3), p.571-585.e6
Main Authors: Dubrot, Juan, Lane-Reticker, Sarah Kate, Kessler, Emily A., Ayer, Austin, Mishra, Gargi, Wolfe, Clara H., Zimmer, Margaret D., Du, Peter P., Mahapatra, Animesh, Ockerman, Kyle M., Davis, Thomas G.R., Kohnle, Ian C., Pope, Hans W., Allen, Peter M., Olander, Kira E., Iracheta-Vellve, Arvin, Doench, John G., Haining, W. Nicholas, Yates, Kathleen B., Manguso, Robert T.
Format: Article
Language:English
Subjects:
Animal models
Antibiotics
antigen presentation
Antigens
Autophagy
Biology
Cancer
checkpoint blockade
CRISPR
Drug resistance
Gene therapy
Genetic engineering
Genetic screening
Genome editing
Genomes
Genomics
Immune response
Immune system
immuno-oncology
Immunology
Immunotherapy
in vivo screen
Kidney cancer
Kinases
lentiviral vectors
Lymphocytes
Major histocompatibility complex
Melanoma
Natural Killer cells
Peptides
Phagocytosis
pooled screen
Recognition
Rejection
Renal cell carcinoma
target discovery
Therapeutic targets
Tumor cells
Tumors
Vectors (Biology)
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Summary:CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of CRISPR technologies in vivo. Here, we characterized immune responses against Cas9 and other expressed CRISPR vector components that cause antigen-specific tumor rejection in several mouse cancer models. To avoid unwanted immune recognition, we designed a lentiviral vector system that allowed selective CRISPR antigen removal (SCAR) from tumor cells. The SCAR system reversed immune-mediated rejection of CRISPR-modified tumor cells in vivo and enabled high-throughput genetic screens in previously intractable models. A pooled in vivo screen using SCAR in a CRISPR-antigen-sensitive renal cell carcinoma revealed resistance pathways associated with autophagy and major histocompatibility complex class I (MHC class I) expression. Thus, SCAR presents a resource that enables CRISPR-based studies of tumor-immune interactions and prevents unwanted immune recognition of genetically engineered cells, with implications for clinical applications. [Display omitted] •CRISPR vector components are immunogenic and cause rejection in mouse cancer models•The SCAR vector system allows removal of immunogens from CRISPR-edited cells•SCAR enables in vivo screening of antigen-sensitive cell lines•Renal cell carcinoma requires autophagy and MHC class I expression for immune evasion Dubrot et al. present the design of a scalable CRISPR vector system that removes Cas9 and other antigens after genome editing. They perform an in vivo genetic screen for immunotherapy dependencies in a murine renal cancer model that is sensitive to vector antigen expression.
ISSN:1074-7613
1097-4180
DOI:10.1016/j.immuni.2021.01.001