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Lamothe RC, Storlie MD, Espinosa DA, Rudlaff R, Browne P, Liu J, Rivas A, Devoto A, Oki J, Khoubyari A, Goltsman DSA, Lin JL, Butterfield CN, Brown CT, Thomas BC, Cost GJ. Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering. CRISPR J 2023. [PMID: 37219969 DOI: 10.1089/crispr.2022.0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery and characterization of improved, novel gene-editing systems from metagenomic data. In this study, we substantially advance this work with three such gene-editing systems, demonstrating their utility for cell therapy development. All three systems are capable of reproducible, high-frequency gene editing in primary immune cells. In human T cells, disruption of the T cell receptor (TCR) alpha-chain was induced in >95% of cells, both paralogs of the TCR beta-chain in >90% of cells, and >90% knockout of β2-microglobulin, TIGIT, FAS, and PDCD1. Simultaneous double knockout of TRAC and TRBC was obtained at a frequency equal to that of the single edits. Gene editing with our systems had minimal effect on T cell viability. Furthermore, we integrate a chimeric antigen receptor (CAR) construct into TRAC (up to ∼60% of T cells), and demonstrate CAR expression and cytotoxicity. We next applied our novel gene-editing tools to natural killer (NK) cells, B cells, hematopoietic stem cells, and induced pluripotent stem cells, generating similarly efficient cell-engineering outcomes including the creation of active CAR-NK cells. Interrogation of our gene-editing systems' specificity reveals a profile comparable with or better than Cas9. Finally, our nucleases lack preexisting humoral and T cell-based immunity, consistent with their sourcing from nonhuman pathogens. In all, we show these new gene-editing systems have the activity, specificity, and translatability necessary for use in cell therapy development.
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Affiliation(s)
| | | | | | | | | | - Jason Liu
- Metagenomi, Inc., Emeryville, California, USA
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Pennell CA, Campbell H, Storlie MD, Bolivar-Wagers S, Osborn MJ, Refaeli Y, Jensen M, Viaud S, Young TS, Blazar BR. Human CD19-specific switchable CAR T-cells are efficacious as constitutively active CAR T-cells but cause less morbidity in a mouse model of human CD19 + malignancy. J Immunother Cancer 2022; 10:e005934. [PMID: 36521930 PMCID: PMC9756162 DOI: 10.1136/jitc-2022-005934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Current Food and Drug Administration (FDA)-approved CD19-specific chimeric antigen receptor (CAR) T-cell therapies for B-cell malignancies are constitutively active and while efficacious, can cause morbidity and mortality. Their toxicities might be reduced if CAR T-cell activity was regulatable rather than constitutive. To test this, we compared the efficacies and morbidities of constitutively active (conventional) and regulatable (switchable) CAR (sCAR) T-cells specific for human CD19 (huCD19) in an immune-competent huCD19+ transgenic mouse model.Conventional CAR (CAR19) and sCAR T-cells were generated by retrovirally transducing C57BL/6 (B6) congenic T-cells with constructs encoding antibody-derived single chain Fv (sFv) fragments specific for huCD19 or a peptide neoepitope (PNE), respectively. Transduced T-cells were adoptively transferred into huCD19 transgenic hemizygous (huCD19Tg/0 ) B6 mice; healthy B-cells in these mice expressed huCD19Tg Prior to transfer, recipients were treated with a lymphodepleting dose of cyclophosphamide to enhance T-cell engraftment. In tumor therapy experiments, CAR19 or sCAR T-cells were adoptively transferred into huCD19Tg/0 mice bearing a syngeneic B-cell lymphoma engineered to express huCD19. To regulate sCAR T cell function, a switch protein was generated that contained the sCAR-specific PNE genetically fused to an anti-huCD19 Fab fragment. Recipients of sCAR T-cells were injected with the switch to link sCAR effector with huCD19+ target cells. Mice were monitored for survival, tumor burden (where appropriate), morbidity (as measured by weight loss and clinical scores), and peripheral blood lymphocyte frequency.CAR19 and sCAR T-cells functioned comparably regarding in vivo expansion and B-cell depletion. However, sCAR T-cells were better tolerated as evidenced by the recipients' enhanced survival, reduced weight loss, and improved clinical scores. Discontinuing switch administration allowed healthy B-cell frequencies to return to pretreatment levels.In our mouse model, sCAR T-cells killed huCD19+ healthy and malignant B-cells and were better tolerated than CAR19 cells. Our data suggest sCAR might be clinically superior to the current FDA-approved therapies for B-cell lymphomas due to the reduced acute and chronic morbidities and mortality, lower incidence and severity of side effects, and B-cell reconstitution on cessation of switch administration.
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Affiliation(s)
- Christopher A Pennell
- Laboratory Medicine and Pathology, Masonic Cancer Center, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
| | - Heather Campbell
- Laboratory Medicine and Pathology, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
| | - Meghan D Storlie
- Laboratory Medicine and Pathology, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
| | - Sara Bolivar-Wagers
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
| | - Mark J Osborn
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
| | - Yosef Refaeli
- Department of Dermatology, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Michael Jensen
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sophie Viaud
- Calibr, The Scripps Research Institute, La Jolla, California, USA
| | - Travis S Young
- Calibr, The Scripps Research Institute, La Jolla, California, USA
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Medical School Twin Cities, Minneapolis, Minnesota, USA
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Pennell CA, Barnum JL, McDonald-Hyman CS, Panoskaltsis-Mortari A, Riddle MJ, Xiong Z, Loschi M, Thangavelu G, Campbell HM, Storlie MD, Refaeli Y, Furlan SN, Jensen MC, Kean LS, Miller JS, Tolar J, Osborn MJ, Blazar BR. Human CD19-Targeted Mouse T Cells Induce B Cell Aplasia and Toxicity in Human CD19 Transgenic Mice. Mol Ther 2018; 26:1423-1434. [PMID: 29735365 PMCID: PMC5986973 DOI: 10.1016/j.ymthe.2018.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 01/28/2023] Open
Abstract
The clinical success of chimeric antigen receptor (CAR) T cell therapy for CD19+ B cell malignancies can be limited by acute toxicities and immunoglobulin replacement needs due to B cell aplasia from persistent CAR T cells. Life-threatening complications include cytokine release syndrome and neurologic adverse events, the exact etiologies of which are unclear. To elucidate the underlying toxicity mechanisms and test potentially safer CAR T cells, we developed a mouse model in which human CD19 (hCD19)-specific mouse CAR T cells were adoptively transferred into mice whose normal B cells express a hCD19 transgene at hemizygous levels. Compared to homozygous hCD19 transgenic mice that have ∼75% fewer circulating B cells, hemizygous mice had hCD19 frequencies and antigen density more closely simulating human B cells. Hemizygous mice given a lethal dose of hCD19 transgene-expressing lymphoma cells and treated with CAR T cells had undetectable tumor levels. Recipients experienced B cell aplasia and antigen- and dose-dependent acute toxicities mirroring patient complications. Interleukin-6 (IL-6), interferon γ (IFN-γ), and inflammatory pathway transcripts were enriched in affected tissues. As in patients, antibody-mediated neutralization of IL-6 (and IFN-γ) blunted toxicity. Apparent behavioral abnormalities associated with decreased microglial cells point to CAR-T-cell-induced neurotoxicity. This model will prove useful in testing strategies designed to improve hCD19-specific CAR T cell safety.
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Affiliation(s)
- Christopher A Pennell
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jessie L Barnum
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cameron S McDonald-Hyman
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Megan J Riddle
- Stem Cell Institute, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhengming Xiong
- Division of Hematology and Oncology, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Loschi
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Govindarajan Thangavelu
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Heather M Campbell
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Meghan D Storlie
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yosef Refaeli
- Department of Dermatology, University of Colorado, Aurora, CO 80045, USA
| | - Scott N Furlan
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Ben Towne Center for Childhood Cancer, The Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98101, USA
| | - Michael C Jensen
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Ben Towne Center for Childhood Cancer, The Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98101, USA
| | - Leslie S Kean
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, The Ben Towne Center for Childhood Cancer, The Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98101, USA
| | - Jeffrey S Miller
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jakub Tolar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark J Osborn
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruce R Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
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