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Tieu V, Sotillo E, Bjelajac JR, Chen C, Malipatlolla M, Guerrero JA, Xu P, Quinn PJ, Fisher C, Klysz D, Mackall CL, Qi LS. A versatile CRISPR-Cas13d platform for multiplexed transcriptomic regulation and metabolic engineering in primary human T cells. Cell 2024; 187:1278-1295.e20. [PMID: 38387457 PMCID: PMC10965243 DOI: 10.1016/j.cell.2024.01.035] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
CRISPR technologies have begun to revolutionize T cell therapies; however, conventional CRISPR-Cas9 genome-editing tools are limited in their safety, efficacy, and scope. To address these challenges, we developed multiplexed effector guide arrays (MEGA), a platform for programmable and scalable regulation of the T cell transcriptome using the RNA-guided, RNA-targeting activity of CRISPR-Cas13d. MEGA enables quantitative, reversible, and massively multiplexed gene knockdown in primary human T cells without targeting or cutting genomic DNA. Applying MEGA to a model of CAR T cell exhaustion, we robustly suppressed inhibitory receptor upregulation and uncovered paired regulators of T cell function through combinatorial CRISPR screening. We additionally implemented druggable regulation of MEGA to control CAR activation in a receptor-independent manner. Lastly, MEGA enabled multiplexed disruption of immunoregulatory metabolic pathways to enhance CAR T cell fitness and anti-tumor activity in vitro and in vivo. MEGA offers a versatile synthetic toolkit for applications in cancer immunotherapy and beyond.
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Affiliation(s)
- Victor Tieu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeremy R Bjelajac
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal Chen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Meena Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justin A Guerrero
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick J Quinn
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chris Fisher
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dorota Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94080, USA.
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Freitas KA, Belk JA, Sotillo E, Quinn PJ, Ramello MC, Malipatlolla M, Daniel B, Sandor K, Klysz D, Bjelajac J, Xu P, Burdsall KA, Tieu V, Duong VT, Donovan MG, Weber EW, Chang HY, Majzner RG, Espinosa JM, Satpathy AT, Mackall CL. Enhanced T cell effector activity by targeting the Mediator kinase module. Science 2022; 378:eabn5647. [PMID: 36356142 PMCID: PMC10335827 DOI: 10.1126/science.abn5647] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
T cells are the major arm of the immune system responsible for controlling and regressing cancers. To identify genes limiting T cell function, we conducted genome-wide CRISPR knockout screens in human chimeric antigen receptor (CAR) T cells. Top hits were MED12 and CCNC, components of the Mediator kinase module. Targeted MED12 deletion enhanced antitumor activity and sustained the effector phenotype in CAR- and T cell receptor-engineered T cells, and inhibition of CDK8/19 kinase activity increased expansion of nonengineered T cells. MED12-deficient T cells manifested increased core Meditator chromatin occupancy at transcriptionally active enhancers-most notably for STAT and AP-1 transcription factors-and increased IL2RA expression and interleukin-2 sensitivity. These results implicate Mediator in T cell effector programming and identify the kinase module as a target for enhancing potency of antitumor T cell responses.
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Affiliation(s)
- Katherine A. Freitas
- Immunology Graduate Program, Stanford University School of
Medicine, Stanford, CA, USA
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally: KAF and JAB
| | - Julia A. Belk
- Department of Computer Science, Stanford University,
Stanford, CA, USA
- These authors contributed equally: KAF and JAB
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick J. Quinn
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Maria C. Ramello
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Meena Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Center for Personal Dynamic Regulomes, Stanford University,
Stanford, CA, USA
- Department of Pathology, Stanford University School of
Medicine, Stanford, CA, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University School of
Medicine, Stanford, CA, USA
| | - Dorota Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Jeremy Bjelajac
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative
Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Kylie A. Burdsall
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
| | - Victor Tieu
- Department of Bioengineering, Stanford University School of
Medicine, Stanford, CA, USA
| | - Vandon T. Duong
- Department of Bioengineering, Stanford University School of
Medicine, Stanford, CA, USA
| | - Micah G. Donovan
- Department of Pharmacology, University of Colorado
Anschutz Medical Campus, Aurora, Colorado, USA
| | - Evan W. Weber
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco,
CA, USA
- Present address: Department of Pediatrics, University of
Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Y. Chang
- Parker Institute for Cancer Immunotherapy, San Francisco,
CA, USA
- Center for Personal Dynamic Regulomes, Stanford University,
Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University,
Stanford, CA, USA
| | - Robbie G. Majzner
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- Division of Pediatric Hematology/Oncology/Stem Cell
Transplant and Regenerative Medicine, Department of Pediatrics, Stanford University
School of Medicine, Stanford, CA, USA
| | - Joaquin M. Espinosa
- Department of Pharmacology, University of Colorado
Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of
Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ansuman T. Satpathy
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco,
CA, USA
- Department of Pathology, Stanford University School of
Medicine, Stanford, CA, USA
- These authors contributed equally: ATS and CLM
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute,
Stanford University School of Medicine, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco,
CA, USA
- Division of Pediatric Hematology/Oncology/Stem Cell
Transplant and Regenerative Medicine, Department of Pediatrics, Stanford University
School of Medicine, Stanford, CA, USA
- Division of BMT and Cell Therapy, Department of Medicine,
Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally: ATS and CLM
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Lynn RC, Weber EW, Sotillo E, Gennert D, Xu P, Good Z, Anbunathan H, Lattin J, Jones R, Tieu V, Nagaraja S, Granja J, de Bourcy CFA, Majzner R, Satpathy AT, Quake SR, Monje M, Chang HY, Mackall CL. c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature 2019; 576:293-300. [PMID: 31802004 PMCID: PMC6944329 DOI: 10.1038/s41586-019-1805-z] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/17/2019] [Indexed: 02/07/2023]
Abstract
Chimeric antigen receptor (CAR) T cells mediate anti-tumour effects in a small subset of patients with cancer1-3, but dysfunction due to T cell exhaustion is an important barrier to progress4-6. To investigate the biology of exhaustion in human T cells expressing CAR receptors, we used a model system with a tonically signaling CAR, which induces hallmark features of exhaustion6. Exhaustion was associated with a profound defect in the production of IL-2, along with increased chromatin accessibility of AP-1 transcription factor motifs and overexpression of the bZIP and IRF transcription factors that have been implicated in mediating dysfunction in exhausted T cells7-10. Here we show that CAR T cells engineered to overexpress the canonical AP-1 factor c-Jun have enhanced expansion potential, increased functional capacity, diminished terminal differentiation and improved anti-tumour potency in five different mouse tumour models in vivo. We conclude that a functional deficiency in c-Jun mediates dysfunction in exhausted human T cells, and that engineering CAR T cells to overexpress c-Jun renders them resistant to exhaustion, thereby addressing a major barrier to progress for this emerging class of therapeutic agents.
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Affiliation(s)
- Rachel C Lynn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Lyell Immunopharma, South San Francisco, CA, USA
| | - Evan W Weber
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - David Gennert
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Peng Xu
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Zinaida Good
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Hima Anbunathan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - John Lattin
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Jones
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Victor Tieu
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Surya Nagaraja
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Charles F A de Bourcy
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Initiative, San Francisco, CA, USA
| | - Robbie Majzner
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Michelle Monje
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurology, Stanford University, Stanford, CA, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Crystal L Mackall
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. .,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Miller JB, Kos P, Tieu V, Zhou K, Siegwart DJ. Development of Cationic Quaternary Ammonium Sulfonamide Amino Lipids for Nucleic Acid Delivery. ACS Appl Mater Interfaces 2018; 10:2302-2311. [PMID: 29286232 DOI: 10.1021/acsami.7b15982] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Lipid nanoparticles (LNPs) currently comprise the most effective carrier class for the delivery of small RNAs. Among lipid carriers, charge-unbalanced lipids are relatively unexplored synthetically. Herein, we developed and evaluated a novel collection of compounds for small interfering RNA (siRNA) delivery, termed cationic quaternary ammonium sulfonamide amino lipids (CSALs). The formulated CSAL LNPs containing cholesterol, 1,2-distearoyl-sn-glycero-3-phosphocholine, and lipid poly(ethylene glycol) exhibited biophysical property trends directly related to the CSAL chemical structure. Lead CSAL LNPs were identified using an siRNA delivery screen. Further chemical synthesis using a rational structure-guided design showed that the head group structure could alter the pKa and other physical properties that modulated delivery efficacy. Shorter-chained dimethylamino head groups, acetate side chains, and higher tail carbon numbers were favorable for delivery. This led to a further study of A3-OAc-C2Me LNPs, which enabled in vivo delivery to normal mouse lungs and subcutaneous and orthotopic lung tumors. Incorporation of CSALs into liver-targeting formulations shifted the in vivo delivery of these carriers to the lungs. This study highlights the importance of the cationic lipid structure in LNPs and provides further design guidelines for nucleic acid carriers.
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Affiliation(s)
- Jason B Miller
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Petra Kos
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Victor Tieu
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Kejin Zhou
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Daniel J Siegwart
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
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