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Lau E, Kwong G, Fowler TW, Sun BC, Donohoue PD, Davis RT, Bryan M, McCawley S, Clarke SC, Williams C, Banh L, Irby M, Edwards L, Storlie M, Kohrs B, Lilley GWJ, Smith SC, Gradia S, Fuller CK, Skoble J, Garner E, van Overbeek M, Kanner SB. Allogeneic chimeric antigen receptor-T cells with CRISPR-disrupted programmed death-1 checkpoint exhibit enhanced functional fitness. Cytotherapy 2023:S1465-3249(23)00091-9. [PMID: 37086241 DOI: 10.1016/j.jcyt.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/23/2023]
Abstract
BACKGROUND AIMS Therapeutic disruption of immune checkpoints has significantly advanced the armamentarium of approaches for treating cancer. The prominent role of the programmed death-1 (PD-1)/programmed death ligand-1 axis for downregulating T cell function offers a tractable strategy for enhancing the disease-modifying impact of CAR-T cell therapy. METHODS To address checkpoint interference, primary human T cells were genome edited with a next-generation CRISPR-based platform (Cas9 chRDNA) by knockout of the PDCD1 gene encoding the PD-1 receptor. Site-specific insertion of a chimeric antigen receptor specific for CD19 into the T cell receptor alpha constant locus was implemented to drive cytotoxic activity. RESULTS These allogeneic CAR-T cells (CB-010) promoted longer survival of mice in a well-established orthotopic tumor xenograft model of a B cell malignancy compared with identically engineered CAR-T cells without a PDCD1 knockout. The persistence kinetics of CB-010 cells in hematologic tissues versus CAR-T cells without PDCD1 disruption were similar, suggesting the robust initial debulking of established tumor xenografts was due to enhanced functional fitness. By single-cell RNA-Seq analyses, CB-010 cells, when compared with identically engineered CAR-T cells without a PDCD1 knockout, exhibited fewer Treg cells, lower exhaustion phenotypes and reduced dysfunction signatures and had higher activation, glycolytic and oxidative phosphorylation signatures. Further, an enhancement of mitochondrial metabolic fitness was observed, including increased respiratory capacity, a hallmark of less differentiated T cells. CONCLUSIONS Genomic PD-1 checkpoint disruption in the context of allogeneic CAR-T cell therapy may provide a compelling option for treating B lymphoid malignancies.
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Affiliation(s)
- Elaine Lau
- Caribou Biosciences, Inc., Berkeley, California, USA
| | - George Kwong
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | - Bee-Chun Sun
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | - Ryan T Davis
- Caribou Biosciences, Inc., Berkeley, California, USA
| | - Mara Bryan
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | | | | | - Lynda Banh
- Caribou Biosciences, Inc., Berkeley, California, USA
| | - Matthew Irby
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | | | - Bryan Kohrs
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | | | - Scott Gradia
- Caribou Biosciences, Inc., Berkeley, California, USA
| | | | - Justin Skoble
- Caribou Biosciences, Inc., Berkeley, California, USA
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2
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Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P. Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol Cell 2021; 81:3637-3649.e5. [PMID: 34478654 DOI: 10.1016/j.molcel.2021.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/28/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022]
Abstract
The off-target activity of the CRISPR-associated nuclease Cas9 is a potential concern for therapeutic genome editing applications. Although high-fidelity Cas9 variants have been engineered, they exhibit varying efficiencies and have residual off-target effects, limiting their applicability. Here, we show that CRISPR hybrid RNA-DNA (chRDNA) guides provide an effective approach to increase Cas9 specificity while preserving on-target editing activity. Across multiple genomic targets in primary human T cells, we show that 2'-deoxynucleotide (dnt) positioning affects guide activity and specificity in a target-dependent manner and that this can be used to engineer chRDNA guides with substantially reduced off-target effects. Crystal structures of DNA-bound Cas9-chRDNA complexes reveal distorted guide-target duplex geometry and allosteric modulation of Cas9 conformation. These structural effects increase specificity by perturbing DNA hybridization and modulating Cas9 activation kinetics to disfavor binding and cleavage of off-target substrates. Overall, these results pave the way for utilizing customized chRDNAs in clinical applications.
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Affiliation(s)
- Paul D Donohoue
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Elaine Lau
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Bastien Vidal
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Matthew J Irby
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - David B Nyer
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Tomer Rotstein
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Lynda Banh
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Mckenzi S Toh
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Jason Gibson
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Bryan Kohrs
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Kevin Baek
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Arthur L G Owen
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Euan M Slorach
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Megan van Overbeek
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Christopher K Fuller
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA
| | - Andrew P May
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Peter Cameron
- Caribou Biosciences, Inc., 2929 Seventh Street, Suite 105, Berkeley, CA 94710, USA.
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3
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Murakami H, Lam I, Huang PC, Song J, van Overbeek M, Keeney S. Multilayered mechanisms ensure that short chromosomes recombine in meiosis. Nature 2020; 582:124-128. [PMID: 32494071 PMCID: PMC7298877 DOI: 10.1038/s41586-020-2248-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/12/2020] [Indexed: 12/17/2022]
Abstract
In most species, homologous chromosomes must recombine in order to segregate accurately during meiosis1. Because small chromosomes would be at risk of missegregation if recombination were randomly distributed, the double-strand breaks (DSBs) that initiate recombination are not located arbitrarily2. How the nonrandomness of DSB distributions is controlled is not understood, although several pathways are known to regulate the timing, location and number of DSBs. Meiotic DSBs are generated by Spo11 and accessory DSB proteins, including Rec114 and Mer2, which assemble on chromosomes3-7 and are nearly universal in eukaryotes8-11. Here we demonstrate how Saccharomyces cerevisiae integrates multiple temporally distinct pathways to regulate the binding of Rec114 and Mer2 to chromosomes, thereby controlling the duration of a DSB-competent state. The engagement of homologous chromosomes with each other regulates the dissociation of Rec114 and Mer2 later in prophase I, whereas the timing of replication and the proximity to centromeres or telomeres influence the accumulation of Rec114 and Mer2 early in prophase I. Another early mechanism enhances the binding of Rec114 and Mer2 specifically on the shortest chromosomes, and is subject to selection pressure to maintain the hyperrecombinogenic properties of these chromosomes. Thus, the karyotype of an organism and its risk of meiotic missegregation influence the shape and evolution of its recombination landscape. Our results provide a cohesive view of a multifaceted and evolutionarily constrained system that allocates DSBs to all pairs of homologous chromosomes.
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Affiliation(s)
- Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Isabel Lam
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Ann Romney Center for Neurologic Disease, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pei-Ching Huang
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Jacquelyn Song
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Megan van Overbeek
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Caribou Biosciences, Inc., Berkeley, CA, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, Russ C, Reece-Hoyes JS, Nye C, Gradia S, Vidal B, Zheng J, Hoffman GR, Fuller CK, May AP. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks. Mol Cell 2016; 63:633-646. [PMID: 27499295 DOI: 10.1016/j.molcel.2016.06.037] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 12/16/2022]
Abstract
The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.
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Affiliation(s)
| | | | | | | | - Elizabeth Frias
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John S Reece-Hoyes
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Scott Gradia
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA
| | | | | | - Gregory R Hoffman
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Andrew P May
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA.
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5
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Sfeir A, Kabir S, van Overbeek M, Celli GB, de Lange T. Loss of Rap1 induces telomere recombination in the absence of NHEJ or a DNA damage signal. Science 2010; 327:1657-61. [PMID: 20339076 DOI: 10.1126/science.1185100] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Shelterin is an essential telomeric protein complex that prevents DNA damage signaling and DNA repair at mammalian chromosome ends. Here we report on the role of the TRF2-interacting factor Rap1, a conserved shelterin subunit of unknown function. We removed Rap1 from mouse telomeres either through gene deletion or by replacing TRF2 with a mutant that does not bind Rap1. Rap1 was dispensable for the essential functions of TRF2--repression of ATM kinase signaling and nonhomologous end joining (NHEJ)--and mice lacking telomeric Rap1 were viable and fertile. However, Rap1 was critical for the repression of homology-directed repair (HDR), which can alter telomere length. The data reveal that HDR at telomeres can take place in the absence of DNA damage foci and underscore the functional compartmentalization within shelterin.
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Affiliation(s)
- Agnel Sfeir
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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6
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Chen Y, Yang Y, van Overbeek M, Donigian JR, Baciu P, de Lange T, Lei M. A shared docking motif in TRF1 and TRF2 used for differential recruitment of telomeric proteins. Science 2008; 319:1092-6. [PMID: 18202258 DOI: 10.1126/science.1151804] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mammalian telomeres are protected by a six-protein complex: shelterin. Shelterin contains two closely related proteins (TRF1 and TRF2), which recruit various proteins to telomeres. We dissect the interactions of TRF1 and TRF2 with their shared binding partner (TIN2) and other shelterin accessory factors. TRF1 recognizes TIN2 using a conserved molecular surface in its TRF homology (TRFH) domain. However, this same surface does not act as a TIN2 binding site in TRF2, and TIN2 binding to TRF2 is mediated by a region outside the TRFH domain. Instead, the TRFH docking site of TRF2 binds a shelterin accessory factor (Apollo), which does not interact with the TRFH domain of TRF1. Conversely, the TRFH domain of TRF1, but not of TRF2, interacts with another shelterin-associated factor: PinX1.
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Affiliation(s)
- Yong Chen
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
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7
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van Overbeek M, de Lange T. Apollo, an Artemis-related nuclease, interacts with TRF2 and protects human telomeres in S phase. Curr Biol 2006; 16:1295-302. [PMID: 16730176 DOI: 10.1016/j.cub.2006.05.022] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [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] [Received: 04/03/2006] [Revised: 05/07/2006] [Accepted: 05/10/2006] [Indexed: 01/03/2023]
Abstract
Human chromosome ends are protected by shelterin, an abundant six-subunit protein complex that binds specifically to the telomeric-repeat sequences, regulates telomere length, and ensures that chromosome ends do not elicit a DNA-damage response (reviewed in). Using mass spectrometry of proteins associated with the shelterin component Rap1, we identified an SMN1/PSO2 nuclease family member that is closely related to Artemis. We refer to this protein as Apollo and report that Apollo has the ability to localize to telomeres through an interaction with the shelterin component TRF2. Although its low abundance at telomeres indicates that Apollo is not a core component of shelterin, Apollo knockdown with RNAi resulted in senescence and the activation of a DNA-damage signal at telomeres as evidenced by telomere-dysfunction-induced foci (TIFs). The TIFs occurred primarily in S phase, suggesting that Apollo contributes to a processing step associated with the replication of chromosome ends. Furthermore, some of the metaphase chromosomes showed two telomeric signals at single-chromatid ends, suggesting an aberrant telomere structure. We propose that the Artemis-like nuclease Apollo is a shelterin accessory factor required for the protection of telomeres during or after their replication.
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Affiliation(s)
- Megan van Overbeek
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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8
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Ye JZS, Donigian JR, van Overbeek M, Loayza D, Luo Y, Krutchinsky AN, Chait BT, de Lange T. TIN2 binds TRF1 and TRF2 simultaneously and stabilizes the TRF2 complex on telomeres. J Biol Chem 2004; 279:47264-71. [PMID: 15316005 DOI: 10.1074/jbc.m409047200] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [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: 11/06/2022] Open
Abstract
Human telomeres contain two related telomeric DNA-binding proteins, TRF1 and TRF2. The TRF1 complex contains the TRF1 interacting partner, TIN2, as well as PIP1 and POT1 and regulates telomere-length homeostasis. The TRF2 complex is primarily involved in telomere protection and contains the TRF2 interacting partner human (h)Rap1 as well as several factors involved in the DNA damage response. A prior report showed that conditional deletion of murine TRF1 reduced the presence of TRF2 on telomeres. Here we showed that TRF2 is also lost from human telomeres upon TRF1 depletion with small interfering RNA prompting a search for the connection between the TRF1 and TRF2 complexes. Using mass spectrometry and co-immunoprecipitation, we found that TRF1, TIN2, PIP1, and POT1 are associated with the TRF2-hRap1 complex. Gel filtration identified a TRF2 complex containing TIN2 and POT1 but not TRF1 indicating that TRF1 is not required for this interaction. Co-immunoprecipitation, Far-Western assays, and two-hybrid assays showed that TIN2, but not POT1 or PIP1, interacts directly with TRF2. Furthermore, TIN2 was found to bind TRF1 and TRF2 simultaneously, showing that TIN2 can link these telomeric proteins. This connection appeared to stabilize TRF2 on the telomeres as the treatment of cells with TIN2 small interfering RNA resulted in a decreased presence of TRF2 and hRap1 at chromosome ends. The TIN2-mediated cooperative binding of TRF1 and TRF2 to telomeres has important implications for the mechanism of telomere length regulation and protection.
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Affiliation(s)
- Jeffrey Zheng-Sheng Ye
- Laboratory for Cell Biology and Genetics, the Rockefeller University, New York, New York 10021, USA
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