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Greig JA, Martins KM, Breton C, Lamontagne RJ, Zhu Y, He Z, White J, Zhu JX, Chichester JA, Zheng Q, Zhang Z, Bell P, Wang L, Wilson JM. Integrated vector genomes may contribute to long-term expression in primate liver after AAV administration. Nat Biotechnol 2024; 42:1232-1242. [PMID: 37932420 PMCID: PMC11324525 DOI: 10.1038/s41587-023-01974-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/29/2023] [Indexed: 11/08/2023]
Abstract
The development of liver-based adeno-associated virus (AAV) gene therapies is facing concerns about limited efficiency and durability of transgene expression. We evaluated nonhuman primates following intravenous dosing of AAV8 and AAVrh10 vectors for over 2 years to better define the mechanism(s) of transduction that affect performance. High transduction of non-immunogenic transgenes was achieved, although expression declined over the first 90 days to reach a lower but stable steady state. More than 10% of hepatocytes contained single nuclear domains of vector DNA that persisted despite the loss of transgene expression. Greater reductions in vector DNA and RNA were observed with immunogenic transgenes. Genomic integration of vector sequences, including complex concatemeric structures, were detected in 1 out of 100 cells at broadly distributed loci that were not in proximity to genes associated with hepatocellular carcinoma. Our studies suggest that AAV-mediated transgene expression in primate hepatocytes occurs in two phases: high but short-lived expression from episomal genomes, followed by much lower but stable expression, likely from integrated vectors.
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Affiliation(s)
- Jenny A Greig
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly M Martins
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Camilo Breton
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Jason Lamontagne
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yanqing Zhu
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhenning He
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John White
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jing-Xu Zhu
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica A Chichester
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qi Zheng
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhe Zhang
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter Bell
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lili Wang
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Wang SY, Scurti GM, Dalheim AV, Quinn S, Stiff PJ, Nishimura MI. Nonactivated and IL-7 cultured CD19-specific CAR T cells are enriched in stem cell phenotypes and functionally superior. Blood Adv 2024; 8:324-335. [PMID: 37967375 PMCID: PMC10788799 DOI: 10.1182/bloodadvances.2023010607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023] Open
Abstract
ABSTRACT CD19-specific chimeric antigen receptor (CAR) T cells have demonstrated impressive responses in patients with relapsed and refractory B cell malignancies. However, many patients relapse or fail to respond to CD19 CAR T cells, demonstrating the need to improve its efficacy and durability. Current protocols for generating CAR T cells involve T cell activation through CD3 stimulation to facilitate efficient CAR transfer followed by ex vivo expansion with exogenous cytokines to obtain adequate cell numbers for treatment. Both T cell activation and expansion inevitably lead to terminal differentiation and replicative senescence, which are suboptimal for therapy. Interleukin-7 (IL-7) was previously shown to allow for lentiviral transduction of T cells in the absence of activation. In these studies, we used IL-7 to generate CD19 CAR T cells without stimulating CD3. Nonactivated and IL-7 cultured (NICE) CD19 CAR T cells were enriched with the T memory stem cell population, retained novel markers of stemness, had lower expression of exhaustion markers, and increased proliferative potential. Furthermore, our findings are consistent with engraftment of NICE CD19 CAR T cells and demonstrate a superior therapeutic response in both intraperitoneal and subcutaneous in vivo B cell lymphoma models. These results suggest that NICE CD19 CAR T cells may improve outcomes for B cell malignancies and warrant clinical evaluation.
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Affiliation(s)
- Siao-Yi Wang
- Department of Medicine, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
| | - Gina M. Scurti
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
| | - Annika V. Dalheim
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
| | - Suzanne Quinn
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
| | - Patrick J. Stiff
- Department of Medicine, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
| | - Michael I. Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL
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3
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Gabrielli G, Shouval R, Ghilardi G, van den Brink M, Ruella M. Harnessing the Gut Microbiota to Potentiate the Efficacy of CAR T Cell Therapy. Hemasphere 2023; 7:e950. [PMID: 37637993 PMCID: PMC10448936 DOI: 10.1097/hs9.0000000000000950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Affiliation(s)
- Giulia Gabrielli
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Italy
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Roni Shouval
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Guido Ghilardi
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Marcel van den Brink
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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4
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Cabrera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE, Deans TL. The sound of silence: Transgene silencing in mammalian cell engineering. Cell Syst 2022; 13:950-973. [PMID: 36549273 PMCID: PMC9880859 DOI: 10.1016/j.cels.2022.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.
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Affiliation(s)
- Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX 77005, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hailey I Edelstein
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Fokion Glykofrydis
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Kasey S Love
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Sarah Lensch
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Mark Livingston
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Urbana, IL 61801, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA
| | - Yvonne Y Chen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy Center at UCLA, Los Angeles, CA 90095, USA
| | - Ahmad S Khalil
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Wilson W Wong
- Biological Design Center and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033-9080, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel 4058, Switzerland
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Joshua N Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; The Eli and Edythe Broad CIRM Center, Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA.
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A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry. Nat Commun 2022; 13:7189. [PMID: 36424374 PMCID: PMC9691722 DOI: 10.1038/s41467-022-34896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
MHC restriction, which describes the binding of TCRs from CD4+ T cells to class II MHC proteins and TCRs from CD8+ T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+ T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.
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Rangan P, Mondino A. Microbial short-chain fatty acids: a strategy to tune adoptive T cell therapy. J Immunother Cancer 2022; 10:jitc-2021-004147. [PMID: 35882448 PMCID: PMC9330349 DOI: 10.1136/jitc-2021-004147] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
The gut microbiota and its metabolites have been shown to play a pivotal role in the regulation of metabolic, endocrine and immune functions. Though the exact mechanism of action remains to be fully elucidated, available knowledge supports the ability of microbiota-fermented short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate, to influence epigenetic and metabolic cascades controlling gene expression, chemotaxis, differentiation, proliferation, and apoptosis in several non-immune and immune cell subsets. While used as preferred metabolic substrates and sources of energy by colonic gut epithelial cells, most recent evidence indicates that these metabolites regulate immune functions, and in particular fine-tune T cell effector, regulatory and memory phenotypes, with direct in vivo consequences on the efficacy of chemotherapy, radiotherapy and immunotherapy. Most recent data also support the use of these metabolites over the course of T cell manufacturing, paving the way for refined adoptive T cell therapy engineering. Here, we review the most recent advances in the field, highlighting in vitro and in vivo evidence for the ability of SCFAs to shape T cell phenotypes and functions.
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Affiliation(s)
- Priya Rangan
- Department of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Anna Mondino
- Department of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
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