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Hu X, Manner K, DeJesus R, White K, Gattis C, Ngo P, Bandoro C, Tham E, Chu EY, Young C, Wells F, Basco R, Friera A, Kangeyan D, Beauchesne P, Dowdle WE, Deuse T, Fry TJ, Foster AE, Schrepfer S. Hypoimmune anti-CD19 chimeric antigen receptor T cells provide lasting tumor control in fully immunocompetent allogeneic humanized mice. Nat Commun 2023; 14:2020. [PMID: 37037829 PMCID: PMC10086027 DOI: 10.1038/s41467-023-37785-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/29/2023] [Indexed: 04/12/2023] Open
Abstract
Manufacturing autologous chimeric antigen receptor (CAR) T cell therapeutics is complex, and many patients experience treatment delays or cannot be treated at all. Although current allogeneic CAR products have the potential to overcome manufacturing bottlenecks, they are subject to immune rejection and failure to persist in the host, and thus do not provide the same level of efficacy as their autologous counterparts. Here, we aimed to develop universal allogeneic CAR T cells that evade the immune system and produce a durable response. We generated human hypoimmune (HIP) T cells with disrupted B2M, CIITA, and TRAC genes using CRISPR-Cas9 editing. In addition, CD47 and anti-CD19 CAR were expressed using lentiviral transduction. These allogeneic HIP CD19 CAR T cells were compared to allogeneic CD19 CAR T cells that only expressed the anti-CD19 CAR (allo CAR T). In vitro assays for cancer killing and exhaustion revealed no differences between allo CAR T and HIP CAR T cells, confirming that the HIP edits did not negatively affect T cell performance. Clearance of CD19+ tumors by HIP CAR T cells in immunodeficient NSG mice was comparable to that of allo CAR T cells. In fully immunocompetent humanized mice, HIP CAR T cells significantly outperformed allo CAR T cells, showed improved persistence and expansion, and provided lasting cancer clearance. Furthermore, CD47-targeting safety strategies reliably and specifically eliminated HIP CAR T cells. These findings suggest that universal allogeneic HIP CAR T cell-based therapeutics might overcome the limitations associated with poor persistence of allogeneic CAR T cells and exert durable anti-tumor responses.
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Affiliation(s)
- Xiaomeng Hu
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Karl Manner
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Rowena DeJesus
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Kathy White
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Corie Gattis
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Priscilla Ngo
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | | | - Eleonore Tham
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Elaine Y Chu
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Chi Young
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Frank Wells
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Ronald Basco
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Annabelle Friera
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Divy Kangeyan
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Pascal Beauchesne
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - William E Dowdle
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Tobias Deuse
- Department of Surgery, Division of Cardiothoracic Surgery, Transplant and Stem Cell Immunobiology (TSI)-Lab, University of California San Francisco, San Francisco, CA, USA
| | - Terry J Fry
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Aaron E Foster
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA
| | - Sonja Schrepfer
- Sana Biotechnology Inc., 1 Tower Place, South San Francisco, CA, USA.
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Hu X, White K, Gattis C, Clarke R, Landry S, Basco R, Tham E, Luo E, Tucker A, Bandoro C, Chu E, Young C, Manner K, Nho P, Lam B, Beauchesne P, Foster A, Dowdle WE, Rebar EJ, Fry TJ, Schrepfer S. Abstract 5598: Engineered hypoimmune allogeneic CAR T cells as potential off-the-shelf CAR T cell immunotherapies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Off-the-shelf CAR T cells may offer advantages over autologous strategies, including ease of manufacturing, improved quality control with avoidance of malignant contamination and T cell dysfunction, and the ability to generate a final product from healthy T cells. However, host-versus-graft immune response against histoincompatible T cells prevents the expansion and persistence of allogeneic CAR T cells and mitigates the efficacy of this approach. A major challenge is that, while HLA deletion can result in adaptive immune evasion, innate reactivity is enhanced. While T cells express CD47, we demonstrate here that CD47 expression above endogenous levels is important for immune evasion. We describe here the engineering of human immune evasive CAR T cells building on our previously described hypoimmune technology (Nat Biotechnol 2019;37(3):252-258 and Proc Natl Acad Sci U S A 2021;118(28):e2022091118). The goal is to achieve improved rates of durable complete remissions by improving allogeneic CD19CAR persistence, since it has been shown that autologous CAR T cells have greater durability over years than allogeneic CAR T cells. Human T cells from healthy donors were obtained by leukapheresis. To generate hypoimmune CD19CAR T cells, gene editing was used to eliminate HLA-I/II and TCR expression and lentiviral transduction was used to express CD47 and CD19CAR containing a 4-1BB costimulatory domain to generate hypoimmune CD19CAR T cells. Control CD19CAR T cells were unmanipulated, i.e., unedited, except for lentiviral transduction used to express CD19CAR. Hypoimmune CD19CAR T cells persist in allogeneic humanized mice and lack T cell activation measured using bioluminescence imaging and ELISPOT analysis, respectively. In contrast, transplantation of control CD19CAR T cells generated from the same human donor resulted in rejection (ELISPOT mean 59 and 558 spot frequencies for hypoimmune CD19CAR T cells and control CD19CAR T cells, respectively; p<0.0001 unpaired t-test). Innate immune cell assays show that CD47 overexpression protects hypoimmune CD19CAR T cells from NK cell and macrophage killing. A blocking antibody against CD47 made the hypoimmune CD19CAR T cells susceptible to macrophage and NK cell killing, confirming the importance of CD47 overexpression to evade innate immune clearance. Importantly, CD47 seemed to provide protection from all NK cell populations while other tested NK cell inhibitory molecules (such as HLA-E/G, PD-L1) seemed to prevent NK cell killing of only certain subpopulations rather than primary NK cells in total. Hypoimmune CD19CAR T cells retain their antitumor activity in the Nalm-6 B cell leukemia model in vitro and in vivo comparable to control CD19CAR T cells derived from various donors. Thus, hypoimmune edits seem to not impact CD19CAR T cell activity and have the potential to provide universal CAR T cells that are able to persist without immunosuppression.
Citation Format: Xiaomeng Hu, Kathy White, Corie Gattis, Ryan Clarke, Sam Landry, Ron Basco, Eleonore Tham, Emily Luo, Andrew Tucker, Christopher Bandoro, Elaine Chu, Chi Young, Karl Manner, Priscilla Nho, Ben Lam, Pascal Beauchesne, Aaron Foster, William E. Dowdle, Edward J. Rebar, Terry J. Fry, Sonja Schrepfer. Engineered hypoimmune allogeneic CAR T cells as potential off-the-shelf CAR T cell immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5598.
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Affiliation(s)
| | | | | | | | - Sam Landry
- 1Sana Biotechnology Inc, San Francisco, CA
| | - Ron Basco
- 1Sana Biotechnology Inc, San Francisco, CA
| | | | - Emily Luo
- 1Sana Biotechnology Inc, San Francisco, CA
| | | | | | - Elaine Chu
- 1Sana Biotechnology Inc, San Francisco, CA
| | - Chi Young
- 1Sana Biotechnology Inc, San Francisco, CA
| | | | | | - Ben Lam
- 1Sana Biotechnology Inc, San Francisco, CA
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Hu X, Dao M, White K, Clarke R, Landry S, Basco R, Gattis C, Tham E, Luo E, Tucker A, Bandoro C, Chu E, Kim J, Young C, Dowdle WE, Rebar EJ, Fry TJ, Schrepfer S. Abstract LB144: Overexpression of CD47 protects hypoimmune CAR T cells from innate immune cell killing. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Off-the-shelf CAR T cells could offer advantages over autologous strategies, including ease of manufacturing, quality control and avoidance of malignant contamination and T cell dysfunction. TCR editing can effectively prevent graft-versus-host reactions. However, the vigorous host-versus-graft immune response against histoincompatible T cells prevents expansion and persistence of allogeneic CAR T cells and mitigates the efficacy of this approach. A major challenge is that, while HLA deletion can result in adaptive immune evasion, innate reactivity is enhanced. CD47 overexpression can block both NK cell and macrophage killing (J Exp Med (2021) 218 (3): e20200839), and we hypothesized that T cells would lose their immunogenicity when human leukocyte antigen (HLA) class I and II genes are inactivated and CD47 is over-expressed. We describe here the engineering of human immune evasive CAR T cells based on our previously described hypoimmune technology. Human T cells from healthy donors were obtained by leukapheresis. CRISPR/Cas9 technology was used to delete b2m, CIITA, and TCR and lentiviral transduction to overexpress CD47 and CD19CAR. Control T cells were unmanipulated except for overexpression of CD19CAR containing a 41BB costimulatory domain. When transplanted into allogeneic humanized mice, hypoimmunogenic HLA-I/II- TCR- CD47+ CD19CAR+ T cells evade immune recognition by T and B cells compared to CD19CAR+ T cells generated from the same human donor using ELISPOT and flow cytometry analysis. Innate immune cell assays show that CD47 overexpression protects HLA-I/II deficient CAR T cells from NK cell and macrophage killing in vitro and in vivo. Relative CD47 expression levels were analyzed to understand the relevance of CD47 for protection from macrophage and NK cell killing. A blocking antibody against CD47 made the hypoimmunogenic CAR T cells susceptible to macrophage and NK cell killing, confirming the importance of CD47 overexpression to evade innate immune clearance. The use of CD47 blocking could additionally be envisioned as a safety strategy for our hypoimmunogenic CAR T cells. Neither isolated CD47 overexpression nor all three hypoimmune modifications or knockout of the TCR showed any effect on the cytotoxic potential of CAR+ T cells. Hypoimmune CAR+ T cells retain their antitumor activity in the Nalm-6 B cell leukemia model in vitro and clear leukemic cells in NSG mice across a range of tumor cell: CAR T cell ratios comparable to unmodified CAR T cells. These findings show that hypoimmunogenic CAR T cells are functionally immune evasive in allogeneic recipients with cytotoxic anti-tumor capacity and suggest they could provide universal CAR T cells that is able to persist without immunosuppression. Blocking CD47 could additionally serve as safety strategy for our hypoimmunogenic CAR T cells.
Citation Format: Xiaomeng Hu, Mo Dao, Kathy White, Ryan Clarke, Sam Landry, Ron Basco, Corie Gattis, Eleonore Tham, Emily Luo, Andrew Tucker, Christopher Bandoro, Elaine Chu, Junmo Kim, Chi Young, William E. Dowdle, Edward J. Rebar, Terry J. Fry, Sonja Schrepfer. Overexpression of CD47 protects hypoimmune CAR T cells from innate immune cell killing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB144.
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Affiliation(s)
| | - Mo Dao
- 1Sana Biotechnology Inc., San Francisco, CA
| | | | | | | | - Ron Basco
- 1Sana Biotechnology Inc., San Francisco, CA
| | | | | | - Emily Luo
- 1Sana Biotechnology Inc., San Francisco, CA
| | | | | | - Elaine Chu
- 1Sana Biotechnology Inc., San Francisco, CA
| | - Junmo Kim
- 1Sana Biotechnology Inc., San Francisco, CA
| | - Chi Young
- 1Sana Biotechnology Inc., San Francisco, CA
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Desforges JP, Bandoro C, Shehata L, Sonne C, Dietz R, Puryear WB, Runstadler JA. Environmental contaminant mixtures modulate in vitro influenza infection. Sci Total Environ 2018; 634:20-28. [PMID: 29626767 DOI: 10.1016/j.scitotenv.2018.03.321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 05/17/2023]
Abstract
Environmental chemicals, particularly organochlorinated contaminants (OCs), are associated with a ranged of adverse health effects, including impairment of the immune system and antiviral immunity. Influenza A virus (IAV) is an infectious disease of major global public health concern and exposure to OCs can increase the susceptibility, morbidity, and mortality to disease. It is however unclear how pollutants are interacting and affecting the outcome of viral infections at the cellular level. In this study, we investigated the effects of a mixture of environmentally relevant OCs on IAV infectivity upon in vitro exposure in Madin Darby Canine Kidney (MDCK) cells and human lung epithelial cells (A549). Exposure to OCs reduced IAV infectivity in MDCK and A549 cells during both short (18-24h) and long-term (72h) infections at 0.05 and 0.5ppm, and effects were more pronounced in cells co-treated with OCs and IAV than pre-treated with OCs prior to IAV (p<0.001). Pre-treatment of host cells with OCs did not affect IAV cell surface attachment or entry. Visualization of IAV by transmission electron microscopy revealed increased envelope deformations and fewer intact virions during OC exposure. Taken together, our results suggest that disruption of IAV infection upon in vitro exposure to OCs was not due to host-cell effects influencing viral attachment and entry, but perhaps mediated by direct effects on viral particles or cellular processes involved in host-virus interactions. In vitro infectivity studies such as ours can shed light on the complex processes underlying host-pathogen-pollutant interactions.
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Affiliation(s)
- Jean-Pierre Desforges
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark.
| | - Christopher Bandoro
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Laila Shehata
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Christian Sonne
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States
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Park AJ, Murphy K, Surette MD, Bandoro C, Krieger JR, Taylor P, Khursigara CM. Tracking the Dynamic Relationship between Cellular Systems and Extracellular Subproteomes in Pseudomonas aeruginosa Biofilms. J Proteome Res 2015; 14:4524-37. [PMID: 26378716 DOI: 10.1021/acs.jproteome.5b00262] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The transition of the opportunistic pathogen Pseudomonas aeruginosa from free-living bacteria into surface-associated biofilm communities represents a viable target for the prevention and treatment of chronic infectious disease. We have established a proteomics platform that identified 2443 and 1142 high-confidence proteins in P. aeruginosa whole cells and outer-membrane vesicles (OMVs), respectively, at three time points during biofilm development (ProteomeXchange identifier PXD002605). The analysis of cellular systems, specifically the phenazine biosynthetic pathway, demonstrates that whole-cell protein abundance correlates to end product (i.e., pyocyanin) concentrations in biofilm but not in planktonic cultures. Furthermore, increased cellular protein abundance in this pathway results in quantifiable pyocyanin in early biofilm OMVs and OMVs from both growth modes isolated at later time points. Overall, our data indicate that the OMVs being released from the surface of the biofilm whole cells have unique proteomes in comparison to their planktonic counterparts. The relative abundance of OMV proteins from various subcellular sources showed considerable differences between the two growth modes over time, supporting the existence and preferential activation of multiple OMV biogenesis mechanisms under different conditions. The consistent detection of cytoplasmic proteins in all of the OMV subproteomes challenges the notion that OMVs are composed of outer membrane and periplasmic proteins alone. Direct comparisons of outer-membrane protein abundance levels between OMVs and whole cells shows ratios that vary greatly from 1:1 and supports previous studies that advocate the specific inclusion, or "packaging", of proteins into OMVs. The quantitative analysis of packaged protein groups suggests biogenesis mechanisms that involve untethered, rather than absent, peptidoglycan-binding proteins. Collectively, individual protein and biological system analyses of biofilm OMVs show that drug-binding cytoplasmic proteins and porins are potentially shuttled from the whole cell into the OMVs and may contribute to the antibiotic resistance of P. aeruginosa whole cells within biofilms.
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Affiliation(s)
- Amber J Park
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada , N1G 2W1
| | - Kathleen Murphy
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada , N1G 2W1
| | - Matthew D Surette
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada , N1G 2W1
| | - Christopher Bandoro
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada , N1G 2W1
| | - Jonathan R Krieger
- SPARC BioCentre, The Hospital for Sick Children , Toronto, Ontario, Canada , M5G 0A4
| | - Paul Taylor
- SPARC BioCentre, The Hospital for Sick Children , Toronto, Ontario, Canada , M5G 0A4
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada , N1G 2W1
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