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Zoine JT, Immadisetty K, Ibanez-Vega J, Moore SE, Nevitt C, Thanekar U, Tian L, Karouni A, Chockley PJ, Arthur B, Sheppard H, Klco JM, Langfitt DM, Krenciute G, Gottschalk S, Babu MM, Velasquez MP. Peptide-scFv antigen recognition domains effectively confer CAR T cell multiantigen specificity. Cell Rep Med 2024; 5:101422. [PMID: 38350450 PMCID: PMC10897625 DOI: 10.1016/j.xcrm.2024.101422] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/06/2023] [Accepted: 01/19/2024] [Indexed: 02/15/2024]
Abstract
The emergence of immune escape is a significant roadblock to developing effective chimeric antigen receptor (CAR) T cell therapies against hematological malignancies, including acute myeloid leukemia (AML). Here, we demonstrate feasibility of targeting two antigens simultaneously by combining a GRP78-specific peptide antigen recognition domain with a CD123-specific scFv to generate a peptide-scFv bispecific antigen recognition domain (78.123). To achieve this, we test linkers with varying length and flexibility and perform immunophenotypic and functional characterization. We demonstrate that bispecific CAR T cells successfully recognize and kill tumor cells that express GRP78, CD123, or both antigens and have improved antitumor activity compared to their monospecific counterparts when both antigens are expressed. Protein structure prediction suggests that linker length and compactness influence the functionality of the generated bispecific CARs. Thus, we present a bispecific CAR design strategy to prevent immune escape in AML that can be extended to other peptide-scFv combinations.
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Affiliation(s)
- Jaquelyn T Zoine
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jorge Ibanez-Vega
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sarah E Moore
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chris Nevitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Unmesha Thanekar
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liqing Tian
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Karouni
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J Chockley
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bright Arthur
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Sheppard
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Deanna M Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - M Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Yan KK, Condori J, Ma Z, Metais JY, Ju B, Ding L, Dhungana Y, Palmer LE, Langfitt DM, Ferrara F, Throm R, Shi H, Risch I, Bhatara S, Shaner B, Lockey TD, Talleur AC, Easton J, Meagher MM, Puck JM, Cowan MJ, Zhou S, Mamcarz E, Gottschalk S, Yu J. Integrome signatures of lentiviral gene therapy for SCID-X1 patients. Sci Adv 2023; 9:eadg9959. [PMID: 37801507 PMCID: PMC10558130 DOI: 10.1126/sciadv.adg9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Lentiviral vector (LV)-based gene therapy holds promise for a broad range of diseases. Analyzing more than 280,000 vector integration sites (VISs) in 273 samples from 10 patients with X-linked severe combined immunodeficiency (SCID-X1), we discovered shared LV integrome signatures in 9 of 10 patients in relation to the genomics, epigenomics, and 3D structure of the human genome. VISs were enriched in the nuclear subcompartment A1 and integrated into super-enhancers close to nuclear pore complexes. These signatures were validated in T cells transduced with an LV encoding a CD19-specific chimeric antigen receptor. Intriguingly, the one patient whose VISs deviated from the identified integrome signatures had a distinct clinical course. Comparison of LV and gamma retrovirus integromes regarding their 3D genome signatures identified differences that might explain the lower risk of insertional mutagenesis in LV-based gene therapy. Our findings suggest that LV integrome signatures, shaped by common features such as genome organization, may affect the efficacy of LV-based cellular therapies.
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Affiliation(s)
- Koon-Kiu Yan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jose Condori
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhijun Ma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jean-Yves Metais
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bensheng Ju
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yogesh Dhungana
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Lance E. Palmer
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Ferrara
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Throm
- Vector Development and Production Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hao Shi
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Isabel Risch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Bridget Shaner
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Timothy D. Lockey
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Aimee C. Talleur
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael M. Meagher
- Department of Therapeutics Production and Quality, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer M. Puck
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Morton J. Cowan
- Department of Pediatrics, Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California San Francisco Benioff Children’s Hospital, San Francisco, CA 94158, USA
| | - Sheng Zhou
- Experimental Cellular Therapeutics Laboratory, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ewelina Mamcarz
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Prinzing B, Zebley CC, Petersen CT, Fan Y, Anido AA, Yi Z, Nguyen P, Houke H, Bell M, Haydar D, Brown C, Boi SK, Alli S, Crawford JC, Riberdy JM, Park JJ, Zhou S, Velasquez MP, DeRenzo C, Lazzarotto CR, Tsai SQ, Vogel P, Pruett-Miller SM, Langfitt DM, Gottschalk S, Youngblood B, Krenciute G. Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity. Sci Transl Med 2021; 13:eabh0272. [PMID: 34788079 PMCID: PMC8733956 DOI: 10.1126/scitranslmed.abh0272] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [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: 12/13/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy is revolutionizing cancer immunotherapy for patients with B cell malignancies and is now being developed for solid tumors and chronic viral infections. Although clinical trials have demonstrated the curative potential of CAR T cell therapy, a substantial and well-established limitation is the heightened contraction and transient persistence of CAR T cells during prolonged antigen exposure. The underlying mechanism(s) for this dysfunctional state, often termed CAR T cell exhaustion, remains poorly defined. Here, we report that exhaustion of human CAR T cells occurs through an epigenetic repression of the T cell’s multipotent developmental potential. Deletion of the de novo DNA methyltransferase 3 alpha (DNMT3A) in T cells expressing first- or second-generation CARs universally preserved the cells’ ability to proliferate and mount an antitumor response during prolonged tumor exposure. The increased functionality of the exhaustion-resistant DNMT3A knockout CAR T cells was coupled to an up-regulation of interleukin-10, and genome-wide DNA methylation profiling defined an atlas of genes targeted for epigenetic silencing. This atlas provides a molecular definition of CAR T cell exhaustion, which includes many transcriptional regulators that limit the “stemness” of immune cells, including CD28, CCR7, TCF7, and LEF1. Last, we demonstrate that this epigenetically regulated multipotency program is firmly coupled to the clinical outcome of prior CAR T cell therapies. These data document the critical role epigenetic mechanisms play in limiting the fate potential of human T cells and provide a road map for leveraging this information for improving CAR T cell efficacy.
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Affiliation(s)
- Brooke Prinzing
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Caitlin C. Zebley
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Christopher T. Petersen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhongzhen Yi
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Haley Houke
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charmaine Brown
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shannon K. Boi
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shanta Alli
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Janice M. Riberdy
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeoungeun J. Park
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sheng Zhou
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mireya Paulina Velasquez
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Chris DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Langfitt
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
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