1
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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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2
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Essawi K, Hakami W, Naeem Khan MB, Martin R, Zeng J, Chu R, Uchida N, Bonifacino AC, Krouse AE, Linde NS, Donahue RE, Blobel GA, Gerdemann U, Kean LS, Maitland SA, Wolfe SA, Metais JY, Gottschalk S, Bauer DE, Tisdale JF, Demirci S. Pre-existing immunity does not impair the engraftment of CRISPR-Cas9-edited cells in rhesus macaques conditioned with busulfan or radiation. Mol Ther Methods Clin Dev 2023; 29:483-493. [PMID: 37273902 PMCID: PMC10236215 DOI: 10.1016/j.omtm.2023.04.004] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/17/2023] [Indexed: 06/06/2023]
Abstract
CRISPR-Cas9-based therapeutic genome editing approaches hold promise to cure a variety of human diseases. Recent findings demonstrate pre-existing immunity for the commonly used Cas orthologs from Streptococcus pyogenes (SpCas9) and Staphylococcus aureus (SaCas9) in humans, which threatens the success of this powerful tool in clinical use. Thus, a comprehensive investigation and potential risk assessment are required to exploit the full potential of the system. Here, we investigated existence of immunity to SpCas9 and SaCas9 in control rhesus macaques (Macaca mulatta) alongside monkeys transplanted with either lentiviral transduced or CRISPR-SpCas9 ribonucleoprotein (RNP)-edited cells. We observed significant levels of Cas9 antibodies in the peripheral blood of all transplanted and non-transplanted control animals. Transplantation of ex vivo transduced or SpCas9-mediated BCL11A enhancer-edited cells did not alter the levels of Cas9 antibodies in rhesus monkeys. Following stimulation of peripheral blood cells with SpCas9 or SaCas9, neither Cas9-specific T cells nor cytokine induction were detected. Robust and durable editing frequencies and expression of high levels of fetal hemoglobin in BCL11A enhancer-edited rhesus monkeys with no evidence of an immune response (>3 years) provide an optimistic outlook for the use of ex vivo CRISPR-SpCas9 (RNP)-edited cells.
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Affiliation(s)
- Khaled Essawi
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Gizan, Saudi Arabia
| | - Waleed Hakami
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Gizan, Saudi Arabia
| | - Muhammad Behroz Naeem Khan
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reid Martin
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
| | - Rebecca Chu
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | | | - Allen E. Krouse
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, MD, USA
| | | | - Robert E. Donahue
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ulrike Gerdemann
- Boston Children’s Hospital, Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leslie S. Kean
- Boston Children’s Hospital, Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Stacy A. Maitland
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jean-Yves Metais
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, USA
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
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3
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Zebley C, Brown CC, Mi T, Fan Y, Alli S, Boi S, Galletti G, Lugli E, Langfitt D, Metais JY, Lockey T, Meagher M, Triplett B, Talleur A, Gottschalk S, Youngblood B. YIA23-003: CD19-CAR T Cells Develop Exhaustion Epigenetic Programs During a Clinical Response. J Natl Compr Canc Netw 2023. [DOI: 10.6004/jnccn.2022.7157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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4
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Naik S, Madden R, Lipsitt A, Lockey T, Bran J, Rubnitz JE, Klco J, Shulkin BL, Patil SL, Schell SS, Park JEJ, Riberdy J, Shang N, Zoine J, Wallace J, Harstead K, Willis C, Metais JY, Langfitt D, Zhou S, Akel S, Meagher M, Triplett BM, Gottschalk S, Velasquez PP. Preliminary Results from a Phase 1 Trial Showing Safety and Anti-Leukemic Activity of CD123-CAR T Cells in Pediatric Patients with AML. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00184-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Wilson TL, Kim H, Chou CH, Langfitt D, Mettelman RC, Minervina AA, Allen EK, Metais JY, Pogorelyy MV, Riberdy JM, Velasquez MP, Kottapalli P, Trivedi S, Olsen SR, Lockey T, Willis C, Meagher MM, Triplett BM, Talleur AC, Gottschalk S, Crawford JC, Thomas PG. Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages. Cancer Discov 2022; 12:2098-2119. [DOI: 10.1158/2159-8290.cd-21-1508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/18/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Abstract
Current chimeric antigen receptor-modified (CAR) T cell products are evaluated in bulk, without assessing functional heterogeneity. We therefore generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using pre- and post-infusion CD19-CAR T cells from blood and bone marrow samples of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified cytotoxic post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. These effector precursor cells exhibited a unique transcriptional profile compared to other pre-infusion cells, corresponding to an unexpected surface phenotype (TIGIT+, CD62Llo, CD27-). Upon stimulation, these cells showed functional superiority and decreased expression of the exhaustion-associated transcription factor, TOX. Collectively, these results demonstrate diverse effector potentials within pre-infusion CAR T cell products, which can be exploited for therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the mechanisms underlying effector development in CAR T cell products.
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Affiliation(s)
- Taylor L. Wilson
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Hyunjin Kim
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Ching-Heng Chou
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Deanna Langfitt
- St. Jude Children's Research Hospital, TN, TN, United States
| | | | | | | | - Jean-Yves Metais
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | | | | | - Sanchit Trivedi
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Scott R. Olsen
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Timothy Lockey
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Catherine Willis
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | - Aimee C. Talleur
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | - Paul G. Thomas
- St. Jude Children's Research Hospital, Memphis, TN, United States
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6
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Zebley CC, Brown C, Mi T, Fan Y, Alli S, Boi S, Galletti G, Lugli E, Langfitt D, Metais JY, Lockey T, Meagher M, Triplett B, Talleur AC, Gottschalk S, Youngblood BA. CD19-CAR T Cells Develop Exhaustion Epigenetic Programs During a Clinical Response. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.122.04] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
The goal of this study was to determine the epigenetic landscape of CD19-CAR T cells pre and post infusion in leukemia patients as an initial step to elucidate intrinsic mechanisms that limit CAR T-cell effector functions in humans. A longitudinal analysis of CD8+ CD19-CAR T cell epigenetic changes was performed by whole-genome DNA methylation profiling of CAR T cells during manufacturing and from peripheral blood mononuclear cells (PBMCs) of 15 patients enrolled on our institutional, autologous CD19-CAR T cell therapy study (NCT03573700). CAR T cell expansion and persistence were determined by measuring vector copy numbers in the PBMCs of treated patients. We had previously established novel exhaustion DNA methylation datasets that delineate between progenitor and fully exhausted T cells. These datasets served as a guide for stratifying our post-infusion CAR T cells along the exhaustion developmental trajectory. Our data show that CD19-CAR T cells lose repressive DNA methylation at effector loci (e.g. PRF1, TBET) while gaining methylation at genes associated with memory potential (e.g. LEF1, TCF7). We confirmed these epigenetic changes are coupled to endogenous human T cell effector and memory differentiation by cross-referencing our epigenetic data with publicly available transcriptional profiles for antigen-specific effector and long-lived memory CD8 T cells from individuals vaccinated for yellow fever. Furthermore, we show that CAR T cells were unable to mount an in vivo recall response after relapse of antigen-positive disease or recovery of endogenous B cells. These observations support the conclusion that CD19-CAR T cells acquire stable epigenetic exhaustion programs that limit their protective capacity.
This work was supported by the National Institutes of Health (1R01AI114442 to BY and LRP to CCZ), the National Comprehensive Cancer Network Young Investigator Award (to CZ), Alex’s Lemonade Stand Foundation Young Investigator Grant (to CZ), Stand Up to Cancer- SU2C (to BY), the American Lebanese Syrian Associated Charities (ALSAC) to BY, and Assisi foundation to BY.
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Affiliation(s)
| | | | - Tian Mi
- 1St. Jude Children’s Research Hospital
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7
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Crawford JC, Wilson TL, Kim H, Chou CH, Langfitt D, Allen EK, Metais JY, Pogorelyy M, Kottapalli P, Trivedi S, Olsen S, Lockey T, Willis C, Meagher MM, Triplett B, Talleur AC, Gottschalk S, Thomas PG. Common trajectories of highly effective CD19-specific CAR T cells identified by endogenous T cell receptor lineages. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.120.15] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Current chimeric antigen receptor-modified (CAR) T cell therapy products are evaluated in bulk, without assessment of the possible heterogeneity in effector potential between cells. Conceivably, only a subset of the pre-infusion product differentiates into optimal effectors. We generated a comprehensive single-cell gene expression and T cell receptor (TCR) sequencing dataset using both pre- and post-infusion CD19-CAR T cells from peripheral blood and bone marrow of pediatric patients with B cell acute lymphoblastic leukemia (B-ALL). We identified potent effector post-infusion cells with identical TCRs to a subset of pre-infusion CAR T cells. Effector precursor CAR T cells exhibited a unique transcriptional profile compared to other pre-infusion cells, and the number of effector precursor cells infused correlated with peak CAR T cell expansion. Additionally, we identified an unexpected cell surface phenotype (TIGIT+, CD62Llo, CD27−), conventionally associated with inhibiting effective T cell responses, that we used to successfully enrich for subsequent effector potential. Collectively, these results demonstrate that highly diverse effector potentials are present among cells in pre-infusion cell products, which can be exploited for diagnostic and therapeutic applications. Furthermore, we provide an integrative experimental and analytical framework for elucidating the biological mechanisms underlying effector development in other CAR T cell therapy products.
This work was supported by the National Institutes of Health (NIH)/National Cancer Institute grant P30CA021765, NIH grants U01AI150747 and R01AI136514 (PGT), the American Society of Transplantation and Cellular Therapy (AT), the American Society of Hematology (AT), the Key for a Cure Foundation (PGT), the Mark Foundation ASPIRE Award (PGT), and the American Lebanese Syrian Associated Charities (SG, PGT). Part of the laboratory studies were performed by the Center for Translational Immunology and Immunotherapy (CeTI2), which is supported by SJCRH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
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Affiliation(s)
| | | | - Hyunjin Kim
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Ching-Heng Chou
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Deanna Langfitt
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - E Kaitlynn Allen
- 1Department of Immunology, St. Jude Children’s Research Hospital
| | - Jean-Yves Metais
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | | | - Pratibha Kottapalli
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Sanchit Trivedi
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Scott Olsen
- 3Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital
| | - Timothy Lockey
- 4Children’s GMP, LLC, St. Jude Children’s Research Hospital
| | | | | | - Brandon Triplett
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - Aimee C Talleur
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
| | - Stephen Gottschalk
- 2Department of Bone Marrow Transplantation & Cellular Therapy, St. Jude Children’s Research Hospital
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8
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Naik S, Talleur AC, Li Y, Madden R, Mamcarz E, Qudeimat A, Sharma A, Srinivasan A, Suliman A, Epperly R, Obeng EA, Velasquez MP, Hijano D, Marón GM, Metais JY, Gottschalk S, Triplett BM. CD45RA-Depleted Haploidentical Transplantation Combined with NK Cell Addback Results in Promising Long-Term Outcomes in Pediatric Patients with High-Risk Hematologic Malignancies. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Naik S, Li Y, Madden R, Mamcarz E, Srinivasan A, Sharma A, Talleur AC, Qudeimat A, Suliman A, Epperly R, Obeng EA, Velasquez MP, Hijano D, Marón GM, Metais JY, Gottschalk S, Triplett BM. CD45RA Depleted T-Cell Addback and Prophylactic Blinatumomab Administration Following Tcrαβ/CD19-Depleted Haploidentical Transplantation in Pediatric Patients with High Risk Acute Leukemia. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Zebley CC, Brown C, Mi T, Fan Y, Alli S, Boi S, Galletti G, Lugli E, Langfitt D, Metais JY, Lockey T, Meagher M, Triplett B, Talleur AC, Gottschalk S, Youngblood B. CD19-CAR T cells undergo exhaustion DNA methylation programming in patients with acute lymphoblastic leukemia. Cell Rep 2021; 37:110079. [PMID: 34852226 PMCID: PMC8800370 DOI: 10.1016/j.celrep.2021.110079] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/08/2021] [Accepted: 11/09/2021] [Indexed: 01/02/2023] Open
Abstract
CD19-CAR T cell therapy has evolved into the standard of care for relapsed/refractory B cell acute lymphoblastic leukemia (ALL); however, limited persistence of the CAR T cells enables tumor relapse for many patients. To gain a deeper understanding of the molecular characteristics associated with CAR T cell differentiation, we performed longitudinal genome-wide DNA methylation profiling of CD8+ CD19-CAR T cells post-infusion in ALL patients. We report that CAR T cells undergo a rapid and broad erasure of repressive DNA methylation reprograms at effector-associated genes. The CAR T cell post-infusion changes are further characterized by repression of genes (e.g., TCF7 and LEF1) associated with memory potential and a DNA methylation signature (e.g., demethylation at CX3CR1, BATF, and TOX) demarcating a transition toward exhaustion-progenitor T cells. Thus, CD19-CAR T cells undergo exhaustion-associated DNA methylation programming, indicating that efforts to prevent this process may be an attractive approach to improve CAR T cell efficacy. Zebley et al. show that CD8+ CD19-CAR T cells undergo genome-wide DNA methylation changes during an antitumor response in patients with B cell acute lymphoblastic leukemia (ALL). Post-infusion CAR T cell differentiation involves acquisition of DNA methylation programs associated with effector function, repression of memory potential, and transition toward exhaustion.
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Affiliation(s)
- 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.
| | - Charmaine Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tian Mi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, 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
| | - Shannon Boi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Giovanni Galletti
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Deanna Langfitt
- 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
| | - Timothy Lockey
- Therapeutics Production and Quality, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael Meagher
- Therapeutics Production and Quality, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brandon Triplett
- Department of Bone Marrow Transplantation and Cellular Therapy, 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
| | - 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.
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11
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Fernández L, Metais JY, Escudero A, Vela M, Valentín J, Vallcorba I, Leivas A, Torres J, Valeri A, Patiño-García A, Martínez J, Leung W, Pérez-Martínez A. Memory T Cells Expressing an NKG2D-CAR Efficiently Target Osteosarcoma Cells. Clin Cancer Res 2017; 23:5824-5835. [DOI: 10.1158/1078-0432.ccr-17-0075] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 06/21/2017] [Indexed: 11/16/2022]
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12
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Talleur AC, Metais JY, Li Y, Rooney B, Moustaki A, Leung WH. Chimeric antigen receptor engineered allogeneic CD27-negative T cells for the treatment of CD19+ leukemia. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.3046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Ying Li
- St. Jude Children's Research Hospital, Memphis, TN
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Wu C, Jares A, Winkler T, Xie J, Metais JY, Dunbar CE. High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias. Hum Gene Ther 2012; 24:38-47. [PMID: 22992116 DOI: 10.1089/hum.2012.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retroviral vectors are an efficient and widely employed means of introducing an exogenous expression cassette into target cells. These vectors have been shown to integrate semi-randomly into the cellular genome, and can be associated with genotoxicity due to impact on expression of proximate genes. Therefore, efficient and accurate integration site analysis, while quantifying contributions of individual vector-containing clones, is desirable. Linear amplification-mediated polymerase chain reaction (LAM-PCR) is a widely used technique for identifying integrated proviral and host genomic DNA junctions. However, LAM-PCR is subject to selection bias inherent in the reliance of the assay on the presence of a restriction enzyme-cutting site adjacent to a retrievable integration site, and it is further limited by an inability to discriminate prior to sequencing between the flanking genomic DNA of interest and uninformative internal vector DNA. We report a modified restriction enzyme-free LAM-PCR (Re-free LAM-PCR) approach that is less time and labor intensive compared to conventional LAM-PCR, but in contrast to some other nonrestrictive methods, compares in efficiency and sensitivity, excludes retrieval of uninformative internal vector sequences, and allows retrieval of integration sites unbiased by the presence of nearby restriction sites. However, we report that Re-free LAM-PCR remains inaccurate for quantitation of the relative contributions of individual integration site-containing clones in a polyclonal setting, suggesting that bias in LAM-PCR retrieval of integration sites is not wholly explained by restriction enzyme-related factors.
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Affiliation(s)
- Chuanfeng Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Coulon S, Metais JY, Chartier M, Briand JP, Baty D. Cyclic peptides selected by phage display mimic the natural epitope recognized by a monoclonal anti-colicin A antibody. J Pept Sci 2004; 10:648-58. [PMID: 15568679 DOI: 10.1002/psc.574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A 10-mer random peptide library displayed on filamentous bacteriophage was used to determine the molecular basis of the interaction between the monoclonal anti-colicin A antibody 1C11 and its cognate epitope. Previous studies established that the putative epitope recognized by 1C11 antibody is composed of amino acid residues 19-25 (RGSGPEP) of colicin A. Using the phage display technique it was confirmed that the epitope of 1C11 antibody was indeed restricted to residues 19-25 and the consensus motif RXXXPEP was identified. Shorter consensus sequences (RXXPEP, RXXEP, KXXEP) were also selected. It was also demonstrated that the disulfide bond found in one group of the selected peptides was crucial for 1C11 antibody recognition. It was shown that cyclization of the peptides by disulfide bond formation could result in a structure that mimics the natural epitope of colicin A.
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Affiliation(s)
- Stephane Coulon
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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van Heeke G, Seamons R, Metais JY, Fozard JR, Goff S, Wheatley A, Dewar J, Hall IP. Single Nucleotide Polymorphism analysis of the human adenosine A2B receptor gene: prevalence of SNPs in asthmatics and normal subjects. ACTA ACUST UNITED AC 2002. [DOI: 10.1002/gnfd.200290003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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