1
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Li R, Lei Y, Rezk A, Diego A Espinoza, Wang J, Feng H, Zhang B, Barcelos IP, Zhang H, Yu J, Huo X, Zhu F, Yang C, Tang H, Goldstein AC, Banwell BL, Hakonarson H, Xu H, Mingueneau M, Sun B, Li H, Bar-Or A. Oxidative phosphorylation regulates B cell effector cytokines and promotes inflammation in multiple sclerosis. Sci Immunol 2024; 9:eadk0865. [PMID: 38701189 DOI: 10.1126/sciimmunol.adk0865] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
Dysregulated B cell cytokine production contributes to pathogenesis of immune-mediated diseases including multiple sclerosis (MS); however, the underlying mechanisms are poorly understood. In this study we investigated how cytokine secretion by pro-inflammatory (GM-CSF-expressing) and anti-inflammatory (IL-10-expressing) B cells is regulated. Pro-inflammatory human B cells required increased oxidative phosphorylation (OXPHOS) compared with anti-inflammatory B cells. OXPHOS reciprocally modulated pro- and anti-inflammatory B cell cytokines through regulation of adenosine triphosphate (ATP) signaling. Partial inhibition of OXPHOS or ATP-signaling including with BTK inhibition resulted in an anti-inflammatory B cell cytokine shift, reversed the B cell cytokine imbalance in patients with MS, and ameliorated neuroinflammation in a myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalitis mouse model. Our study identifies how pro- and anti-inflammatory cytokines are metabolically regulated in B cells and identifies ATP and its metabolites as a "fourth signal" that shapes B cell responses and is a potential target for restoring the B cell cytokine balance in autoimmune diseases.
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Affiliation(s)
- Rui Li
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Immunotherapy and Department of Neurology of First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Yanting Lei
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Ayman Rezk
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diego A Espinoza
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jing Wang
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Huiru Feng
- Institute of Immunotherapy and Department of Neurology of First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Bo Zhang
- Institute of Immunotherapy and Department of Neurology of First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Isabella P Barcelos
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hang Zhang
- Department of Immunology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jing Yu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xinrui Huo
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Fangyi Zhu
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Changxin Yang
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hao Tang
- MS Research Unit, Biogen, Cambridge, MA 02142, USA
| | - Amy C Goldstein
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brenda L Banwell
- Division of Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongwei Xu
- Department of Immunology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | | | - Bo Sun
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hulun Li
- Department of Neurobiology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Amit Bar-Or
- Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- MS Research Unit, Biogen, Cambridge, MA 02142, USA
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2
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Espinoza DA, Le Coz C, Cruz Cabrera E, Romberg N, Bar-Or A, Li R. Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue. JCI Insight 2023; 8:155199. [PMID: 36809296 PMCID: PMC10132144 DOI: 10.1172/jci.insight.155199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
B cells within secondary lymphoid tissues (SLTs) encompass a diversity of activation states and multiple maturation processes that reflect antigen recognition and transition through the germinal center (GC) reaction, in which mature B cells differentiate into memory and antibody-secreting cells (ASCs). Here, utilizing single-cell RNA-seq, we identify a range of distinct activation and maturation states of tonsillar-derived B cells. In particular, we identify a previously uncharacterized CCL4/CCL3 chemokine-expressing B-cell population with an expression pattern consistent with BCR/CD40 activation. Furthermore, we present a computational method leveraging regulatory network inference and pseudotemporal modeling to identify upstream transcription factor modulation along a GC to ASC axis of transcriptional maturation. Our dataset provides valuable insight into diverse B-cell functional profiles and will be a useful resource for further studies into the B-cell immune compartment.
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Affiliation(s)
- Diego A Espinoza
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Carole Le Coz
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Emylette Cruz Cabrera
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Amit Bar-Or
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
| | - Rui Li
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States of America
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3
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Abraham DM, Lozano RJ, Guitart X, Liang JA, Mortlock RD, Espinoza DA, Fan X, Krouse A, Bonifacino A, Hong SG, Singh K, Tisdale JF, Wu C, Dunbar CE. Comparison of busulfan and total body irradiation conditioning on hematopoietic clonal dynamics following lentiviral gene transfer in rhesus macaques. Mol Ther Methods Clin Dev 2022; 28:62-75. [PMID: 36620072 PMCID: PMC9798201 DOI: 10.1016/j.omtm.2022.12.001] [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: 09/09/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The clonal dynamics following hematopoietic stem progenitor cell (HSPC) transplantation with busulfan conditioning are of great interest to the development of HSPC gene therapies. Compared with total body irradiation (TBI), busulfan is less toxic and more clinically relevant. We used a genetic barcoded HSPC autologous transplantation model to investigate the impact of busulfan conditioning on hematopoietic reconstitution in rhesus macaques. Two animals received lower busulfan dose and demonstrated lower vector marking levels compared with the third animal given a higher busulfan dose, despite similar busulfan pharmacokinetic analysis. We observed uni-lineage clonal engraftment at 1 month post-transplant, replaced by multilineage clones by 2 to 3 months in all animals. The initial multilineage clones in the first two animals were replaced by a second multilineage wave at 9 months; this clonal pattern disappeared at 13 months in the first animal, though was maintained in the second animal. The third animal maintained stable multilineage clones from 3 months to the most recent time point. In addition, busulfan animals exhibit more rapid HSPC clonal mixing across bone marrow sites and less CD16+ NK-biased clonal expansion compared with TBI animals. Therefore, busulfan conditioning regimens can variably impact the marrow niche, resulting in differences in clonal patterns with implications for HSPC gene therapies.
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Affiliation(s)
- Diana M. Abraham
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J. Lozano
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xavi Guitart
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jialiu A. Liang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryland D. Mortlock
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diego A. Espinoza
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allen Krouse
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aylin Bonifacino
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Komudi Singh
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author Chuanfeng Wu, Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Building 10 CRC, Room 5E-3288, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author Cynthia E. Dunbar, Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Building 10 CRC, Room 5E-3332, 10 Center Drive, Bethesda, MD 20892, USA.
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4
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Zuroff L, Rezk A, Shinoda K, Espinoza DA, Elyahu Y, Zhang B, Chen AA, Shinohara RT, Jacobs D, Alcalay RN, Tropea TF, Chen-Plotkin A, Monsonego A, Li R, Bar-Or A. Immune aging in multiple sclerosis is characterized by abnormal CD4 T cell activation and increased frequencies of cytotoxic CD4 T cells with advancing age. EBioMedicine 2022; 82:104179. [PMID: 35868128 PMCID: PMC9305354 DOI: 10.1016/j.ebiom.2022.104179] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 11/17/2021] [Revised: 06/12/2022] [Accepted: 07/05/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Immunosenescence (ISC) describes age-related changes in immune-system composition and function. Multiple sclerosis (MS) is a lifelong inflammatory condition involving effector and regulatory T-cell imbalance, yet little is known about T-cell ISC in MS. We examined age-associated changes in circulating T cells in MS compared to normal controls (NC). METHODS Forty untreated MS (Mean Age 43·3, Range 18-72) and 49 NC (Mean Age 48·6, Range 20-84) without inflammatory conditions were included in cross-sectional design. T-cell subsets were phenotypically and functionally characterized using validated multiparametric flow cytometry. Their aging trajectories, and differences between MS and NC, were determined using linear mixed-effects models. FINDINGS MS patients demonstrated early and persistent redistribution of naïve and memory CD4 T-cell compartments. While most CD4 and CD8 T-cell aging trajectories were similar between groups, MS patients exhibited abnormal age-associated increases of activated (HLA-DR+CD38+; (P = 0·013) and cytotoxic CD4 T cells, particularly in patients >60 (EOMES: P < 0·001). Aging MS patients also failed to upregulate CTLA-4 expression on both CD4 (P = 0·014) and CD8 (P = 0·009) T cells, coupled with abnormal age-associated increases in frequencies of B cells expressing costimulatory molecules. INTERPRETATION While many aspects of T-cell aging in MS are conserved, the older MS patients harbour abnormally increased frequencies of CD4 T cells with activated and cytotoxic effector profiles. Age-related decreased expression of T-cell co-inhibitory receptor CTLA-4, and increased B-cell costimulatory molecule expression, may provide a mechanism that drives aberrant activation of effector CD4 T cells that have been implicated in progressive disease. FUNDING Stated in Acknowledgements section of manuscript.
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Affiliation(s)
- Leah Zuroff
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ayman Rezk
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Koji Shinoda
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Diego A Espinoza
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yehezqel Elyahu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences; Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center; and National Institute for Biotechnology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Bo Zhang
- Department of Cardiology, The fourth affiliated hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Andrew A Chen
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Russell T Shinohara
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dina Jacobs
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY 10032, USA; The Center for Movement Disorders, Neurological Institute, Tel Aviv Medical Center, Tel Aviv 6423914, Israel
| | - Thomas F Tropea
- Department of Neurology, Perelman school of medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alice Chen-Plotkin
- Department of Neurology, Perelman school of medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alon Monsonego
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences; Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center; and National Institute for Biotechnology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Rui Li
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Amit Bar-Or
- The Center for Neuroinflammation and Experimental Therapeutics and the Department of Neurology, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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5
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Espinoza DA, Mexhitaj I, Smiler J, Mafra F, Da Silva RP, Fadda G, Yeh EA, Marrie RA, Arnold DL, Li R, Banwell B, Bar-Or A. Proteogenomic immune signatures delineate the landscape of pediatric acquired demyelinating syndromes. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.108.04] [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
Approximately 20–30% of children presenting with acquired inflammatory demyelinating syndromes (ADS) have multiple sclerosis (MS). Another 30% harbor serum antibodies against myelin oligodendrocyte glycoprotein and are referred to as having MOG-associated disease (MOGAD). While MS and MOGAD can have similar features, differences in response to immune therapies point to distinct underlying immune mechanisms.
To assess potentially distinct immune mechanisms underlying MS and MOGAD, we applied proteogenomics to high quality cryopreserved peripheral blood mononuclear cells collected from patients with ADS prior to institution of immune therapy, as well as from healthy controls. CITE-Seq profiling was applied to a total of 92,716 single cells with equal contribution from 24 children (6 healthy donors; 6 with ADS but neither MS or MOGAD; 6 with MOGAD; and 6 with MS, ascertained with long-term follow-up).
Analysis revealed a pan-ADS enrichment of atypical (CD11c+) B cells compared to healthy controls. Children with MS were distinguished from children with MOGAD by MS-specific enrichments of checkpoint-molecule (TIGIT and CD137)-expressing CD8 memory T cells, STAT4+ Th1 CD4 memory T cells and CD56dim/CD16+ NK cells.
Overall, our study identifies distinct features of circulating cellular immune profiles that may serve to distinguish children with MS and MOGAD, and provides novel insights into early immune mechanisms that may be involved in each of these conditions.
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Affiliation(s)
- Diego A Espinoza
- 1Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania
| | - Ina Mexhitaj
- 2Perelman School of Medicine, University of Pennsylvania
| | | | - Fernanda Mafra
- 3Center for Applied Genomics, Children's Hospital of Philadelphia
| | | | - Giulia Fadda
- 2Perelman School of Medicine, University of Pennsylvania
| | - E Ann Yeh
- 5Hospital for Sick Children, University of Toronto, Canada
| | - Ruth Ann Marrie
- 6Max Rady College of Medicine, University of Manitoba, Canada
| | | | - Rui Li
- 2Perelman School of Medicine, University of Pennsylvania
| | | | - Amit Bar-Or
- 2Perelman School of Medicine, University of Pennsylvania
- 4Children's Hospital of Philadelphia
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6
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Apostolidis SA, Kakara M, Painter MM, Goel RR, Mathew D, Lenzi K, Rezk A, Patterson KR, Espinoza DA, Kadri JC, Markowitz DM, E Markowitz C, Mexhitaj I, Jacobs D, Babb A, Betts MR, Prak ETL, Weiskopf D, Grifoni A, Lundgreen KA, Gouma S, Sette A, Bates P, Hensley SE, Greenplate AR, Wherry EJ, Li R, Bar-Or A. Cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy. Nat Med 2021; 27:1990-2001. [PMID: 34522051 PMCID: PMC8604727 DOI: 10.1038/s41591-021-01507-2] [Citation(s) in RCA: 333] [Impact Index Per Article: 111.0] [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: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 messenger RNA vaccination in healthy individuals generates immune protection against COVID-19. However, little is known about SARS-CoV-2 mRNA vaccine-induced responses in immunosuppressed patients. We investigated induction of antigen-specific antibody, B cell and T cell responses longitudinally in patients with multiple sclerosis (MS) on anti-CD20 antibody monotherapy (n = 20) compared with healthy controls (n = 10) after BNT162b2 or mRNA-1273 mRNA vaccination. Treatment with anti-CD20 monoclonal antibody (aCD20) significantly reduced spike-specific and receptor-binding domain (RBD)-specific antibody and memory B cell responses in most patients, an effect ameliorated with longer duration from last aCD20 treatment and extent of B cell reconstitution. By contrast, all patients with MS treated with aCD20 generated antigen-specific CD4 and CD8 T cell responses after vaccination. Treatment with aCD20 skewed responses, compromising circulating follicular helper T (TFH) cell responses and augmenting CD8 T cell induction, while preserving type 1 helper T (TH1) cell priming. Patients with MS treated with aCD20 lacking anti-RBD IgG had the most severe defect in circulating TFH responses and more robust CD8 T cell responses. These data define the nature of the SARS-CoV-2 vaccine-induced immune landscape in aCD20-treated patients and provide insights into coordinated mRNA vaccine-induced immune responses in humans. Our findings have implications for clinical decision-making and public health policy for immunosuppressed patients including those treated with aCD20.
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Grants
- U19AI082630 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 AR076951 NIAMS NIH HHS
- AI082630 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R21 AI142638 NIAID NIH HHS
- AI108545 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R01 AI152236 NIAID NIH HHS
- 75N9301900065 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- AI149680 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 CA009140 NCI NIH HHS
- R01 AI118694 NIAID NIH HHS
- U19 AI082630 NIAID NIH HHS
- AI152236 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- P30-AI0450080 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- T32 AR076951-01 U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- R01 AI105343 NIAID NIH HHS
- AI105343 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- R01 AI155577 NIAID NIH HHS
- UM1 AI144288 NIAID NIH HHS
- U19 AI149680 NIAID NIH HHS
- AI155577 U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)
- SI-2011-37160 National Multiple Sclerosis Society (National MS Society)
- UC4 DK112217 NIDDK NIH HHS
- P01 AI108545 NIAID NIH HHS
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)
- Penn | Perelman School of Medicine, University of Pennsylvania (Perelman School of Medicine at the University of Pennsylvania)
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Affiliation(s)
- Sokratis A Apostolidis
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mihir Kakara
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark M Painter
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rishi R Goel
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kerry Lenzi
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayman Rezk
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kristina R Patterson
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Diego A Espinoza
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessy C Kadri
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel M Markowitz
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Clyde E Markowitz
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ina Mexhitaj
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Dina Jacobs
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison Babb
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kendall A Lundgreen
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Center for Research on Coronavirus and Other Emerging Pathogens, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sigrid Gouma
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Center for Research on Coronavirus and Other Emerging Pathogens, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott E Hensley
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Rui Li
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Amit Bar-Or
- Center for Neuroinflammation and Experimental Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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7
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Espinoza DA, Mortlock RD, Koelle SJ, Wu C, Dunbar CE. Interrogation of clonal tracking data using barcodetrackR. Nat Comput Sci 2021; 1:280-289. [PMID: 37621673 PMCID: PMC10449013 DOI: 10.1038/s43588-021-00057-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 08/26/2023]
Abstract
Clonal tracking methods provide quantitative insights into the cellular output of genetically labelled progenitor cells across time and cellular compartments. In the context of gene and cell therapies, clonal tracking methods have enabled the tracking of progenitor cell output both in humans receiving therapies and in corresponding animal models, providing valuable insight into lineage reconstitution, clonal dynamics, and vector genotoxicity. However, the absence of a toolbox for analysis of clonal tracking data has precluded the development of standardized analytical frameworks within the field. Thus, we developed barcodetrackR, an R package and accompanying Shiny app containing diverse tools for the analysis and visualization of clonal tracking data. We demonstrate the utility of barcodetrackR in exploring longitudinal clonal patterns and lineage relationships in a number of clonal tracking studies of hematopoietic stem and progenitor cells (HSPCs) in humans receiving HSPC gene therapy and in animals receiving lentivirally transduced HSPC transplants or tumor cells.
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Affiliation(s)
- Diego A. Espinoza
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryland D. Mortlock
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samson J. Koelle
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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8
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Truitt LL, Yang D, Espinoza DA, Fan X, Ram DR, Moström MJ, Tran D, Sprehe LM, Reeves RK, Donahue RE, Kaur A, Dunbar CE, Wu C. Impact of CMV Infection on Natural Killer Cell Clonal Repertoire in CMV-Naïve Rhesus Macaques. Front Immunol 2019; 10:2381. [PMID: 31649681 PMCID: PMC6794559 DOI: 10.3389/fimmu.2019.02381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 07/30/2019] [Accepted: 09/23/2019] [Indexed: 02/01/2023] Open
Abstract
Recent functional, gene expression, and epigenetic studies have suggested the presence of a subset of mature natural killer (NK) cells responsible for maintaining NK cell memory. The lack of endogenous clonal markers in NK cells impedes understanding the genesis of these cell populations. In humans, primates, and mice, this phenotype and memory or adaptive functions have been strongly linked to cytomegalovirus or related herpes virus infections. We have used transplantation of lentivirally-barcoded autologous hematopoietic stem and progenitor cells (HSPC) to track clonal hematopoiesis in rhesus macaques and previously reported striking oligoclonal expansions of NK-biased barcoded clones within the CD56−CD16+ NK cell subpopulation, clonally distinct from ongoing output of myeloid, B cell, T cell, and CD56+16− NK cells from HSPC. These CD56−CD16+ NK cell clones segregate by expression of specific KIR surface receptors, suggesting clonal expansion in reaction to specific environmental stimuli. We have now used this model to investigate the impact of rhesus CMV(RhCMV) infection on NK clonal dynamics. Following transplantation, RhCMVneg rhesus macaques display less dominant and oligoclonal CD16+ NK cells biased clones compared to RhCMVpos animals, however these populations of cells are still clearly present. Upon RhCMV infection, CD16+ NK cells proliferate, followed by appearance of new groups of expanded NK clones and disappearance of clones present prior to RhCMV infection. A second superinfection with RhCMV resulted in rapid viral clearance without major change in the mature NK cell clonal landscape. Our findings suggest that RhCMV is not the sole driver of clonal expansion and peripheral maintenance of mature NK cells; however, infection of macaques with this herpesvirus does result in selective expansion and persistence of specific NK cell clones, providing further information relevant to adaptive NK cells and the development of NK cell therapies.
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Affiliation(s)
- Lauren L Truitt
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Di Yang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States.,Institute of Hematology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Diego A Espinoza
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Daniel R Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Matilda J Moström
- Tulane National Primate Research Center, Covington, LA, United States
| | - Dollnovan Tran
- Tulane National Primate Research Center, Covington, LA, United States
| | - Lesli M Sprehe
- Tulane National Primate Research Center, Covington, LA, United States
| | - R Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
| | - Robert E Donahue
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Amitinder Kaur
- Tulane National Primate Research Center, Covington, LA, United States
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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9
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Fan X, Wu C, Truitt LL, Espinoza DA, Sellers S, Bonifacino A, Zhou Y, Cordes SF, Krouse A, Metzger M, Donahue RE, Lu R, Dunbar CE. Clonal tracking of erythropoiesis in rhesus macaques. Haematologica 2019; 105:1813-1824. [PMID: 31582555 PMCID: PMC7327626 DOI: 10.3324/haematol.2019.231811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/03/2019] [Indexed: 12/25/2022] Open
Abstract
The classical model of hematopoietic hierarchies is being reconsidered on the basis of data from in vitro assays and single cell expression profiling. Recent experiments suggested that the erythroid lineage might differentiate directly from multipotent hematopoietic stem cells / progenitors or from a highly biased subpopulation of stem cells, rather than transiting through common myeloid progenitors or megakaryocyte-erythrocyte progenitors. We genetically barcoded autologous rhesus macaque stem and progenitor cells, allowing quantitative tracking of the in vivo clonal output of thousands of individual cells over time following transplantation. CD34+ cells were lentiviral-transduced with a high diversity barcode library, with the barcode in an expressed region of the provirus, allowing barcode retrieval from DNA or RNA, with each barcode representing an individual stem or progenitor cell clone. Barcode profiles from bone marrow CD45-CD71+ maturing nucleated red blood cells were compared with other lineages purified from the same bone marrow sample. There was very high correlation of barcode contributions between marrow nucleated red blood cells and other lineages, with the highest correlation between nucleated red blood cells and myeloid lineages, whether at earlier or later time points post transplantation, without obvious clonal contributions from highly erythroid-biased or restricted clones. A similar profile occurred even under stressors such as aging or erythropoietin stimulation. RNA barcode analysis on circulating mature red blood cells followed over long time periods demonstrated stable erythroid clonal contributions. Overall, in this nonhuman primate model with great relevance to human hematopoiesis, we documented continuous production of erythroid cells from multipotent, non-biased hematopoietic stem cell clones at steady-state or under stress.
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Affiliation(s)
- Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Lauren L Truitt
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Diego A Espinoza
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie Sellers
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Aylin Bonifacino
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Stefan F Cordes
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Allen Krouse
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Mark Metzger
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Robert E Donahue
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
| | - Rong Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MA, USA
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10
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Wu C, Espinoza DA, Koelle SJ, Yang D, Truitt L, Schlums H, Lafont BA, Davidson-Moncada JK, Lu R, Kaur A, Hammer Q, Li B, Panch S, Allan DA, Donahue RE, Childs RW, Romagnani C, Bryceson YT, Dunbar CE. Clonal expansion and compartmentalized maintenance of rhesus macaque NK cell subsets. Sci Immunol 2019; 3:3/29/eaat9781. [PMID: 30389798 DOI: 10.1126/sciimmunol.aat9781] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
Natural killer (NK) cells recognize and eliminate infected and malignant cells. Their life histories are poorly understood, particularly in humans, due to lack of informative models and endogenous clonal markers. Here, we apply transplantation of barcoded rhesus macaque hematopoietic cells to interrogate the landscape of NK cell production, expansion, and life histories at a clonal level long term and after proliferative challenge. We identify oligoclonal populations of rhesus CD56-CD16+ NK cells that are characterized by marked expansions and contractions over time yet remained long-term clonally uncoupled from other hematopoietic lineages, including CD56+CD16- NK cells. Individual or groups of CD56-CD16+ expanded clones segregated with surface expression of specific killer immunoglobulin-like receptors. These clonally distinct NK cell subpopulation patterns persisted for more than 4 years, including after transient in vivo anti-CD16-mediated depletion and subsequent regeneration. Profound and sustained interleukin-15-mediated depletion was required to generate new oligoclonal CD56-CD16+ NK cells. Together, our results indicate that linear NK cell production from multipotent hematopoietic progenitors or less mature CD56+CD16- cells is negligible during homeostasis and moderate proliferative stress. In such settings, peripheral compartmentalized self-renewal can maintain the composition of distinct, differentiated NK cell subpopulations.
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Affiliation(s)
- Chuanfeng Wu
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Diego A Espinoza
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samson J Koelle
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Department of Statistics, University of Washington, Seattle, WA, USA
| | - Di Yang
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lauren Truitt
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Heinrich Schlums
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Bernard A Lafont
- Viral Immunology Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jan K Davidson-Moncada
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Clinical Development and Translational Research, MacroGenics Inc. Rockville, MD, USA
| | - Rong Lu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, Covington, LA, USA
| | - Quirin Hammer
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Deutsches Rheuma-Forschungszentrum-A Leibnitz Institute, Charite Medical University, Berlin, Germany
| | - Brian Li
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Department of Medicine, Beth Israel Hospital, Boston, MA, USA
| | - Sandhya Panch
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - David A Allan
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Robert E Donahue
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Richard W Childs
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Chiara Romagnani
- Deutsches Rheuma-Forschungszentrum-A Leibnitz Institute, Charite Medical University, Berlin, Germany
| | - Yenan T Bryceson
- Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Stockholm, Sweden. .,Department of Clinical Sciences, University of Bergen, Bergen, Norway
| | - Cynthia E Dunbar
- Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.
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11
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Espinoza DA, Fan X, Yang D, Cordes SF, Truitt LL, Calvo KR, Yabe IM, Demirci S, Hope KJ, Hong SG, Krouse A, Metzger M, Bonifacino A, Lu R, Uchida N, Tisdale JF, Wu X, DeRavin SS, Malech HL, Donahue RE, Wu C, Dunbar CE. Aberrant Clonal Hematopoiesis following Lentiviral Vector Transduction of HSPCs in a Rhesus Macaque. Mol Ther 2019; 27:1074-1086. [PMID: 31023523 DOI: 10.1016/j.ymthe.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 01/21/2023] Open
Abstract
Lentiviral vectors (LVs) are used for delivery of genes into hematopoietic stem and progenitor cells (HSPCs) in clinical trials worldwide. LVs, in contrast to retroviral vectors, are not associated with insertion site-associated malignant clonal expansions and, thus, are considered safer. Here, however, we present a case of markedly abnormal dysplastic clonal hematopoiesis affecting the erythroid, myeloid, and megakaryocytic lineages in a rhesus macaque transplanted with HSPCs that were transduced with a LV containing a strong retroviral murine stem cell virus (MSCV) constitutive promoter-enhancer in the LTR. Nine insertions were mapped in the abnormal clone, resulting in overexpression and aberrant splicing of several genes of interest, including the cytokine stem cell factor and the transcription factor PLAG1. This case represents the first clear link between lentiviral insertion-induced clonal expansion and a clinically abnormal transformed phenotype following transduction of normal primate or human HSPCs, which is concerning, and suggests that strong constitutive promoters should not be included in LVs.
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Affiliation(s)
- Diego A Espinoza
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Di Yang
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Stefan F Cordes
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Lauren L Truitt
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Katherine R Calvo
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Idalia M Yabe
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Selami Demirci
- Sickle Cell and Vascular Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Kristin J Hope
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON, Canada
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Allen Krouse
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Mark Metzger
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Aylin Bonifacino
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Rong Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Naoya Uchida
- Sickle Cell and Vascular Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - John F Tisdale
- Sickle Cell and Vascular Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Robert E Donahue
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
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12
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Yabe IM, Truitt LL, Espinoza DA, Wu C, Koelle S, Panch S, Corat MA, Winkler T, Yu KR, Hong SG, Bonifacino A, Krouse A, Metzger M, Donahue RE, Dunbar CE. Barcoding of Macaque Hematopoietic Stem and Progenitor Cells: A Robust Platform to Assess Vector Genotoxicity. Mol Ther Methods Clin Dev 2018; 11:143-154. [PMID: 30547048 PMCID: PMC6258888 DOI: 10.1016/j.omtm.2018.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/19/2018] [Indexed: 12/19/2022]
Abstract
Gene therapies using integrating retrovirus vectors to modify hematopoietic stem and progenitor cells have shown great promise for the treatment of immune system and hematologic diseases. However, activation of proto-oncogenes via insertional mutagenesis has resulted in the development of leukemia. We have utilized cellular bar coding to investigate the impact of different vector designs on the clonal behavior of hematopoietic stem and progenitor cells (HSPCs) during in vivo expansion, as a quantitative surrogate assay for genotoxicity in a non-human primate model with high relevance for human biology. We transplanted two rhesus macaques with autologous CD34+ HSPCs transduced with three lentiviral vectors containing different promoters and/or enhancers of a predicted range of genotoxicities, each containing a high-diversity barcode library that uniquely tags each individual transduced HSPC. Analysis of clonal output from thousands of individual HSPCs transduced with these barcoded vectors revealed sustained clonal diversity, with no progressive dominance of clones containing any of the three vectors for up to almost 3 years post-transplantation. Our data support a low genotoxic risk for lentivirus vectors in HSPCs, even those containing strong promoters and/or enhancers. Additionally, this flexible system can be used for the testing of future vector designs.
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Affiliation(s)
- Idalia M. Yabe
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Lauren L. Truitt
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Diego A. Espinoza
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Chuanfeng Wu
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Samson Koelle
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Sandhya Panch
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marcus A.F. Corat
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Multidisciplinary Center for Biological Research, University of Campinas, Campinas, SP 13083-877, Brazil
| | - Thomas Winkler
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kyung-Rok Yu
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - So Gun Hong
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Aylin Bonifacino
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Allen Krouse
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Mark Metzger
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Robert E. Donahue
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Cynthia E. Dunbar
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Corresponding author: Cynthia E. Dunbar, National Heart, Lung and Blood Institute, NIH, Building 10 CRC Room 4E-5132, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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13
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Wu C, Espinoza DA, Koelle SJ, Potter EL, Lu R, Li B, Yang D, Fan X, Donahue RE, Roederer M, Dunbar CE. Geographic clonal tracking in macaques provides insights into HSPC migration and differentiation. J Exp Med 2017; 215:217-232. [PMID: 29141868 PMCID: PMC5748860 DOI: 10.1084/jem.20171341] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 10/12/2017] [Indexed: 01/13/2023] Open
Abstract
Wu et al. use barcode tracking to uncover prolonged geographic bone marrow segregation of regenerating hematopoietic stem and progenitor cell clones after transplantation and provide evidence for local bone marrow production of T cells. The geographic distribution of hematopoiesis at a clonal level is of interest in understanding how hematopoietic stem and progenitor cells (HSPCs) and their progeny interact with bone marrow (BM) niches during regeneration. We tagged rhesus macaque autologous HSPCs with genetic barcodes, allowing clonal tracking over time and space after transplantation. We found marked geographic segregation of CD34+ HSPCs for at least 6 mo posttransplantation, followed by very gradual clonal mixing at different BM sites over subsequent months to years. Clonal mapping was used to document local production of granulocytes, monocytes, B cells, and CD56+ natural killer (NK) cells. In contrast, CD16+CD56− NK cells were not produced in the BM, and in fact were clonally distinct from multipotent progenitors producing all other lineages. Most surprisingly, we documented local BM production of CD3+ T cells early after transplantation, using both clonal mapping and intravascular versus tissue-resident T cell staining, suggesting a thymus-independent T cell developmental pathway operating during BM regeneration, perhaps before thymic recovery.
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Affiliation(s)
- Chuanfeng Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Diego A Espinoza
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Samson J Koelle
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - E Lake Potter
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Rong Lu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Brian Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Di Yang
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.,Institute of hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Fan
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Robert E Donahue
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Cynthia E Dunbar
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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Yu IW, Espinoza DA, McAlexander MA, Witwer KW. OpenArray profiling reveals no differential modulation of miRNA by positive and negative CD4+ T cell immunoselection. Exp Hematol 2014; 42:11-3. [PMID: 24096121 PMCID: PMC4136421 DOI: 10.1016/j.exphem.2013.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/11/2013] [Accepted: 09/19/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Ian W Yu
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Diego A Espinoza
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa A McAlexander
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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