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Bullock ME, Hogan T, Williams C, Morris S, Nowicka M, Sharjeel M, van Dorp C, Yates AJ, Seddon B. The dynamics and longevity of circulating CD4+ memory T cells depend on cell age and not the chronological age of the host. PLoS Biol 2024; 22:e3002380. [PMID: 39137219 PMCID: PMC11321570 DOI: 10.1371/journal.pbio.3002380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 06/24/2024] [Indexed: 08/15/2024] Open
Abstract
Quantifying the kinetics with which memory T cell populations are generated and maintained is essential for identifying the determinants of the duration of immunity. The quality and persistence of circulating CD4 effector memory (TEM) and central memory (TCM) T cells in mice appear to shift with age, but it is unclear whether these changes are driven by the aging host environment, by cell age effects, or both. Here, we address these issues by combining DNA labelling methods, established fate-mapping systems, a novel reporter mouse strain, and mathematical models. Together, these allow us to quantify the dynamics of both young and established circulating memory CD4 T cell subsets, within both young and old mice. We show that that these cells and their descendents become more persistent the longer they reside within the TCM and TEM pools. This behaviour may limit memory CD4 T cell diversity by skewing TCR repertoires towards clones generated early in life, but may also compensate for functional defects in new memory cells generated in old age.
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Affiliation(s)
- M. Elise Bullock
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - Cayman Williams
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - Sinead Morris
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Maria Nowicka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Minahil Sharjeel
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - Christiaan van Dorp
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
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2
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Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E. Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma. PLoS Comput Biol 2024; 20:e1012266. [PMID: 38995971 PMCID: PMC11288457 DOI: 10.1371/journal.pcbi.1012266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 07/30/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Tuberculosis (TB) remains a global public health threat. Understanding the dynamics of host-pathogen interactions within TB granulomas will assist in identifying what leads to the successful elimination of infection. In vitro TB models provide a controllable environment to study these granuloma dynamics. Previously we developed a biomimetic 3D spheroid granuloma model that controls bacteria better than a traditional monolayer culture counterpart. We used agent-based simulations to predict the mechanistic reason for this difference. Our calibrated simulations were able to predict heterogeneous bacterial dynamics that are consistent with experimental data. In one group of simulations, spheroids are found to have higher macrophage activation than their traditional counterparts, leading to better bacterial control. This higher macrophage activation in the spheroids was not due to higher counts of activated T cells, instead fewer activated T cells were able to activate more macrophages due to the proximity of these cells to each other within the spheroid. In a second group of simulations, spheroids again have more macrophage activation but also more T cell activation, specifically CD8+ T cells. This higher level of CD8+ T cell activation is predicted to be due to the proximity of these cells to the cells that activate them. Multiple mechanisms of control were predicted. Simulations removing individual mechanisms show that one group of simulations has a CD4+ T cell dominant response, while the other has a mixed/CD8+ T cell dominant response. Lastly, we demonstrated that in spheroids the initial structure and movement rules work synergistically to reduce bacterial load. These findings provide valuable insights into how the structural complexity of in vitro models impacts immune responses. Moreover, our study has implications for engineering more physiologically relevant in vitro models and advancing our understanding of TB pathogenesis and potential therapeutic interventions.
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Affiliation(s)
- Alexa Petrucciani
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Alexis Hoerter
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Leigh Kotze
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nelita Du Plessis
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, Indiana, United States of America
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3
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Bullock ME, Hogan T, Williams C, Morris S, Nowicka M, Sharjeel M, van Dorp C, Yates AJ, Seddon B. The dynamics and longevity of circulating CD4 + memory T cells depend on cell age and not the chronological age of the host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562650. [PMID: 38948729 PMCID: PMC11212895 DOI: 10.1101/2023.10.16.562650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Quantifying the kinetics with which memory T cell populations are generated and maintained is essential for identifying the determinants of the duration of immunity. The quality and persistence of circulating CD4+ effector memory (TEM) and central memory (TCM) T cells in mice appear to shift with age, but it is unclear whether these changes are driven by the aging host environment, by cell age effects, or both. Here we address these issues by combining DNA labelling methods, established fate-mapping systems, a novel reporter mouse strain, and mathematical models. Together, these allow us to quantify the dynamics of both young and established circulating memory CD4+ T cell subsets, within both young and old mice. We show that that these cells and their descendents become more persistent the longer they reside within the TCM and TEM pools. This behaviour may limit memory CD4 T cell diversity by skewing TCR repertoires towards clones generated early in life, but may also compensate for functional defects in new memory cells generated in old age.
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Affiliation(s)
- M. Elise Bullock
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Cayman Williams
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Sinead Morris
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Maria Nowicka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Minahil Sharjeel
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Christiaan van Dorp
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
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4
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Chen JJ, Vincent MY, Shepard D, Peereboom D, Mahalingam D, Battiste J, Patel MR, Juric D, Wen PY, Bullock A, Selfridge JE, Pant S, Liu J, Li W, Fyfe S, Wang S, Zota V, Mahoney J, Watnick RS, Cieslewicz M, Watnick J. Phase 1 dose expansion and biomarker study assessing first-in-class tumor microenvironment modulator VT1021 in patients with advanced solid tumors. COMMUNICATIONS MEDICINE 2024; 4:95. [PMID: 38773224 PMCID: PMC11109328 DOI: 10.1038/s43856-024-00520-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/03/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Preclinical studies have demonstrated that VT1021, a first-in-class therapeutic agent, inhibits tumor growth via stimulation of thrombospondin-1 (TSP-1) and reprograms the tumor microenvironment. We recently reported data from the dose escalation part of a phase I study of VT1021 in solid tumors. Here, we report findings from the dose expansion phase of the same study. METHODS We analyzed the safety and tolerability, clinical response, and biomarker profile of VT1021 in the expansion portion of the phase I study (NCT03364400). Safety/tolerability is determined by adverse events related to the treatment. Clinical response is determined by RECIST v1.1 and iRECIST. Biomarkers are measured by multiplexed ion beam imaging and enzyme-linked immunoassay (ELISA). RESULTS First, we report the safety and tolerability data as the primary outcome of this study. Adverse events (AE) suspected to be related to the study treatment (RTEAEs) are mostly grade 1-2. There are no grade 4 or 5 adverse events. VT1021 is safe and well tolerated in patients with solid tumors in this study. We report clinical responses as a secondary efficacy outcome. VT1021 demonstrates promising single-agent clinical activity in recurrent GBM (rGBM) in this study. Among 22 patients with rGBM, the overall disease control rate (DCR) is 45% (95% confidence interval, 0.24-0.67). Finally, we report the exploratory outcomes of this study. We show the clinical confirmation of TSP-1 induction and TME remodeling by VT1021. Our biomarker analysis identifies several plasmatic cytokines as potential biomarkers for future clinical studies. CONCLUSIONS VT1021 is safe and well-tolerated in patients with solid tumors in a phase I expansion study. VT1021 has advanced to a phase II/III clinical study in glioblastoma (NCT03970447).
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Affiliation(s)
| | | | | | | | | | | | - Manish R Patel
- Florida Cancer Specialists/Sarah Cannon Research Institute, Sarasota, FL, USA
| | - Dejan Juric
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | - Shubham Pant
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joyce Liu
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Wendy Li
- Vigeo Therapeutics, Cambridge, MA, USA
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5
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Gurrola TE, Effah SN, Sariyer IK, Dampier W, Nonnemacher MR, Wigdahl B. Delivering CRISPR to the HIV-1 reservoirs. Front Microbiol 2024; 15:1393974. [PMID: 38812680 PMCID: PMC11133543 DOI: 10.3389/fmicb.2024.1393974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/22/2024] [Indexed: 05/31/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is well known as one of the most complex and difficult viral infections to cure. The difficulty in developing curative strategies arises in large part from the development of latent viral reservoirs (LVRs) within anatomical and cellular compartments of a host. The clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system shows remarkable potential for the inactivation and/or elimination of integrated proviral DNA within host cells, however, delivery of the CRISPR/Cas9 system to infected cells is still a challenge. In this review, the main factors impacting delivery, the challenges for delivery to each of the LVRs, and the current successes for delivery to each reservoir will be discussed.
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Affiliation(s)
- Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Samuel N. Effah
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Microbiology, Immunology, and Inflammation and Center for Neurovirology and Gene Editing, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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6
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Tręda C, Włodarczyk A, Rieske P. The hope, hype and obstacles surrounding cell therapy. J Cell Mol Med 2024; 28:e18359. [PMID: 38770886 PMCID: PMC11107145 DOI: 10.1111/jcmm.18359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Cell therapy offers hope, but it also presents challenges, most particularly the limited ability of human organs and tissues to regenerate. Since many diseases are associated with irreversible pathophysiological or traumatic changes, stem cells and their derivatives are unable to secure healing. Although regenerative medicine offers chances for improvements in many diseases, such as type one diabetes and Parkinson's disease, it cannot eliminate the primary cause of many of them. While successes can be expected for diseases such as sickle cell disease, this is not the case for hereditary diseases with varied mutation types or for ciliopathies, which start in embryogenesis. In this complicated medical environment, synthetic biology offers some solutions, but their implementation will take many years. Still, positive examples such as CAR-T therapy offer hope.
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Affiliation(s)
- Cezary Tręda
- Department of Tumor BiologyMedical University of LodzLodzPoland
| | | | - Piotr Rieske
- Department of Tumor BiologyMedical University of LodzLodzPoland
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7
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Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E. In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models. PLoS One 2024; 19:e0299107. [PMID: 38517920 PMCID: PMC10959380 DOI: 10.1371/journal.pone.0299107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/05/2024] [Indexed: 03/24/2024] Open
Abstract
In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool for examining host-pathogen interactions and screening drugs. With the development of more complex in vitro models, there is a need for tools to help analyze and integrate data from these models. To this end, we introduce an agent-based model (ABM) representation of the interactions between immune cells and bacteria in an in vitro setting. This in silico model was used to simulate both traditional and spheroid cell culture models by changing the movement rules and initial spatial layout of the cells in accordance with the respective in vitro models. The traditional and spheroid simulations were calibrated to published experimental data in a paired manner, by using the same parameters in both simulations. Within the calibrated simulations, heterogeneous outputs are seen for bacterial count and T cell infiltration into the macrophage core of the spheroid. The simulations also predict that equivalent numbers of activated macrophages do not necessarily result in similar bacterial reductions; that host immune responses can control bacterial growth in both spheroid structure dependent and independent manners; that STAT1 activation is the limiting step in macrophage activation in spheroids; and that drug screening and macrophage activation studies could have different outcomes depending on the in vitro culture used. Future model iterations will be guided by the limitations of the current model, specifically which parts of the output space were harder to reach. This ABM can be used to represent more in vitro Mtb infection models due to its flexible structure, thereby accelerating in vitro discoveries.
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Affiliation(s)
- Alexa Petrucciani
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Alexis Hoerter
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Leigh Kotze
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nelita Du Plessis
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elsje Pienaar
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States of America
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN, United States of America
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Lindgren H, Eneslätt K, Golovliov I, Gelhaus C, Sjöstedt A. Analyses of human immune responses to Francisella tularensis identify correlates of protection. Front Immunol 2023; 14:1238391. [PMID: 37781364 PMCID: PMC10540638 DOI: 10.3389/fimmu.2023.1238391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Francisella tularensis is the etiological agent of the potentially severe infection tularemia. An existing F: tularensis vaccine, the live vaccine strain (LVS), has been used to protect at-risk personnel, but it is not licensed in any country and it has limited efficacy. Therefore, there is a need of a new, efficacious vaccine. The aim of the study was to perform a detailed analysis of the characteristics of the human immune response to F. tularensis, since this will generate crucial knowledge required to develop new vaccine candidates. Nine individuals were administered the LVS vaccine and peripheral blood mononuclear cells (PBMC) were collected before and at four time points up to one year after vaccination. The properties of the PBMC were characterized by flow cytometry analysis of surface markers and intracellular cytokine staining. In addition, the cytokine content of supernatants from F. tularensis-infected PBMC cultures was determined and the protective properties of the supernatants investigated by adding them to cultures with infected monocyte-derived macrophages (MDM). Unlike before vaccination, PBMC collected at all four time points after vaccination demonstrated F. tularensis-specific cell proliferation, cytokine secretion and cytokine-expressing memory cells. A majority of 17 cytokines were secreted at higher levels by PBMC collected at all time points after vaccination than before vaccination. A discriminative analysis based on IFN-γ and IL-13 secretion correctly classified samples obtained before and after vaccination. Increased expression of IFN-γ, IL-2, and MIP-1β were observed at all time points after vaccination vs. before vaccination and the most significant changes occurred among the CD4 transient memory, CD8 effector memory, and CD8 transient memory T-cell populations. Growth restriction of the highly virulent F. tularensis strain SCHU S4 in MDM was conferred by supernatants and protection correlated to levels of IFN-γ, IL-2, TNF, and IL-17. The findings demonstrate that F. tularensis vaccination induces long-term T-cell reactivity, including TEM and TTM cell populations. Individual cytokine levels correlated with the degree of protection conferred by the supernatants. Identification of such memory T cells and effector mechanisms provide an improved understanding of the protective mechanisms against F. tularensis. mechanisms against F. tularensis.
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Affiliation(s)
- Helena Lindgren
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Kjell Eneslätt
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Igor Golovliov
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | | | - Anders Sjöstedt
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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9
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Kut C, Midthune D, Lee E, Fair P, Cheunkarndee T, McNutt T, DeWeese T, Fakhry C, Kipnis V, Quon H. Developing the POTOMAC Model: A Novel Prediction Model to Study the Impact of Lymphopenia Kinetics on Survival Outcomes in Head and Neck Cancer Via an Ensemble Tree-Based Machine Learning Approach. JCO Clin Cancer Inform 2023; 7:e2300058. [PMID: 38096467 PMCID: PMC10735077 DOI: 10.1200/cci.23.00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/25/2023] [Accepted: 10/19/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE Lymphopenia is associated with poor survival outcomes in head and neck squamous cell carcinoma (HNSCC), yet there is no consensus on whether we should limit lymphopenia risks during treatment. To fully elucidate the prognostic role of baseline versus treatment-related lymphopenia, a robust analysis is necessary to investigate the relative importance of various lymphopenia metrics (LMs) in predicting survival outcomes. METHODS In this prospective cohort study, 363 patients were eligible for analysis (patients with newly diagnosed, nonmetastatic HNSCC treated with neck radiation with or without chemotherapy in 2015-2019). Data were acquired on 28 covariates: seven baseline, five disease, seven treatment, and nine LMs, including static and time-varying features for absolute lymphocyte count (ALC), neutrophil-to-lymphocyte ratio, and immature granulocytes (IGs). IGs were included, given their hypothesized role in inhibiting lymphocyte function. Overall, there were 4.0% missing data. Median follow-up was 2.9 years. We developed a model (POTOMAC) to predict survival outcomes using a random survival forest (RSF) procedure. RSF uses an ensemble approach to reduce the risk of overfitting and provides internal validation of the model using data that are not used in model development. The ability to predict survival risk was assessed using the AUC for the predicted risk score. RESULTS POTOMAC predicted 2-year survival with AUCs at 0.78 for overall survival (primary end point) and 0.73 for progression-free survival (secondary end point). Top modifiable risk factors included radiation dose and max ALC decrease. Top baseline risk factors included age, Charlson Comorbidity Index, Karnofsky Performance Score, and baseline IGs. Top-ranking LMs had superior prognostic performance when compared with human papillomavirus status, chemotherapy type, and dose (up to 2, 8, and 65 times higher in variable importance score). CONCLUSION POTOMAC provides important insights into potential approaches to reduce mortality in patients with HNSCC treated by chemoradiation but needs to be validated in future studies.
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Affiliation(s)
- Carmen Kut
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Doug Midthune
- Biometric Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Emerson Lee
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Peyton Fair
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Tia Cheunkarndee
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Todd McNutt
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Theodore DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Carole Fakhry
- Department of Otolaryngology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Victor Kipnis
- Biometric Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Harry Quon
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Otolaryngology, Johns Hopkins School of Medicine, Baltimore, MD
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10
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Lukas E, Hogan T, Williams C, Seddon B, Yates AJ. Quantifying cellular dynamics in mice using a novel fluorescent division reporter system. Front Immunol 2023; 14:1157705. [PMID: 37575229 PMCID: PMC10412932 DOI: 10.3389/fimmu.2023.1157705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/20/2023] [Indexed: 08/15/2023] Open
Abstract
The dynamics of cell populations are frequently studied in vivo using pulse-chase DNA labeling techniques. When combined with mathematical models, the kinetic of label uptake and loss within a population of interest then allows one to estimate rates of cell production and turnover through death or onward differentiation. Here we explore an alternative method of quantifying cellular dynamics, using a cell fate-mapping mouse model in which dividing cells can be induced to constitutively express a fluorescent protein, using a Ki67 reporter construct. We use a pulse-chase approach with this reporter mouse system to measure the lifespans and division rates of naive CD4 and CD8 T cells using a variety of modeling approaches, and show that they are all consistent with estimates derived from other published methods. However we propose that to obtain unbiased parameter estimates and full measures of their uncertainty one should simultaneously model the timecourses of the frequencies of labeled cells within both the population of interest and its precursor. We conclude that Ki67 reporter mice provide a promising system for modeling cellular dynamics.
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Affiliation(s)
- Eva Lukas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Cayman Williams
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
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11
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Zhang Y, Yan AW, Boelen L, Hadcocks L, Salam A, Gispert DP, Spanos L, Bitria LM, Nemat-Gorgani N, Traherne JA, Roberts C, Koftori D, Taylor GP, Forton D, Norman PJ, Marsh SG, Busch R, Macallan DC, Asquith B. KIR-HLA interactions extend human CD8+ T cell lifespan in vivo. J Clin Invest 2023; 133:e169496. [PMID: 37071474 PMCID: PMC10266773 DOI: 10.1172/jci169496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUNDThere is increasing evidence, in transgenic mice and in vitro, that inhibitory killer cell immunoglobulin-like receptors (iKIRs) can modulate T cell responses. Furthermore, we have previously shown that iKIRs are an important determinant of T cell-mediated control of chronic viral infection and that these results are consistent with an increase in the CD8+ T cell lifespan due to iKIR-ligand interactions. Here, we tested this prediction and investigated whether iKIRs affect T cell lifespan in humans in vivo.METHODSWe used stable isotope labeling with deuterated water to quantify memory CD8+ T cell survival in healthy individuals and patients with chronic viral infections.RESULTSWe showed that an individual's iKIR-ligand genotype was a significant determinant of CD8+ T cell lifespan: in individuals with 2 iKIR-ligand gene pairs, memory CD8+ T cells survived, on average, for 125 days; in individuals with 4 iKIR-ligand gene pairs, the memory CD8+ T cell lifespan doubled to 250 days. Additionally, we showed that this survival advantage was independent of iKIR expression by the T cell of interest and, further, that the iKIR-ligand genotype altered the CD8+ and CD4+ T cell immune aging phenotype.CONCLUSIONSTogether, these data reveal an unexpectedly large effect of iKIR genotype on T cell survival.FUNDINGWellcome Trust; Medical Research Council; EU Horizon 2020; EU FP7; Leukemia and Lymphoma Research; National Institute of Health Research (NIHR) Imperial Biomedical Research Centre; Imperial College Research Fellowship; National Institutes of Health; Jefferiss Trust.
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Affiliation(s)
- Yan Zhang
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Ada W.C. Yan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Linda Hadcocks
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Arafa Salam
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | | | - Loiza Spanos
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
- School of Life and Health Sciences, University of Roehampton, London, United Kingdom
| | - Laura Mora Bitria
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Neda Nemat-Gorgani
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - James A. Traherne
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Chrissy Roberts
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Danai Koftori
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Graham P. Taylor
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- National Centre for Human Retrovirology, St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Daniel Forton
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
- Department of Gastroenterology and Hepatology, St George’s University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Biomedical Informatics and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Steven G.E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
- UCL Cancer Institute, UCL, London, United Kingdom
| | - Robert Busch
- School of Life and Health Sciences, University of Roehampton, London, United Kingdom
| | - Derek C. Macallan
- Institute for Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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12
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Fang F, Andersen AM, Philibert R, Hancock DB. Epigenetic biomarkers for smoking cessation. ADDICTION NEUROSCIENCE 2023; 6:100079. [PMID: 37123087 PMCID: PMC10136056 DOI: 10.1016/j.addicn.2023.100079] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cigarette smoking has been associated with epigenetic alterations that may be reversible upon cessation. As the most-studied epigenetic modification, DNA methylation is strongly associated with smoking exposure, providing a potential mechanism that links smoking to adverse health outcomes. Here, we reviewed the reversibility of DNA methylation in accessible peripheral tissues, mainly blood, in relation to cigarette smoking cessation and the utility of DNA methylation as a biomarker signature to differentiate current, former, and never smokers and to quantify time since cessation. We summarized thousands of differentially methylated Cytosine-Guanine (CpG) dinucleotides and regions associated with smoking cessation from candidate gene and epigenome-wide association studies, as well as the prediction accuracy of the multi-CpG predictors for smoking status. Overall, there is robust evidence for DNA methylation signature of cigarette smoking cessation. However, there are still gaps to fill, including (1) cell-type heterogeneity in measuring blood DNA methylation; (2) underrepresentation of non-European ancestry populations; (3) limited longitudinal data to quantitatively measure DNA methylation after smoking cessation over time; and (4) limited data to study the impact of smoking cessation on other epigenetic features, noncoding RNAs, and histone modifications. Epigenetic machinery provides promising biomarkers that can improve success in smoking cessation in the clinical setting. To achieve this goal, larger and more-diverse samples with longitudinal measures of a broader spectrum of epigenetic marks will be essential to developing a robust DNA methylation biomarker assay, followed by meeting validation requirements for the assay before being implemented as a clinically useful tool.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
| | - Allan M. Andersen
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
- Behavioral Diagnostics LLC, 2500 Crosspark Rd, Coralville, IA 52241, USA
- Department of Biomedical Engineering, 5601 Seamans Center for the Engineering Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
- Corresponding author. (D.B. Hancock)
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13
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Derksen LY, Tesselaar K, Borghans JAM. Memories that last: Dynamics of memory T cells throughout the body. Immunol Rev 2023. [PMID: 37114435 DOI: 10.1111/imr.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Memory T cells form an essential part of immunological memory, which can last for years or even a lifetime. Much experimental work has shown that the individual cells that make up the memory T-cell pool are in fact relatively short-lived. Memory T cells isolated from the blood of humans, or the lymph nodes and spleen of mice, live about 5-10 fold shorter than naive T cells, and much shorter than the immunological memory they convey. The commonly accepted view is, therefore, that long-term T-cell memory is maintained dynamically rather than by long-lived cells. This view is largely based on memory T cells in the circulation, identified using rather broad phenotypic markers, and on research in mice living in overly clean conditions. We wondered to what extent there may be heterogeneity in the dynamics and lifespans of memory T cells. We here review what is currently known about the dynamics of memory T cells in different memory subsets, locations in the body and conditions of microbial exposure, and discuss how this may be related to immunometabolism and how this knowledge can be used in various clinical settings.
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Affiliation(s)
- Lyanne Y Derksen
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kiki Tesselaar
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - José A M Borghans
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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14
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Lu D, Yadav R, Holder P, Chiang E, Sanjabi S, Poon V, Bernett M, Varma R, Liu K, Leung I, Bogaert L, Desjarlais J, Shivva V, Hosseini I, Ramanujan S. Complex PK-PD of an engineered IL-15/IL-15Rα-Fc fusion protein in cynomolgus monkeys: QSP modeling of lymphocyte dynamics. Eur J Pharm Sci 2023; 186:106450. [PMID: 37084985 DOI: 10.1016/j.ejps.2023.106450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 04/23/2023]
Abstract
XmAb24306 is a lymphoproliferative interleukin (IL)-15/IL-15 receptor α (IL-15Rα) Fc-fusion protein currently under clinical investigation as an immunotherapeutic agent for cancer treatment. XmAb24306 contains mutations in IL-15 that attenuate its affinity to the heterodimeric IL-15 receptor βγ (IL-15R). We observe substantially prolonged pharmacokinetics (PK) (half-life ∼ 2.5 to 4.5 days) in single- and repeat-dose cynomolgus monkey (cyno) studies compared to wild-type IL-15 (half-life ∼ 1 hour), leading to increased exposure and enhanced and durable expansion of NK cells, CD8+ T cells and CD4-CD8- (double negative [DN]) T cells. Drug clearance varied with dose level and time post-dose, and PK exposure decreased upon repeated dosing, which we attribute to increased target-mediated drug disposition (TMDD) resulting from drug-induced lymphocyte expansion (i.e., pharmacodynamic (PD)-enhanced TMDD). We developed a quantitative systems pharmacology (QSP) model to quantify the complex PKPD behaviors due to the interactions of XmAb24306 with multiple cell types (CD8+, CD4+, DN T cells, and NK cells) in the peripheral blood (PB) and lymphoid tissues. The model, which includes nonspecific drug clearance, binding to and TMDD by IL15R differentially expressed on lymphocyte subsets, and resultant lymphocyte margination/migration out of PB, expansion in lymphoid tissues, and redistribution to the blood, successfully describes the systemic PK and lymphocyte kinetics observed in the cyno studies. Results suggest that after 3 doses of every-two-week (Q2W) doses up to 70 days, the relative contributions of each elimination pathway to XmAb24306 clearance are: DN T cells > NK cells > CD8+ T cells > nonspecific clearance > CD4+ T cells. Modeling suggests that observed cellular expansion in blood results from the influx of cells expanded by the drug in lymphoid tissues. The model is used to predict lymphoid tissue expansion and to simulate PK-PD for different dose regimens. Thus, the model provides insight into the mechanisms underlying the observed PK-PD behavior of an engineered cytokine and can serve as a framework for the rapid integration and analysis of data that emerges from ongoing clinical studies in cancer patients as single-agent or given in combination.
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Affiliation(s)
- Dan Lu
- Genentech, Inc., South San Francisco, CA, USA.
| | | | | | | | | | - Victor Poon
- Genentech, Inc., South San Francisco, CA, USA
| | | | | | - Ke Liu
- Xencor, Inc. Monrovia, CA, USA
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15
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Gaare JJ, Dölle C, Brakedal B, Brügger K, Haugarvoll K, Nido GS, Tzoulis C. Nicotinamide riboside supplementation is not associated with altered methylation homeostasis in Parkinson's disease. iScience 2023; 26:106278. [PMID: 36936793 PMCID: PMC10014306 DOI: 10.1016/j.isci.2023.106278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/19/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Replenishing nicotinamide adenine dinucleotide (NAD) via supplementation of nicotinamide riboside (NR) has been shown to confer neuroprotective effects in models of aging and neurodegenerative diseases, including Parkinson's disease (PD). Although generally considered safe, concerns have been raised that NR supplementation could impact methylation dependent reactions, including DNA methylation, because of increased production and methylation dependent breakdown of nicotinamide (NAM). We investigated the effect of NR supplementation on DNA methylation in a double blinded, placebo-controlled trial of 29 human subjects with PD, in blood cells and muscle tissue. Our results show that NR had no impact on DNA methylation homeostasis, including individuals with common pathogenic mutations in the MTHFR gene known to affect one-carbon metabolism. Pathway and methylation variance analyses indicate that there might be minor regulatory responses to NR. We conclude that short-term therapy with high-dose NR for up to 30 days has no deleterious impact on methylation homeostasis.
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Affiliation(s)
- Johannes J. Gaare
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Christian Dölle
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Brage Brakedal
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kim Brügger
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kristoffer Haugarvoll
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Gonzalo S. Nido
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson’s Disease, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Corresponding author
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16
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Leon C, Tokarev A, Bouchnita A, Volpert V. Modelling of the Innate and Adaptive Immune Response to SARS Viral Infection, Cytokine Storm and Vaccination. Vaccines (Basel) 2023; 11:vaccines11010127. [PMID: 36679972 PMCID: PMC9861811 DOI: 10.3390/vaccines11010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023] Open
Abstract
In this work, we develop mathematical models of the immune response to respiratory viral infection, taking into account some particular properties of the SARS-CoV infections, cytokine storm and vaccination. Each model consists of a system of ordinary differential equations that describe the interactions of the virus, epithelial cells, immune cells, cytokines, and antibodies. Conventional analysis of the existence and stability of stationary points is completed by numerical simulations in order to study the dynamics of solutions. The behavior of the solutions is characterized by large peaks of virus concentration specific to acute respiratory viral infections. At the first stage, we study the innate immune response based on the protective properties of interferon secreted by virus-infected cells. Viral infection down-regulates interferon production. This competition can lead to the bistability of the system with different regimes of infection progression with high or low intensity. After that, we introduce the adaptive immune response with antigen-specific T- and B-lymphocytes. The resulting model shows how the incubation period and the maximal viral load depend on the initial viral load and the parameters of the immune response. In particular, an increase in the initial viral load leads to a shorter incubation period and higher maximal viral load. The model shows that a deficient production of antibodies leads to an increase in the incubation period and even higher maximum viral loads. In order to study the emergence and dynamics of cytokine storm, we consider proinflammatory cytokines produced by cells of the innate immune response. Depending on the parameters of the model, the system can remain in the normal inflammatory state specific for viral infections or, due to positive feedback between inflammation and immune cells, pass to cytokine storm characterized by the excessive production of proinflammatory cytokines. Finally, we study the production of antibodies due to vaccination. We determine the dose-response dependence and the optimal interval of vaccine dose. Assumptions of the model and obtained results correspond to the experimental and clinical data.
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Affiliation(s)
- Cristina Leon
- Interdisciplinary Center for Mathematical Modelling in Biomedicine, S.M. Nikol’skii Mathematical Institute, Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., 117198 Moscow, Russia
- M&S Decisions, 5 Naryshkinskaya Alley, 125167 Moscow, Russia
- Department of Foreign Languages No. 2, Plekhanov Russian University of Economics, 36 Stremyanny Lane, 115093 Moscow, Russia
- Correspondence:
| | - Alexey Tokarev
- Interdisciplinary Center for Mathematical Modelling in Biomedicine, S.M. Nikol’skii Mathematical Institute, Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., 117198 Moscow, Russia
- Semenov Institute of Chemical Physics, 4 Kosygin St., 119991 Moscow, Russia
- Bukhara Engineering Technological Institute, 15 Murtazoyeva Street, Bukhara 200100, Uzbekistan
| | - Anass Bouchnita
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79902, USA
| | - Vitaly Volpert
- Interdisciplinary Center for Mathematical Modelling in Biomedicine, S.M. Nikol’skii Mathematical Institute, Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., 117198 Moscow, Russia
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France
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17
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Baliu-Piqué M, Tesselaar K, Borghans JAM. Are homeostatic mechanisms aiding the reconstitution of the T-cell pool during lymphopenia in humans? Front Immunol 2022; 13:1059481. [PMID: 36483556 PMCID: PMC9723355 DOI: 10.3389/fimmu.2022.1059481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
A timely recovery of T-cell numbers following haematopoietic stem-cell transplantation (HSCT) is essential for preventing complications, such as increased risk of infection and disease relapse. In analogy to the occurrence of lymphopenia-induced proliferation in mice, T-cell dynamics in humans are thought to be homeostatically regulated in a cell density-dependent manner. The idea is that T cells divide faster and/or live longer when T-cell numbers are low, thereby helping the reconstitution of the T-cell pool. T-cell reconstitution after HSCT is, however, known to occur notoriously slowly. In fact, the evidence for the existence of homeostatic mechanisms in humans is quite ambiguous, since lymphopenia is often associated with infectious complications and immune activation, which confound the study of homeostatic regulation. This calls into question whether homeostatic mechanisms aid the reconstitution of the T-cell pool during lymphopenia in humans. Here we review the changes in T-cell dynamics in different situations of T-cell deficiency in humans, including the early development of the immune system after birth, healthy ageing, HIV infection, thymectomy and hematopoietic stem cell transplantation (HSCT). We discuss to what extent these changes in T-cell dynamics are a side-effect of increased immune activation during lymphopenia, and to what extent they truly reflect homeostatic mechanisms.
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Affiliation(s)
| | | | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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18
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Cell-based therapeutics for the treatment of hematologic diseases inside the bone marrow. J Control Release 2021; 339:1-13. [PMID: 34536449 DOI: 10.1016/j.jconrel.2021.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022]
Abstract
Cell-based therapies could overcome the limitations of traditional drugs for the treatment of refractory diseases. Cell exchange between the bone marrow and blood is bidirectional. Several kinds of cells in the blood have the capability to enter the bone marrow by interacting with sinusoidal cells under specific physiological or pathological conditions. These cells are the potential living therapeutics or delivery vehicles to treat or prevent bone marrow-related hematologic diseases. In this review, we summarized the in vivo molecular mechanisms and kinetics of these cells in entering the bone marrow. The advances in the fabrication of living cell drugs and the strategies to design cell-based carriers into the bone marrow were discussed. The latest studies on how to use blood cells as living drugs or as drug carriers to improve therapeutic outcomes of hematologic diseases inside the bone marrow were highlighted.
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19
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Zarnitsyna VI, Akondy RS, Ahmed H, McGuire DJ, Zarnitsyn VG, Moore M, Johnson PLF, Ahmed R, Li KW, Hellerstein MK, Antia R. Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination. PLoS Comput Biol 2021; 17:e1009468. [PMID: 34648489 PMCID: PMC8568194 DOI: 10.1371/journal.pcbi.1009468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 11/04/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding how immunological memory lasts a lifetime requires quantifying changes in the number of memory cells as well as how their division and death rates change over time. We address these questions by using a statistically powerful mixed-effects differential equations framework to analyze data from two human studies that follow CD8 T cell responses to the yellow fever vaccine (YFV-17D). Models were first fit to the frequency of YFV-specific memory CD8 T cells and deuterium enrichment in those cells 42 days to 1 year post-vaccination. A different dataset, on the loss of YFV-specific CD8 T cells over three decades, was used to assess out of sample predictions of our models. The commonly used exponential and bi-exponential decline models performed relatively poorly. Models with the cell loss following a power law (exactly or approximately) were most predictive. Notably, using only the first year of data, these models accurately predicted T cell frequencies up to 30 years post-vaccination. Our analyses suggest that division rates of these cells drop and plateau at a low level (0.1% per day, ∼ double the estimated values for naive T cells) within one year following vaccination, whereas death rates continue to decline for much longer. Our results show that power laws can be predictive for T cell memory, a finding that may be useful for vaccine evaluation and epidemiological modeling. Moreover, since power laws asymptotically decline more slowly than any exponential decline, our results help explain the longevity of immune memory phenomenologically. Immunological memory, generated in response to infection or vaccination, may provide complete or partial protection from antigenically similar infections for the lifetime. Memory CD8 T cells are important players in protection from secondary viral infections but quantitative understanding of their dynamics in humans is limited. We analyze data from two studies where immunization with the yellow fever virus vaccine (YFV-17D) generates a mild acute infection and long-term memory. We find that: (i) the division rate of YFV-17D-specific CD8 T cells drops and stabilizes at ∼ 0.1% per day during the first year following vaccination whereas the death rate declines more gradually, and (ii) the number of these cells declines approximately in accordance with a power law (∝ time−0.75) for at least several decades following vaccination.
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Affiliation(s)
- Veronika I. Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (VIZ); (RAn)
| | - Rama S. Akondy
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, India
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Donald J. McGuire
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | | | - Mia Moore
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philip L. F. Johnson
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kelvin W. Li
- Department of Nutritional Sciences and Toxicology, UC Berkeley, Berkeley, California, United States of America
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, UC Berkeley, Berkeley, California, United States of America
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (VIZ); (RAn)
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20
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Lentiviral Vectors for T Cell Engineering: Clinical Applications, Bioprocessing and Future Perspectives. Viruses 2021; 13:v13081528. [PMID: 34452392 PMCID: PMC8402758 DOI: 10.3390/v13081528] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
Lentiviral vectors have played a critical role in the emergence of gene-modified cell therapies, specifically T cell therapies. Tisagenlecleucel (Kymriah), axicabtagene ciloleucel (Yescarta) and most recently brexucabtagene autoleucel (Tecartus) are examples of T cell therapies which are now commercially available for distribution after successfully obtaining EMA and FDA approval for the treatment of blood cancers. All three therapies rely on retroviral vectors to transduce the therapeutic chimeric antigen receptor (CAR) into T lymphocytes. Although these innovations represent promising new therapeutic avenues, major obstacles remain in making them readily available tools for medical care. This article reviews the biological principles as well as the bioprocessing of lentiviral (LV) vectors and adoptive T cell therapy. Clinical and engineering successes, shortcomings and future opportunities are also discussed. The development of Good Manufacturing Practice (GMP)-compliant instruments, technologies and protocols will play an essential role in the development of LV-engineered T cell therapies.
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21
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Boehme M, Guzzetta KE, Bastiaanssen TFS, van de Wouw M, Moloney GM, Gual-Grau A, Spichak S, Olavarría-Ramírez L, Fitzgerald P, Morillas E, Ritz NL, Jaggar M, Cowan CSM, Crispie F, Donoso F, Halitzki E, Neto MC, Sichetti M, Golubeva AV, Fitzgerald RS, Claesson MJ, Cotter PD, O'Leary OF, Dinan TG, Cryan JF. Microbiota from young mice counteracts selective age-associated behavioral deficits. NATURE AGING 2021; 1:666-676. [PMID: 37117767 DOI: 10.1038/s43587-021-00093-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/25/2021] [Indexed: 04/30/2023]
Abstract
The gut microbiota is increasingly recognized as an important regulator of host immunity and brain health. The aging process yields dramatic alterations in the microbiota, which is linked to poorer health and frailty in elderly populations. However, there is limited evidence for a mechanistic role of the gut microbiota in brain health and neuroimmunity during aging processes. Therefore, we conducted fecal microbiota transplantation from either young (3-4 months) or old (19-20 months) donor mice into aged recipient mice (19-20 months). Transplant of a microbiota from young donors reversed aging-associated differences in peripheral and brain immunity, as well as the hippocampal metabolome and transcriptome of aging recipient mice. Finally, the young donor-derived microbiota attenuated selective age-associated impairments in cognitive behavior when transplanted into an aged host. Our results reveal that the microbiome may be a suitable therapeutic target to promote healthy aging.
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Affiliation(s)
- Marcus Boehme
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Katherine E Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | | | | | - Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Minal Jaggar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Francisco Donoso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Evelyn Halitzki
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marta C Neto
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marzia Sichetti
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Anna V Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Rachel S Fitzgerald
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Olivia F O'Leary
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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22
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Nikolaou C, Muehle K, Schlickeiser S, Japp AS, Matzmohr N, Kunkel D, Frentsch M, Thiel A. High-dimensional single cell mass cytometry analysis of the murine hematopoietic system reveals signatures induced by ageing and physiological pathogen challenges. IMMUNITY & AGEING 2021; 18:20. [PMID: 33879187 PMCID: PMC8056611 DOI: 10.1186/s12979-021-00230-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/26/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Immune ageing is a result of repetitive microbial challenges along with cell intrinsic or systemic changes occurring during ageing. Mice under 'specific-pathogen-free' (SPF) conditions are frequently used to assess immune ageing in long-term experiments. However, physiological pathogenic challenges are reduced in SPF mice. The question arises to what extent murine experiments performed under SPF conditions are suited to analyze immune ageing in mice and serve as models for human immune ageing. Our previous comparisons of same aged mice with different microbial exposures, unambiguously identified distinct clusters of immune cells characteristic for numerous previous pathogen encounters in particular in pet shop mice. RESULTS We here performed single cell mass cytometry assessing splenic as secondary and bone marrow as primary lymphoid organ-derived leukocytes isolated from young versus aged SPF mice in order to delineate alterations of the murine hematopoietic system induced during ageing. We then compared immune clusters from young and aged SPF mice to pet shop mice in order to delineate alterations of the murine hematopoietic system induced by physiological pathogenic challenges and those caused by cell intrinsic or systemic changes during ageing. Notably, distinct immune signatures were similarly altered in both pet shop and aged SPF mice in comparison to young SPF mice, including increased frequencies of memory T lymphocytes, effector-cytokine producing T cells, plasma cells and mature NK cells. However, elevated frequencies of CD4+ T cells, total NK cells, granulocytes, pDCs, cDCs and decreased frequencies of naïve B cells were specifically identified only in pet shop mice. In aged SPF mice specifically the frequencies of splenic IgM+ plasma cells, CD8+ T cells and CD4+ CD25+ Treg were increased as compared to pet shop mice and young mice. CONCLUSIONS Our study dissects firstly how ageing impacts both innate and adaptive immune cells in primary and secondary lymphoid organs. Secondly, it partly distinguishes murine intrinsic immune ageing alterations from those induced by physiological pathogen challenges highlighting the importance of designing mouse models for their use in preclinical research including vaccines and immunotherapies.
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Affiliation(s)
- Christos Nikolaou
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany. .,Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany. .,Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Kerstin Muehle
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Stephan Schlickeiser
- Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Flow & Mass Cytometry Core Facility, Charité - Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Alberto Sada Japp
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nadine Matzmohr
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Desiree Kunkel
- Flow & Mass Cytometry Core Facility, Charité - Universitätsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany
| | - Marco Frentsch
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Thiel
- Regenerative Immunology and Aging, BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
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23
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Fu J, Zuber J, Shonts B, Obradovic A, Wang Z, Frangaj K, Meng W, Rosenfeld AM, Waffarn EE, Liou P, Lau SP, Savage TM, Yang S, Rogers K, Danzl NM, Ravella S, Satwani P, Iuga A, Ho SH, Griesemer A, Shen Y, Prak ETL, Martinez M, Kato T, Sykes M. Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation. J Clin Invest 2021; 131:141698. [PMID: 33630757 DOI: 10.1172/jci141698] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
In humans receiving intestinal transplantation (ITx), long-term multilineage blood chimerism often develops. Donor T cell macrochimerism (≥4%) frequently occurs without graft-versus-host disease (GVHD) and is associated with reduced rejection. Here we demonstrate that patients with macrochimerism had high graft-versus-host (GvH) to host-versus-graft (HvG) T cell clonal ratios in their allografts. These GvH clones entered the circulation, where their peak levels were associated with declines in HvG clones early after transplant, suggesting that GvH reactions may contribute to chimerism and control HvG responses without causing GVHD. Consistently, donor-derived T cells, including GvH clones, and CD34+ hematopoietic stem and progenitor cells (HSPCs) were simultaneously detected in the recipients' BM more than 100 days after transplant. Individual GvH clones appeared in ileal mucosa or PBMCs before detection in recipient BM, consistent with an intestinal mucosal origin, where donor GvH-reactive T cells expanded early upon entry of recipient APCs into the graft. These results, combined with cytotoxic single-cell transcriptional profiles of donor T cells in recipient BM, suggest that tissue-resident GvH-reactive donor T cells migrated into the recipient circulation and BM, where they destroyed recipient hematopoietic cells through cytolytic effector functions and promoted engraftment of graft-derived HSPCs that maintain chimerism. These mechanisms suggest an approach to achieving intestinal allograft tolerance.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Julien Zuber
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Brittany Shonts
- Columbia Center for Translational Immunology, Department of Medicine and
| | | | - Zicheng Wang
- Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Kristjana Frangaj
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Sai-Ping Lau
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Thomas M Savage
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Suxiao Yang
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Kortney Rogers
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Nichole M Danzl
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Shilpa Ravella
- Division of Digestive and Liver Diseases, Department of Medicine
| | | | - Alina Iuga
- Department of Pathology and Cell Biology, and
| | - Siu-Hong Ho
- Columbia Center for Translational Immunology, Department of Medicine and
| | - Adam Griesemer
- Columbia Center for Translational Immunology, Department of Medicine and.,Department of Surgery
| | - Yufeng Shen
- Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, New York, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine and.,Department of Surgery.,Department of Microbiology and Immunology, Columbia University, New York, New York, USA
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24
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Wang A, Chao T, Ji Z, Xuan R, Liu S, Guo M, Wang G, Wang J. Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages. PeerJ 2020; 8:e9947. [PMID: 33083113 PMCID: PMC7547598 DOI: 10.7717/peerj.9947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/25/2020] [Indexed: 01/03/2023] Open
Abstract
Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen receptor-mediated signalling pathway, positive regulation of lymphocyte proliferation) that may play key roles in the immune functions of the goat submandibular glands at different developmental stages were identified. Moreover, we found that eight antibacterial peptide-encoding genes were downregulated in the tuberculosis and salivary secretion pathways, while all immunoglobulins were upregulated in 10 immune system pathways. These findings indicate that the submandibular glands may be important immunological organs during the growth process of goats and that the immune function of these glands gradually weakens with age up to 12 months but remains relatively stable after 12 months of age. Overall, this study will improve our understanding of transcriptional regulation related to goat submandibular gland immune function.
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Affiliation(s)
- Aili Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Shuang Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Maosen Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, P.R. China
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25
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Verstegen RHJ, Aui PM, Watson E, De Jong S, Bartol SJW, Bosco JJ, Cameron PU, Stirling RG, de Vries E, van Dongen JJM, van Zelm MC. Quantification of T-Cell and B-Cell Replication History in Aging, Immunodeficiency, and Newborn Screening. Front Immunol 2019; 10:2084. [PMID: 31543882 PMCID: PMC6730487 DOI: 10.3389/fimmu.2019.02084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/19/2019] [Indexed: 11/23/2022] Open
Abstract
Quantification of T-cell receptor excision circles (TRECs) has impacted on human T-cell research, but interpretations on T-cell replication have been limited due to the lack of a genomic coding joint. We here overcome this limitation with multiplex TRG rearrangement quantification (detecting ~0.98 alleles per TCRαβ+ T cell) and the HSB-2 cell line with a retrovirally introduced TREC construct. We uncovered <5 cell divisions in naive and >10 cell divisions in effector memory T-cell subsets. Furthermore, we show that TREC dilution with age in healthy adults results mainly from increased T cell replication history. This proliferation was significantly increased in patients with predominantly antibody deficiency. Finally, Guthrie cards of neonates with Down syndrome have fewer T and B cells than controls, with similar T-cell and slightly higher B-cell replication. Thus, combined analysis of TRG coding joints and TREC signal joints can be utilized to quantify in vivo T-cell replication, and has direct applications for research into aging, immunodeficiency, and newborn screening.
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Affiliation(s)
- Ruud H J Verstegen
- Department of Immunology, Erasmus MC, University Medical Centre, Rotterdam, Netherlands.,Division of Rheumatology, Department of Paediatrics, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Pei M Aui
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
| | - Eliza Watson
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
| | - Samuel De Jong
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
| | - Sophinus J W Bartol
- Department of Immunology, Erasmus MC, University Medical Centre, Rotterdam, Netherlands
| | - Julian J Bosco
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.,Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia
| | - Paul U Cameron
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.,Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia
| | - Robert G Stirling
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.,Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia
| | - Esther de Vries
- Tranzo, Scientific Center for Care and Welfare, Tilburg University, Tilburg, Netherlands.,Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | - Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, Netherlands
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, University Medical Centre, Rotterdam, Netherlands.,Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia.,The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.,Department of Allergy, Immunology and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia
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26
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Gabel M, Baumann NS, Oxenius A, Graw F. Investigating the Dynamics of MCMV-Specific CD8 + T Cell Responses in Individual Hosts. Front Immunol 2019; 10:1358. [PMID: 31281313 PMCID: PMC6595046 DOI: 10.3389/fimmu.2019.01358] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/29/2019] [Indexed: 01/03/2023] Open
Abstract
Infection by Cytomegalovirus (CMV) is characterized by the massive expansion and continued maintenance of CMV-specific CD8+ T cells for certain CMV-derived peptides. This phenomenon called “memory inflation" has made CMV a primary target for the generation of T cell based vaccine vectors against various diseases. However, many aspects concerning the generation and maintenance of the inflationary CD8+ T cell response still remain to be resolved. In this study, we combined experimental data and mathematical models to analyze the dynamics of circulatory inflationary CD8+ T cells within individual mice infected by MCMV. Obtaining frequent measurements on the number and frequency of CMV-specific CD8+ T cells up to 70 days post infection, we find that mathematical models assuming differing viral stimuli during acute infection and the inflationary phase provide a better description for the observed dynamics than models relying on similar viral stimuli during both phases. In addition, our analysis allowed a detailed quantification of the different phases of memory inflation within individual mice (1st-expansion - contraction - 2nd expansion/maintenance) indicating remarkable consistency of the timing of these phases across mice, but considerable variation in the size of the individual responses between mice. Our analysis provides a first step toward generating a mechanistic framework for analyzing the generation and maintenance of inflationary CD8+ T cells while accounting for individual heterogeneity. Extending these analyses by incorporating measurements from additional compartments and more prolonged sampling will help to obtain a systematic and quantitative understanding of the factors regulating the process of memory inflation.
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Affiliation(s)
- Michael Gabel
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, Heidelberg, Germany
| | - Nicolas S Baumann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Frederik Graw
- Center for Modelling and Simulation in the Biosciences, BioQuant-Center, Heidelberg University, Heidelberg, Germany
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27
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Baliu-Piqué M, Otto SA, Borghans JAM, Tesselaar K. In vivo deuterium labelling in mice supports a dynamic model for memory T-cell maintenance in the bone marrow. Immunol Lett 2019; 210:29-32. [PMID: 31004681 DOI: 10.1016/j.imlet.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
The maintenance and dynamics of memory T-cells in the bone marrow are a matter of ongoing debate. It has been suggested that memory T-cells in the bone marrow are maintained as long-lived, quiescent cells. We have recently shown that memory T-cells isolated from goat bone marrow undergo self-renewal and recirculate via the blood and lymph. Using the well-established memory T-cell markers CD44 and CD62L we here show very similar results in mice. This provides further support for the concept that memory T-cells are continuously self-renewing and recirculating between blood, bone marrow, spleen and lymph nodes.
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Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid A Otto
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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28
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Baliu-Piqué M, Kurniawan H, Ravesloot L, Verheij MW, Drylewicz J, Lievaart-Peterson K, Borghans JAM, Koets A, Tesselaar K. Age-related distribution and dynamics of T-cells in blood and lymphoid tissues of goats. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 93:1-10. [PMID: 30550777 DOI: 10.1016/j.dci.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Neonatal mammals have increased disease susceptibility and sub-optimal vaccine responses. This raises problems in both humans and farm animals. The high prevalence of paratuberculosis in goats and the lack of an effective vaccine against it have a strong impact on the dairy sector, and calls for vaccines optimized for the neonatal immune system. We characterized the composition of the T-cell pool in neonatal kids and adult goats and quantified their turnover rates using in vivo deuterium labelling. From birth to adulthood, CD4+ T-cells were the predominant subset in the thymus and lymph nodes, while spleen and bone marrow contained mainly CD8+ lymphocytes. In blood, CD4+ T-cells were the predominant subset during the neonatal period, while CD8+ T-cells predominated in adults. We observed that thymic mass and cellularity increased during the first 5 months after birth, but decreased later in life. Deuterium labelling revealed that T-cell turnover rates in neonatal kids are considerably higher than in adult animals.
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Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Henry Kurniawan
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lars Ravesloot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Myrddin W Verheij
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ad Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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29
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Siracusa F, Durek P, McGrath MA, Sercan-Alp Ö, Rao A, Du W, Cendón C, Chang HD, Heinz GA, Mashreghi MF, Radbruch A, Dong J. CD69 + memory T lymphocytes of the bone marrow and spleen express the signature transcripts of tissue-resident memory T lymphocytes. Eur J Immunol 2019; 49:966-968. [PMID: 30673129 PMCID: PMC6563480 DOI: 10.1002/eji.201847982] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/11/2018] [Accepted: 01/21/2019] [Indexed: 11/08/2022]
Abstract
It is a matter of current debate whether the bone marrow is a hub for circulating memory T lymphocytes and/or the home of resident memory T lymphocytes. Here we demonstrate for CD69+ murine CD8+ , and CD69+ murine and human CD4+ memory T lymphocytes of the bone marrow, making up between 30 and 60% of bone marrow memory T lymphocytes, that they express the gene expression signature of tissue-resident memory T lymphocytes. This suggests that a substantial proportion of bone marrow memory T lymphocytes are resident. It adds to previous evidence that bone marrow memory T cells are resting in terms of mobility and proliferation, and maintain exclusive long-term memory to distinct, systemic antigens.
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Affiliation(s)
- Francesco Siracusa
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Pawel Durek
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Mairi A McGrath
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Özen Sercan-Alp
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Anna Rao
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Weijie Du
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Carla Cendón
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Hyun-Dong Chang
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany.,Schwiete-Laboratory for Microbiota and Inflammation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Gitta Anne Heinz
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Andreas Radbruch
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany.,Experimental Rheumatology, Charité University Medicine Berlin, Berlin, Germany
| | - Jun Dong
- Cell Biology, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
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