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Winford E, Lutshumba J, Martin BJ, Wilcock DM, Jicha GA, Nikolajczyk BS, Stowe AM, Bachstetter AD. Terminally differentiated effector memory T cells associate with cognitive and AD-related biomarkers in an aging-based community cohort. Immun Ageing 2024; 21:36. [PMID: 38867294 PMCID: PMC11167815 DOI: 10.1186/s12979-024-00443-2] [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] [Received: 11/21/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND AND PURPOSE The immune response changes during aging and the progression of Alzheimer's disease (AD) and related dementia (ADRD). Terminally differentiated effector memory T cells (called TEMRA) are important during aging and AD due to their cytotoxic phenotype and association with cognitive decline. However, it is not clear if the changes seen in TEMRAs are specific to AD-related cognitive decline specifically or are more generally correlated with cognitive decline. This study aimed to examine whether TEMRAs are associated with cognition and plasma biomarkers of AD, neurodegeneration, and neuroinflammation in a community-based cohort of older adults. METHODS Study participants from a University of Kentucky Alzheimer's Disease Research Center (UK-ADRC) community-based cohort of aging and dementia were used to test our hypothesis. There were 84 participants, 44 women and 40 men. Participants underwent physical examination, neurological examination, medical history, cognitive testing, and blood collection to determine plasma biomarker levels (Aβ42/Aβ40 ratio, total tau, Neurofilament Light chain (Nf-L), Glial Fibrillary Acidic Protein (GFAP)) and to isolate peripheral blood mononuclear cells (PBMCs). Flow cytometry was used to analyze PBMCs from study participants for effector and memory T cell populations, including CD4+ and CD8+ central memory T cells (TCM), Naïve T cells, effector memory T cells (TEM), and effector memory CD45RA+ T cells (TEMRA) immune cell markers. RESULTS CD8+ TEMRAs were positively correlated with Nf-L and GFAP. We found no significant difference in CD8+ TEMRAs based on cognitive scores and no associations between CD8+ TEMRAs and AD-related biomarkers. CD4+ TEMRAs were associated with cognitive impairment on the MMSE. Gender was not associated with TEMRAs, but it did show an association with other T cell populations. CONCLUSION These findings suggest that the accumulation of CD8+ TEMRAs may be a response to neuronal injury (Nf-L) and neuroinflammation (GFAP) during aging or the progression of AD and ADRD. As our findings in a community-based cohort were not clinically-defined AD participants but included all ADRDs, this suggests that TEMRAs may be associated with changes in systemic immune T cell subsets associated with the onset of pathology.
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Affiliation(s)
- Edric Winford
- Department of Neuroscience, University of Kentucky, 741 S. Limestone St. Rm B459, Lexington, KY, 40536, USA
| | - Jenny Lutshumba
- Department of Neuroscience, University of Kentucky, 741 S. Limestone St. Rm B459, Lexington, KY, 40536, USA
| | - Barbara J Martin
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Donna M Wilcock
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, Lexington, KY, USA
| | - Gregory A Jicha
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Barbara S Nikolajczyk
- Department of Pharmacology and Nutritional Science, and Barnstable Brown Diabetes and Obesity Center, University of Kentucky, Lexington, KY, USA
| | - Ann M Stowe
- Department of Neuroscience, University of Kentucky, 741 S. Limestone St. Rm B459, Lexington, KY, 40536, USA
- Department of Neurology, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Adam D Bachstetter
- Department of Neuroscience, University of Kentucky, 741 S. Limestone St. Rm B459, Lexington, KY, 40536, USA.
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA.
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Hodson D, Mistry H, Yates J, Guzzetti S, Davies M, Aarons L, Ogungbenro K. Hierarchical cluster analysis and nonlinear mixed-effects modelling for candidate biomarker detection in preclinical models of cancer. Eur J Pharm Sci 2024; 197:106774. [PMID: 38641123 DOI: 10.1016/j.ejps.2024.106774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Preclinical models of cancer can be of translational benefit when assessing how different biomarkers are regulated in response to particular treatments. Detection of molecular biomarkers in preclinical models of cancer is difficult due inter-animal variability in responses, combined with limited accessibility of longitudinal data. METHODS Nonlinear mixed-effects modelling (NLME) was used to analyse tumour growth data based on expected tumour growth rates observed 7 days after initial doses (DD7) of Radiotherapy (RT) and Combination of RT with DNA Damage Response Inhibitors (DDRi). Cox regression was performed to confirm an association between DD7 and survival. Hierarchical Cluster Analysis (HCA) was then used to identify candidate biomarkers impacting responses to RT and RT/DDRi and these were validated using NLME. RESULTS Cox regression confirmed significant associations between DD7 and survival. HCA of RT treated samples, combined with NLME confirmed significant associations between DD7 and Cluster specific CD8+ Ki67 MFI, as well as DD7 and cluster specific Natural Killer cell density in RT treated mice. CONCLUSION Application of NLME, as well as HCA of candidate biomarkers may provide additional avenues to assess the effect of RT in MC38 syngeneic tumour models. Additional studies would need to be conducted to confirm association between DD7 and biomarkers in RT/DDRi treated mice.
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Affiliation(s)
- David Hodson
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, Stopford Building, University of Manchester, Manchester M13 9PT, UK
| | - Hitesh Mistry
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, Stopford Building, University of Manchester, Manchester M13 9PT, UK
| | - James Yates
- DMPK, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Sofia Guzzetti
- DMPK, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Michael Davies
- DMPK, Research and Early Development, Neuroscience R&D, AstraZeneca, Cambridge, UK
| | - Leon Aarons
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, Stopford Building, University of Manchester, Manchester M13 9PT, UK
| | - Kayode Ogungbenro
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, Stopford Building, University of Manchester, Manchester M13 9PT, UK.
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Firestone RS, McAvoy D, Shekarkhand T, Serrano E, Hamadeh I, Wang A, Zhu M, Qin WG, Patel D, Tan CR, Hultcrantz M, Mailankody S, Hassoun H, Shah US, Korde N, Maclachlan KH, Landau HJ, Scordo M, Shah GL, Lahoud OB, Giralt S, Murata K, Hosszu KK, Chung DJ, Lesokhin AM, Usmani SZ. CD8 effector T cells enhance teclistamab response in BCMA-exposed and -naïve multiple myeloma. Blood Adv 2024; 8:1600-1611. [PMID: 37878808 PMCID: PMC10987849 DOI: 10.1182/bloodadvances.2023011225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
ABSTRACT Teclistamab, a B-cell maturation antigen (BCMA)- and CD3-targeting bispecific antibody, is an effective novel treatment for relapsed/refractory multiple myeloma (R/RMM), but efficacy in patients exposed to BCMA-directed therapies and mechanisms of resistance have yet to be fully delineated. We conducted a real-world retrospective study of commercial teclistamab, capturing both clinical outcomes and immune correlates of treatment response in a cohort of patients (n = 52) with advanced R/RMM. Teclistamab was highly effective with an overall response rate (ORR) of 64%, including an ORR of 50% for patients with prior anti-BCMA therapy. Pretreatment plasma cell BCMA expression levels had no bearing on response. However, comprehensive pretreatment immune profiling identified that effector CD8+ T-cell populations were associated with response to therapy and a regulatory T-cell population associated with nonresponse, indicating a contribution of immune status in outcomes with potential utility as a biomarker signature to guide patient management.
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Affiliation(s)
- Ross S. Firestone
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Devin McAvoy
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tala Shekarkhand
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Edith Serrano
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Issam Hamadeh
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alice Wang
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Ge Qin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dhwani Patel
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carlyn R. Tan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sham Mailankody
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hani Hassoun
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Urvi S. Shah
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neha Korde
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kylee H. Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Heather J. Landau
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Scordo
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunjan L. Shah
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Oscar B. Lahoud
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kazunori Murata
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kinga K. Hosszu
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David J. Chung
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander M. Lesokhin
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Saad Z. Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Cellular Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Spasic M, Ogayo ER, Parsons AM, Mittendorf EA, van Galen P, McAllister SS. Spectral Flow Cytometry Methods and Pipelines for Comprehensive Immunoprofiling of Human Peripheral Blood and Bone Marrow. CANCER RESEARCH COMMUNICATIONS 2024; 4:895-910. [PMID: 38466569 PMCID: PMC10962315 DOI: 10.1158/2767-9764.crc-23-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Profiling hematopoietic and immune cells provides important information about disease risk, disease status, and therapeutic responses. Spectral flow cytometry enables high-dimensional single-cell evaluation of large cohorts in a high-throughput manner. Here, we designed, optimized, and implemented new methods for deep immunophenotyping of human peripheral blood and bone marrow by spectral flow cytometry. Two blood antibody panels capture 48 cell-surface markers to assess more than 58 cell phenotypes, including subsets of T cells, B cells, monocytes, natural killer (NK) cells, and dendritic cells, and their respective markers of exhaustion, activation, and differentiation in less than 2 mL of blood. A bone marrow antibody panel captures 32 markers for 35 cell phenotypes, including stem/progenitor populations, T-cell subsets, dendritic cells, NK cells, and myeloid cells in a single tube. We adapted and developed innovative flow cytometric analysis algorithms, originally developed for single-cell genomics, to improve data integration and visualization. We also highlight technical considerations for users to ensure data fidelity. Our protocol and analysis pipeline accurately identifies rare cell types, discerns differences in cell abundance and phenotype across donors, and shows concordant immune landscape trends in patients with known hematologic malignancy. SIGNIFICANCE This study introduces optimized methods and analysis algorithms that enhance capabilities in comprehensive immunophenotyping of human blood and bone marrow using spectral flow cytometry. This approach facilitates detection of rare cell types, enables measurement of cell variations across donors, and provides proof-of-concept in identifying known hematologic malignancies. By unlocking complexities of hematopoietic and immune landscapes at the single-cell level, this advancement holds potential for understanding disease states and therapeutic responses.
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Affiliation(s)
- Milos Spasic
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Esther R. Ogayo
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Adrienne M. Parsons
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A. Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Peter van Galen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Sandra S. McAllister
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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Brooks HL, de Castro Brás LE, Brunt KR, Sylvester MA, Parvatiyar MS, Sirish P, Bansal SS, Sule R, Eadie AL, Knepper MA, Fenton RA, Lindsey ML, DeLeon-Pennell KY, Gomes AV. Guidelines on antibody use in physiology research. Am J Physiol Renal Physiol 2024; 326:F511-F533. [PMID: 38234298 DOI: 10.1152/ajprenal.00347.2023] [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: 10/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
Antibodies are one of the most used reagents in scientific laboratories and are critical components for a multitude of experiments in physiology research. Over the past decade, concerns about many biological methods, including those that use antibodies, have arisen as several laboratories were unable to reproduce the scientific data obtained in other laboratories. The lack of reproducibility could be largely attributed to inadequate reporting of detailed methods, no or limited verification by authors, and the production and use of unvalidated antibodies. The goal of this guideline article is to review best practices concerning commonly used techniques involving antibodies, including immunoblotting, immunohistochemistry, and flow cytometry. Awareness and integration of best practices will increase the rigor and reproducibility of these techniques and elevate the quality of physiology research.
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Affiliation(s)
- Heddwen L Brooks
- Department of Physiology, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | | | - Keith R Brunt
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Saint John, New Brunswick, Canada
| | - Megan A Sylvester
- Department of Physiology, College of Medicine, University of Arizona, Tucson, Arizona, United States
| | - Michelle S Parvatiyar
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, Florida, United States
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, California, United States
| | - Shyam S Bansal
- Department of Cellular and Molecular Physiology, Heart and Vascular Institute, Pennsylvania State University Hershey Medical Center, Hershey, Pennsylvania, United States
| | - Rasheed Sule
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, United States
| | - Ashley L Eadie
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Saint John, New Brunswick, Canada
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Merry L Lindsey
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, United States
- Research Service, Nashville Veterans Affairs Medical Center, Nashville, Tennessee, United States
| | - Kristine Y DeLeon-Pennell
- Division of Cardiology, Department of Medicine, School of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- Research Service, Ralph H Johnson Veterans Affairs Medical Center, Charleston, South Carolina, United States
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, United States
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Zweifach A. Samples in many cell-based experiments are matched/paired but taking this into account does not always increase power of statistical tests for differences in means. Mol Biol Cell 2024; 35:br1. [PMID: 37910179 PMCID: PMC10881176 DOI: 10.1091/mbc.e23-05-0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/25/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023] Open
Abstract
Power of statistical tests for differences in means is the probability of obtaining a statistically significant p value when means differ. When samples in experimental replicates come from a single cell culture, they are matched or paired because they share between-trials biological variability. This can cause positive correlation between values from conditions in a replicate. Correlation can also be caused in otherwise independent samples by shared technical variability. However, correlation is reduced by noise that affects samples individually. I investigated how to maximize power in experiments with two conditions over a range of correlations. Normalizing data to control increases the rate of false positives, if Student's t test is used. Paired t tests, theoretically the correct test for matched samples, have higher power than Student's t test when correlation is high, but lower power when correlation is low. Testing correlation to select a test for differences in mean can affect the subsequent rate of false positives. Ultimately, components of experimental variability must be considered to choose the most powerful two sample test for differences in mean. This contrasts with experiments with more than two conditions, where random-block ANOVA, a matched samples test, can be used as a default.
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Affiliation(s)
- Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT 06269-3125
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Winford E, Lutshumba J, Martin BJ, Wilcock DM, Jicha GA, Nikolajczyk BS, Stowe AM, Bachstetter AD. Terminally differentiated effector memory T cells associate with cognitive and AD-related biomarkers in an aging-based community cohort. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568812. [PMID: 38077088 PMCID: PMC10705256 DOI: 10.1101/2023.11.27.568812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Background and Purpose The immune response changes during aging and the progression of Alzheimer's disease (AD) and related dementia (ADRD). Terminally differentiated effector memory T cells (called TEMRA) are important during aging and AD due to their cytotoxic phenotype and association with cognitive decline. However, it is not clear if the changes seen in TEMRAs are specific to AD-related cognitive decline specifically or are more generally correlated with cognitive decline. This study aimed to examine whether TEMRAs are associated with cognition and plasma biomarkers of AD, neurodegeneration, and neuroinflammation in a community-based cohort of older adults. Methods Study participants from a University of Kentucky Alzheimer's Disease Research Center (UK-ADRC) community-based cohort of aging and dementia were used to test our hypothesis. There were 84 participants, 44 women and 40 men. Participants underwent physical examination, neurological examination, medical history, cognitive testing, and blood collection to determine plasma biomarker levels (Aβ42/Aβ40 ratio, total tau, Neurofilament Light chain (Nf-L), Glial Fibrillary Acidic Protein (GFAP)) and to isolate peripheral blood mononuclear cells (PBMCs). Flow cytometry was used to analyze PBMCs from study participants for effector and memory T cell populations, including CD4+ and CD8+ central memory T cells (TCM), Naïve T cells, effector memory T cells (TEM), and effector memory CD45RA+ T cells (TEMRA) immune cell markers. Results CD8+ TEMRAs were positively correlated with Nf-L and GFAP. We found no significant difference in CD8+ TEMRAs based on cognitive scores and no associations between CD8+ TEMRAs and AD-related biomarkers. CD4+ TEMRAs were associated with cognitive impairment on the MMSE. Gender was not associated with TEMRAs, but it did show an association with other T cell populations. Conclusion These findings suggest that the accumulation of CD8+ TEMRAs may be a response to neuronal injury (Nf-L) and neuroinflammation (GFAP) during aging or the progression of AD and ADRD. As our findings in a community-based cohort were not clinically-defined AD participants but included all ADRDs, this suggests that TEMRAs may be associated with changes in systemic immune T cell subsets associated with the onset of pathology.
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Affiliation(s)
- Edric Winford
- Department of Neuroscience, University of Kentucky; Lexington, Kentucky, USA
| | - Jenny Lutshumba
- Department of Neuroscience, University of Kentucky; Lexington, Kentucky, USA
| | - Barbara J. Martin
- Sanders-Brown Center on Aging, University of Kentucky; Lexington, Kentucky, USA
| | - Donna M. Wilcock
- Sanders-Brown Center on Aging, University of Kentucky; Lexington, Kentucky, USA
- Department of Physiology, University of Kentucky, Lexington; Lexington, Kentucky, USA
| | - Gregory A. Jicha
- Department of Neurology, University of Kentucky; Lexington, Kentucky, USA
- Sanders-Brown Center on Aging, University of Kentucky; Lexington, Kentucky, USA
| | - Barbara S. Nikolajczyk
- Department of Pharmacology and Nutritional Science, and Barnstable Brown Diabetes and Obesity Center, University of Kentucky; Lexington, Kentucky, USA
| | - Ann M Stowe
- Department of Neuroscience, University of Kentucky; Lexington, Kentucky, USA
- Department of Neurology, University of Kentucky; Lexington, Kentucky, USA
- Sanders-Brown Center on Aging, University of Kentucky; Lexington, Kentucky, USA
| | - Adam D. Bachstetter
- Department of Neuroscience, University of Kentucky; Lexington, Kentucky, USA
- Sanders-Brown Center on Aging, University of Kentucky; Lexington, Kentucky, USA
- Spinal Cord and Brain Injury Research Center, University of Kentucky; Lexington, Kentucky, USA
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Li J, Jing Q, Hu Z, Wang X, Hu Y, Zhang J, Li L. Mycobacterium tuberculosis-specific memory T cells in bronchoalveolar lavage of patients with pulmonary tuberculosis. Cytokine 2023; 171:156374. [PMID: 37782984 DOI: 10.1016/j.cyto.2023.156374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis(MTB) most often infects the lungs and results in pulmonary tuberculosis(TB). MTB-specific memory T cells are able to respond quickly against antigens and help reduce the burden of pulmonary bacteria. The characteristics, function and chemotaxis axis of memory T cells in the lung remain unclear. The current study aimed to clarify the classification, function and recruitment of local antigen-specific memory T cells in the lung and the periphery blood of patients with pulmonary TB. METHODS A total of 85 patients with active pulmonary TB were included in the study. Bronchoalveolar lavage fluid (BALF) and Peripheral blood were collected for further detection. The cell-surface markers and intracellular staining of memory T cell subtypes were measured by flow cytometry. The level of CXCL9, CXCL10 and CXCL11 in Bronchoalveolar lavage fluid cells and peripheral blood mononuclear cells (PBMC) were measured by Real-time PCR. RESULTS The ratio of effective Memory T cells (TEM) were the highest in BALF of patients with pulmonary TB. In patients, CXCR3 and its ligands was increased in memory T cells of BALF compared with PBMC. IFN-γ+TNF-α+ effective Memory T cells and central memory T cells from BALF were increased after antigen stimulation. CXCR3 was higher in IFN-γ+ compared with IFN-γ- in CD4+ TCM and TEM from BALF of patients. Compared with PBMC, the PD-1 levels of terminal effector memory RA+(TEMRA) and TEM cells in CD4+ memory T cells of BALF were significantly increased. In addition, PD-1 was increased in IFN-γ+ compared with IFN-γ- in CD4+TEM from BALF of patients. There was no difference in Treg ratio between PBMC and BALF of TB patients. CONCLUSIONS The CXCL9/CXCL11-CXCR3 axis may participate in the chemotaxis of memory T cells from the peripheral to lung. CD4+TEM and TEMRA in BALF may have exhausted, especially the cytokine producing TEM. Our study clarified the characteristics of antigen-specific memory T cells in local lung and may have impact on strategies of therapy and vaccine.
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Affiliation(s)
- Jun Li
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Qiusheng Jing
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Zhimin Hu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Xuan Wang
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Yan Hu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Jing Zhang
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Li Li
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China.
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9
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Limoges MA, Lortie A, Demontier É, Quenum AJI, Lessard F, Drouin Z, Carrier N, Nguimbus LM, Beaulieu MC, Boire G, Piché A, Allard-Chamard H, Ramanathan S, Roux S. SARS-CoV-2 mRNA vaccine-induced immune responses in rheumatoid arthritis. J Leukoc Biol 2023; 114:358-367. [PMID: 37478373 PMCID: PMC10533224 DOI: 10.1093/jleuko/qiad086] [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: 12/20/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
Our objective was to characterize T and B cell responses to vaccination with SARS-CoV-2 antigens in immunocompromised rheumatoid arthritis (RA) patients. In 22 RA patients, clinical and biological variables were analyzed before and 4 weeks after each of 3 messenger RNA (mRNA) vaccine doses and compared with unmatched healthy individuals. Sequentially sampled peripheral blood mononuclear cells and sera were collected to determine immune profiles and to analyze the T cell response to a spike peptide pool and B cell specificity to the receptor-binding domain (RBD). Anti-spike antibodies were detectable in 6 of 22 RA patients after 1 dose of vaccine with increasing titers after each booster dose, although the overall response was lower compared with that in healthy control individuals. Responding patients after the first dose were more likely to have RA antibodies and a higher baseline proportion of circulating follicular B cells. In RA patients, the mRNA vaccine elicited a robust CD4+ T response to a spike peptide pool following the first and second doses. Consistent with the serologies, RBD-specific B cells exhibited a modest increase after the first dose and the second dose resulted in marked increases only in a fraction of the RA patients to both ancestral and omicron RBD. Our results highlight the importance of multidose COVID-19 vaccination in RA patients to develop a protective humoral response. However, these patients rapidly develop specific T CD4+ responses, despite delayed B cell responses.
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Affiliation(s)
- Marc-André Limoges
- Department of Immunology and Cell Biology, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Audrey Lortie
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Élodie Demontier
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Akouavi Julite Irmine Quenum
- Department of Immunology and Cell Biology, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Félix Lessard
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Zacharie Drouin
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Nathalie Carrier
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Leopold Mbous Nguimbus
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Marie-Claude Beaulieu
- Department of Family and Emergency Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Gilles Boire
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Alain Piché
- Division of Infectious Diseases, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Hugues Allard-Chamard
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
| | - Sophie Roux
- Division of Rheumatology, Department of Medicine, Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, 3001, 12th avenue N, Sherbrooke, PQ, Canada, J1H5N4
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10
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Prospective Evaluation of CD45RA+/CCR7- Effector Memory T (T EMRA) Cell Subsets in Patients with Primary and Secondary Brain Tumors during Radiotherapy of the Brain within the Scope of the Prospective Glio-CMV-01 Clinical Trial. Cells 2023; 12:cells12040516. [PMID: 36831183 PMCID: PMC9954596 DOI: 10.3390/cells12040516] [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: 11/29/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Radiotherapy (RT) of the brain is a common treatment for patients with high-grade gliomas and brain metastases. It has previously been shown that reactivation of cytomegalovirus (CMV) frequently occurs during RT of the brain. This causes neurological decline, demands antiviral treatment, and is associated with a worse prognosis. CMV-specific T cells are characterized by a differentiated effector memory phenotype and CD45RA+ CCR7- effector memory T (TEMRA) cells were shown to be enriched in CMV seropositive individuals. In this study, we investigated the distribution of TEMRA cells and their subsets in the peripheral blood of healthy donors and, for the first time, prospectively within the scope of the prospective Glio-CMV-01 clinical trial of patients with high-grade glioma and brain metastases during radiation therapy as a potential predictive marker. First, we developed a multicolor flow cytometry-based assay to monitor the frequency and distribution of TEMRA cells in a longitudinal manner. The CMV serostatus and age were considered as influencing factors. We revealed that patients who had a reactivation of CMV have significantly higher amounts of CD8+ TEMRA cells. Further, the distribution of the subsets of TEMRA cells based on the expression of CD27, CD28, and CD57 is highly dependent on the CMV serostatus. We conclude that the percentage of CD8+ TEMRA cells out of all CD8+ T cells has the potential to serve as a biomarker for predicting the risk of CMV reactivation during RT of the brain. Furthermore, this study highlights the importance of taking the CMV serostatus into account when analyzing TEMRA cells and their subsets.
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11
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Meskas J, Yokosawa D, Wang S, Segat GC, Brinkman RR. flowCut: An R package for automated removal of outlier events and flagging of files based on time versus fluorescence analysis. Cytometry A 2023; 103:71-81. [PMID: 35796000 PMCID: PMC9823164 DOI: 10.1002/cyto.a.24670] [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: 08/04/2021] [Revised: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 01/30/2023]
Abstract
Technical artifacts such as clogging that occur during the data acquisition process of flow cytometry data can cause spurious events and fluorescence intensity shifting that impact the quality of the data and its analysis results. These events should be identified and potentially removed before being passed to the next stage of analysis. flowCut, an R package, automatically detects anomaly events in flow cytometry experiments and flags files for potential review. Its results are on par with manual analysis and it outperforms existing automated approaches.
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Affiliation(s)
- Justin Meskas
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Daniel Yokosawa
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Sherrie Wang
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
- Cytapex Bioinformatics Inc, Vancouver, British Columbia, Canada
| | - Gabriela C Segat
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Ryan Remy Brinkman
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
- Faculty of Science, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Gorrese M, Bertolini A, Fresolone L, Campana A, Pezzullo L, Guariglia R, Mettivier L, Manzo P, Cuffa B, D'Alto F, Serio B, Selleri C, Giudice V. Inter-intra instrument comparison and standardization of a 10-color immunophenotyping for B and T cell non-Hodgkin lymphoma diagnosis and monitoring. J Immunol Methods 2022; 511:113374. [PMID: 36243108 DOI: 10.1016/j.jim.2022.113374] [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: 08/25/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Harmonization of flow cytometry protocols from instrument settings to antibody panel and reagents is highly encouraged for inter-laboratory data comparison in both research and clinical settings, especially for minimal residual disease monitoring evaluation in hematological diseases across centers. Here, we described inter-intra instrument comparison of two standardized 10-color staining dried tubes for B- and T-cell lymphoproliferative disorder diagnosis and monitoring on two different flow cytometers, a Beckman Coulter NaviosEx and a Beckman Coulter DxFlex. A total of 47 consecutive patients were enrolled, and 39 of them were evaluable for further studies. We show highly comparable results between the two cytometers for cell frequency and fluorescence intensity signals for both standardized 10-color staining dried tubes. For this latter, fluorescence of each antibody and subject was normalized on the mean value obtained from the entire study cohort thus reducing the effects of biological variability and allowing comparison between instruments with different detector sensitivity. In summary, dried tubes were confirmed as an optimal standardized diagnostic tool, especially when associated with EuroFlow standardized procedures by minimizing technical and biological variability. However, data analysis is still operator-dependent, and more efforts are needed to develop automated or semi-automated software for flow cytometry data analysis for diagnostic purposes.
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Affiliation(s)
- Marisa Gorrese
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Angela Bertolini
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Lucia Fresolone
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Annapaola Campana
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Luca Pezzullo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Roberto Guariglia
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Laura Mettivier
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Paola Manzo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Bianca Cuffa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Francesca D'Alto
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy; Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy.
| | - Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy; Department of Medicine, Surgery, and Dentistry, University of Salerno, Baronissi, Italy
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13
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Lindestam Arlehamn CS, Benson B, Kuan R, Dill-McFarland KA, Peterson GJ, Paul S, Nguyen FK, Gilman RH, Saito M, Taplitz R, Arentz M, Goss CH, Aitken ML, Horne DJ, Shah JA, Sette A, Hawn TR. T-cell deficiency and hyperinflammatory monocyte responses associate with Mycobacterium avium complex lung disease. Front Immunol 2022; 13:1016038. [PMID: 36263044 PMCID: PMC9574438 DOI: 10.3389/fimmu.2022.1016038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Immunological mechanisms of susceptibility to nontuberculous mycobacterial (NTM) disease are poorly understood. To understand NTM pathogenesis, we evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex (MAC) in asymptomatic individuals with a previous history of MAC lung disease (MACDZ). We hypothesized that Mav-specific immune responses are associated with susceptibility to MAC lung disease. We measured MAC-, NTM-, or MAC/Mtb-specific T-cell responses by cytokine production, expression of surface markers, and analysis of global gene expression in 27 MACDZ individuals and 32 healthy controls. We also analyzed global gene expression in Mycobacterium avium-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls. We were unable to detect increased T-cell responses against MAC-specific reagents in MACDZ compared to controls, while the responses to non-mycobacteria derived antigens were preserved. MACDZ individuals had a lower frequency of Th1 and Th1* T-cell populations. In addition, MACDZ subjects had lower transcriptional responses in PBMCs stimulated with a mycobacterial peptide pool (MTB300). By contrast, global gene expression analysis demonstrated upregulation of proinflammatory pathways in uninfected and M. avium-infected monocytes, i.e. a hyperinflammatory in vitro response, derived from MACDZ subjects compared to controls. Together, these data suggest a novel immunologic defect which underlies MAC pathogenesis and includes concurrent innate and adaptive dysregulation which persists years after completion of treatment.
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Affiliation(s)
- Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- *Correspondence: Cecilia S. Lindestam Arlehamn,
| | - Basilin Benson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Rebecca Kuan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Glenna J. Peterson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Sinu Paul
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Felicia K. Nguyen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Robert H. Gilman
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States
- Department of Microbiology, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Matthew Arentz
- Department of Global Health, University of Washington, Seattle, WA, United States
- FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Christopher H. Goss
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Moira L. Aitken
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - David J. Horne
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Javeed A. Shah
- Department of Medicine, University of Washington, Seattle, WA, United States
- VA Puget Sound Healthcare System, Seattle, WA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, United States
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14
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Chen Y, Ye Y, Krauß PL, Löwe P, Pfeiffenberger M, Damerau A, Ehlers L, Buttgereit T, Hoff P, Buttgereit F, Gaber T. Age-related increase of mitochondrial content in human memory CD4+ T cells contributes to ROS-mediated increased expression of proinflammatory cytokines. Front Immunol 2022; 13:911050. [PMID: 35935995 PMCID: PMC9353942 DOI: 10.3389/fimmu.2022.911050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Cellular metabolism modulates effector functions in human CD4+ T (Th) cells by providing energy and building blocks. Conversely, cellular metabolic responses are modulated by various influences, e.g., age. Thus, we hypothesized that metabolic reprogramming in human Th cells during aging modulates effector functions and contributes to “inflammaging”, an aging-related, chronic, sterile, low-grade inflammatory state characterized by specific proinflammatory cytokines. Analyzing the metabolic response of human naive and memory Th cells from young and aged individuals, we observed that memory Th cells exhibit higher glycolytic and mitochondrial fluxes than naive Th cells. In contrast, the metabolism of the latter was not affected by donor age. Memory Th cells from aged donors showed a higher respiratory capacity, mitochondrial content, and intracellular ROS production than those from young donors without altering glucose uptake and cellular ATP levels, which finally resulted in higher secreted amounts of proinflammatory cytokines, e.g., IFN-γ, IP-10 from memory Th cells taken from aged donors after TCR-stimulation which were sensitive to ROS inhibition. These findings suggest that metabolic reprogramming in human memory Th cells during aging results in an increased expression of proinflammatory cytokines through enhanced ROS production, which may contribute to the pathogenesis of inflammaging.
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Affiliation(s)
- Yuling Chen
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Yuanchun Ye
- Department of Gastroenterology, Fujian Medical University Affiliated First Quanzhou Hospital, Quanzhou, China
- Department of Hematology, Oncology and Tumor Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pierre-Louis Krauß
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Pelle Löwe
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Moritz Pfeiffenberger
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Alexandra Damerau
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Lisa Ehlers
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Thomas Buttgereit
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Dermatology, Venerology, and Allergology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Hoff
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Rheumatologie, Endokrinologikum Berlin, Berlin, Germany
| | - Frank Buttgereit
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
| | - Timo Gaber
- Department of Rheumatology and Clinical Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Centre (DRFZ) Berlin, A Leibniz Institute, Berlin, Germany
- *Correspondence: Timo Gaber,
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15
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Browning AP, Ansari N, Drovandi C, Johnston APR, Simpson MJ, Jenner AL. Identifying cell-to-cell variability in internalization using flow cytometry. J R Soc Interface 2022; 19:20220019. [PMID: 35611619 PMCID: PMC9131125 DOI: 10.1098/rsif.2022.0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Biological heterogeneity is a primary contributor to the variation observed in experiments that probe dynamical processes, such as the internalization of material by cells. Given that internalization is a critical process by which many therapeutics and viruses reach their intracellular site of action, quantifying cell-to-cell variability in internalization is of high biological interest. Yet, it is common for studies of internalization to neglect cell-to-cell variability. We develop a simple mathematical model of internalization that captures the dynamical behaviour, cell-to-cell variation, and extrinsic noise introduced by flow cytometry. We calibrate our model through a novel distribution-matching approximate Bayesian computation algorithm to flow cytometry data of internalization of anti-transferrin receptor antibody in a human B-cell lymphoblastoid cell line. This approach provides information relating to the region of the parameter space, and consequentially the nature of cell-to-cell variability, that produces model realizations consistent with the experimental data. Given that our approach is agnostic to sample size and signal-to-noise ratio, our modelling framework is broadly applicable to identify biological variability in single-cell data from internalization assays and similar experiments that probe cellular dynamical processes.
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Affiliation(s)
- Alexander P Browning
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia.,QUT Centre for Data Science, Queensland University of Technology, Brisbane, Australia
| | - Niloufar Ansari
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher Drovandi
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia.,QUT Centre for Data Science, Queensland University of Technology, Brisbane, Australia
| | - Angus P R Johnston
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Matthew J Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.,QUT Centre for Data Science, Queensland University of Technology, Brisbane, Australia
| | - Adrianne L Jenner
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia.,QUT Centre for Data Science, Queensland University of Technology, Brisbane, Australia
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16
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Jones RP, Ponomarenko A. System Complexity in Influenza Infection and Vaccination: Effects upon Excess Winter Mortality. Infect Dis Rep 2022; 14:287-309. [PMID: 35645214 PMCID: PMC9149983 DOI: 10.3390/idr14030035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Unexpected outcomes are usually associated with interventions in complex systems. Excess winter mortality (EWM) is a measure of the net effect of all competing forces operating each winter, including influenza(s) and non-influenza pathogens. In this study over 2400 data points from 97 countries are used to look at the net effect of influenza vaccination rates in the elderly aged 65+ against excess winter mortality (EWM) each year from the winter of 1980/81 through to 2019/20. The observed international net effect of influenza vaccination ranges from a 7.8% reduction in EWM estimated at 100% elderly vaccination for the winter of 1989/90 down to a 9.3% increase in EWM for the winter of 2018/19. The average was only a 0.3% reduction in EWM for a 100% vaccinated elderly population. Such outcomes do not contradict the known protective effect of influenza vaccination against influenza mortality per se—they merely indicate that multiple complex interactions lie behind the observed net effect against all-causes (including all pathogen causes) of winter mortality. This range from net benefit to net disbenefit is proposed to arise from system complexity which includes environmental conditions (weather, solar cycles), the antigenic distance between constantly emerging circulating influenza clades and the influenza vaccine makeup, vaccination timing, pathogen interference, and human immune diversity (including individual history of host-virus, host-antigen interactions and immunosenescence) all interacting to give the observed outcomes each year. We propose that a narrow focus on influenza vaccine effectiveness misses the far wider complexity of winter mortality. Influenza vaccines may need to be formulated in different ways, and perhaps administered over a shorter timeframe to avoid the unanticipated adverse net outcomes seen in around 40% of years.
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Affiliation(s)
- Rodney P. Jones
- Healthcare Analysis & Forecasting, Wantage OX12 0NE, UK
- Correspondence:
| | - Andriy Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine;
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17
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Eskandari G, Subedi S, Christensen P, Olsen RJ, Zu Y, Long SW. Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population. J Pathol Inform 2022; 12:49. [PMID: 35070478 PMCID: PMC8721865 DOI: 10.4103/jopi.jopi_12_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/27/2021] [Indexed: 11/04/2022] Open
Abstract
Introduction Manual gating of flow cytometry (FCM) data for marrow cell analysis is a standard approach in current practice, although it is time- and labor-consuming. Recent advances in cytometry technology have led to significant efforts in developing partially or fully automated analysis methods. Although multiple supervised and unsupervised FCM data analysis algorithms have been developed, they have not been widely adopted by the clinical and research laboratories. In this study, we evaluated flowDensity, an open source freely available algorithm, as an automated analysis tool for classification of lymphocyte subsets in the bone marrow biopsy specimens. Materials and Methods FlowDensity-based gating was applied to 102 normal bone marrow samples and compared with the manual analysis. Independent expression of each cell marker was assessed for comprehensive expression analysis and visualization. Results Our findings showed a correlation between the manual and flowDensity-based gating in the lymphocyte subsets. However, flowDensity-based gating in the populations with a small number of cells in each cluster showed a low degree of correlation. Comprehensive expression analysis successfully identified and visualized the lymphocyte subsets. Discussion Our study found that although flowDensity might be a promising method for FCM data analysis, more optimization is required before implementing this algorithm into day-to-day workflow.
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Affiliation(s)
- Ghazaleh Eskandari
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Paul Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Scott W Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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18
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Yang JHM, Ward-Hartstonge KA, Perry DJ, Blanchfield JL, Posgai AL, Wiedeman AE, Diggins K, Rahman A, Tree TIM, Brusko TM, Levings MK, James EA, Kent SC, Speake C, Homann D, Long SA. Guidelines for standardizing T cell cytometry assays to link biomarkers, mechanisms, and disease outcomes in type 1 diabetes. Eur J Immunol 2022; 52:372-388. [PMID: 35025103 DOI: 10.1002/eji.202049067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 11/10/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Cytometric immunophenotyping is a powerful tool to discover and implement T cell biomarkers of type 1 diabetes (T1D) progression and response to clinical therapy. Although many discovery-based T cell biomarkers have been described, to date, no such markers have been widely adopted in standard practice. The heterogeneous nature of T1D and lack of standardized assays and experimental design across studies is a major barrier to the broader adoption of T cell immunophenotyping assays. There is an unmet need to harmonize the design of immunophenotyping assays, including those that measure antigen-agnostic cell populations, such that data collected from different clinical trial sites and T1D cohorts are comparable, yet account for cohort-specific features and different drug mechanisms of action. In these Guidelines, we aim to provide expert advice on how to unify aspects of study design and practice. We provide recommendations for defining cohorts, method implementation, as well as tools for data analysis and reporting by highlighting and building on selected successes. Harmonization of cytometry-based T cell assays will allow researchers to better integrate findings across trials, ultimately enabling the identification and validation of biomarkers of disease progression and treatment response in T1D. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jennie H M Yang
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, London, UK.,National Institute of Health Research Biomedical Research Centre at Guy's and St. Thomas' National Health Service Foundation Trust and King's College London, London, UK
| | - Kirsten A Ward-Hartstonge
- Department of Surgery, The University of British Columbia, Vancouver, CA.,BC Children's Hospital Research Institute, British Columbia, Vancouver, CA
| | - Daniel J Perry
- Department of Pathology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - J Lori Blanchfield
- Center for Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Amanda L Posgai
- Department of Pathology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Alice E Wiedeman
- Center for Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Kirsten Diggins
- Center for Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy I M Tree
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, London, UK.,National Institute of Health Research Biomedical Research Centre at Guy's and St. Thomas' National Health Service Foundation Trust and King's College London, London, UK
| | - Todd M Brusko
- Department of Pathology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Megan K Levings
- Department of Surgery, The University of British Columbia, Vancouver, CA.,BC Children's Hospital Research Institute, British Columbia, Vancouver, CA.,School of Biomedical Engineering, The University of British Columbia, CA
| | - Eddie A James
- Center for Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Sally C Kent
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Dirk Homann
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Diabetes, Obesity & Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Alice Long
- Center for Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | -
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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19
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DePasquale EAK, Ssozi D, Ainciburu M, Good J, Noel J, Villanueva MA, Couturier CP, Shalek AK, Aranki SF, Mallidi HR, Griffin GK, Lane AA, van Galen P. Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm. Front Immunol 2022; 13:809414. [PMID: 35359938 PMCID: PMC8960171 DOI: 10.3389/fimmu.2022.809414] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
The immune system represents a major barrier to cancer progression, driving the evolution of immunoregulatory interactions between malignant cells and T-cells in the tumor environment. Blastic plasmacytoid dendritic cell neoplasm (BPDCN), a rare acute leukemia with plasmacytoid dendritic cell (pDC) differentiation, provides a unique opportunity to study these interactions. pDCs are key producers of interferon alpha (IFNA) that play an important role in T-cell activation at the interface between the innate and adaptive immune system. To assess how uncontrolled proliferation of malignant BPDCN cells affects the tumor environment, we catalog immune cell heterogeneity in the bone marrow (BM) of five healthy controls and five BPDCN patients by analyzing 52,803 single-cell transcriptomes, including 18,779 T-cells. We test computational techniques for robust cell type classification and find that T-cells in BPDCN patients consistently upregulate interferon alpha (IFNA) response and downregulate tumor necrosis factor alpha (TNFA) pathways. Integrating transcriptional data with T-cell receptor sequencing via shared barcodes reveals significant T-cell exhaustion in BPDCN that is positively correlated with T-cell clonotype expansion. By highlighting new mechanisms of T-cell exhaustion and immune evasion in BPDCN, our results demonstrate the value of single-cell multiomics to understand immune cell interactions in the tumor environment.
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Affiliation(s)
- Erica A. K. DePasquale
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
| | - Daniel Ssozi
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Marina Ainciburu
- Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IDISNA), Pamplona, Spain
| | - Jonathan Good
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Human Biology, Sattler College, Boston, MA, United States
| | - Jenny Noel
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Martin A. Villanueva
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States
| | - Charles P. Couturier
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sary F. Aranki
- Division of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital, Boston, MA, United States
| | - Hari R. Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital, Boston, MA, United States
| | - Gabriel K. Griffin
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Andrew A. Lane
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Peter van Galen
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States
- *Correspondence: Peter van Galen,
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20
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Hillman H, Khan N, Singhania A, Dubelko P, Soldevila F, Tippalagama R, DeSilva AD, Gunasena B, Perera J, Scriba TJ, Ontong C, Fisher M, Luabeya A, Taplitz R, Seumois G, Vijayanand P, Hedrick CC, Peters B, Burel JG. Single-cell profiling reveals distinct subsets of CD14+ monocytes drive blood immune signatures of active tuberculosis. Front Immunol 2022; 13:1087010. [PMID: 36713384 PMCID: PMC9874319 DOI: 10.3389/fimmu.2022.1087010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Previous studies suggest that monocytes are an important contributor to tuberculosis (TB)-specific immune signatures in blood. Methods Here, we carried out comprehensive single-cell profiling of monocytes in paired blood samples of active TB (ATB) patients at diagnosis and mid-treatment, and healthy controls. Results At diagnosis, ATB patients displayed increased monocyte-to-lymphocyte ratio, increased frequency of CD14+CD16- and intermediate CD14+CD16+ monocytes, and upregulation of interferon signaling genes that significantly overlapped with previously reported blood TB signatures in both CD14+ subsets. In this cohort, we identified additional transcriptomic and functional changes in intermediate CD14+CD16+ monocytes, such as the upregulation of inflammatory and MHC-II genes, and increased capacity to activate T cells, reflecting overall increased activation in this population. Single-cell transcriptomics revealed that distinct subsets of intermediate CD14+CD16+ monocytes were responsible for each gene signature, indicating significant functional heterogeneity within this population. Finally, we observed that changes in CD14+ monocytes were transient, as they were no longer observed in the same ATB patients mid-treatment, suggesting they are associated with disease resolution. Discussion Together, our study demonstrates for the first time that both intermediate and classical monocytes individually contribute to blood immune signatures of ATB and identifies novel subsets and associated gene signatures that may hold disease relevance.
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Affiliation(s)
- Hannah Hillman
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Nabeela Khan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Akul Singhania
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Paige Dubelko
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Ferran Soldevila
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Rashmi Tippalagama
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Aruna D DeSilva
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Paraclinical Sciences, Faculty of Medicine, General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Bandu Gunasena
- Medical Unit, National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | - Judy Perera
- Department of Paraclinical Sciences, Faculty of Medicine, General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Cynthia Ontong
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Angelique Luabeya
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Gregory Seumois
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Pandurangan Vijayanand
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Catherine C Hedrick
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Julie G Burel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
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21
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Singhania A, Dubelko P, Kuan R, Chronister WD, Muskat K, Das J, Phillips EJ, Mallal SA, Seumois G, Vijayanand P, Sette A, Lerm M, Peters B, Lindestam Arlehamn C. CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature. EBioMedicine 2021; 74:103746. [PMID: 34902786 PMCID: PMC8671872 DOI: 10.1016/j.ebiom.2021.103746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The century-old Mycobacterium bovis Bacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. METHODS We investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or a Mycobacterium tuberculosis (Mtb)-derived peptide pool. FINDINGS Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* (CXCR3+CCR6+) and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects. INTERPRETATION The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.
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Affiliation(s)
- Akul Singhania
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Paige Dubelko
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Rebecca Kuan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - William D Chronister
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kaylin Muskat
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Jyotirmoy Das
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Grégory Seumois
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Lerm
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Cecilia Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
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22
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Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman AH, Jehi L, Mayadas TN. Protective heterologous T cell immunity in COVID-19 induced by the trivalent MMR and Tdap vaccine antigens. MED 2021; 2:1050-1071.e7. [PMID: 34414383 PMCID: PMC8363466 DOI: 10.1016/j.medj.2021.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND T cells control viral infection, promote vaccine durability, and in coronavirus disease 2019 (COVID-19) associate with mild disease. We investigated whether prior measles-mumps-rubella (MMR) or tetanus-diphtheria-pertussis (Tdap) vaccination elicits cross-reactive T cells that mitigate COVID-19. METHODS Antigen-presenting cells (APC) loaded ex vivo with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), MMR, or Tdap antigens and autologous T cells from COVID-19-convalescent participants, uninfected individuals, and COVID-19 mRNA-vaccinated donors were co-cultured. T cell activation and phenotype were detected by interferon-γ (IFN-γ) enzyme-linked immunospot (ELISpot) assays and flow cytometry. ELISAs (enzyme-linked immunosorbant assays) and validation studies identified the APC-derived cytokine(s) driving T cell activation. TCR clonotyping and single-cell RNA sequencing (scRNA-seq) identified cross-reactive T cells and their transcriptional profile. A propensity-weighted analysis of COVID-19 patients estimated the effects of MMR and Tdap vaccination on COVID-19 outcomes. FINDINGS High correlation was observed between T cell responses to SARS-CoV-2 (spike-S1 and nucleocapsid) and MMR and Tdap proteins in COVID-19-convalescent and -vaccinated individuals. The overlapping T cell population contained an effector memory T cell subset (effector memory re-expressing CD45RA on T cells [TEMRA]) implicated in protective, anti-viral immunity, and their detection required APC-derived IL-15, known to sensitize T cells to activation. Cross-reactive TCR repertoires detected in antigen-experienced T cells recognizing SARS-CoV-2, MMR, and Tdap epitopes had TEMRA features. Indices of disease severity were reduced in MMR- or Tdap-vaccinated individuals by 32%-38% and 20%-23%, respectively, among COVID-19 patients. CONCLUSIONS Tdap and MMR memory T cells reactivated by SARS-CoV-2 may provide protection against severe COVID-19. FUNDING This study was supported by a National Institutes of Health (R01HL065095, R01AI152522, R01NS097719) donation from Barbara and Amos Hostetter and the Chleck Foundation.
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Affiliation(s)
- Vijayashree Mysore
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Xavier Cullere
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Matthew L Settles
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xinge Ji
- Quantitative Health Science Department, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael W Kattan
- Quantitative Health Science Department, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michaël Desjardins
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | | | - Tal Gilboa
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Lindsey R Baden
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Andrew H Lichtman
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Lara Jehi
- Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tanya N Mayadas
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
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23
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Tippalagama R, Singhania A, Dubelko P, Lindestam Arlehamn CS, Crinklaw A, Pomaznoy M, Seumois G, deSilva AD, Premawansa S, Vidanagama D, Gunasena B, Goonawardhana NDS, Ariyaratne D, Scriba TJ, Gilman RH, Saito M, Taplitz R, Vijayanand P, Sette A, Peters B, Burel JG. HLA-DR Marks Recently Divided Antigen-Specific Effector CD4 T Cells in Active Tuberculosis Patients. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:523-533. [PMID: 34193602 PMCID: PMC8516689 DOI: 10.4049/jimmunol.2100011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023]
Abstract
Upon Ag encounter, T cells can rapidly divide and form an effector population, which plays an important role in fighting acute infections. In humans, little is known about the molecular markers that distinguish such effector cells from other T cell populations. To address this, we investigated the molecular profile of T cells present in individuals with active tuberculosis (ATB), where we expect Ag encounter and expansion of effector cells to occur at higher frequency in contrast to Mycobacterium tuberculosis-sensitized healthy IGRA+ individuals. We found that the frequency of HLA-DR+ cells was increased in circulating CD4 T cells of ATB patients, and was dominantly expressed in M. tuberculosis Ag-specific CD4 T cells. We tested and confirmed that HLA-DR is a marker of recently divided CD4 T cells upon M. tuberculosis Ag exposure using an in vitro model examining the response of resting memory T cells from healthy IGRA+ to Ags. Thus, HLA-DR marks a CD4 T cell population that can be directly detected ex vivo in human peripheral blood, whose frequency is increased during ATB disease and contains recently divided Ag-specific effector T cells. These findings will facilitate the monitoring and study of disease-specific effector T cell responses in the context of ATB and other infections.
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Affiliation(s)
- Rashmi Tippalagama
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Akul Singhania
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Paige Dubelko
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | | | - Austin Crinklaw
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Mikhail Pomaznoy
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Gregory Seumois
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Aruna D deSilva
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | | | | | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | | | - Dinuka Ariyaratne
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Baltimore, MD
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA; and
| | - Pandurangan Vijayanand
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Alessandro Sette
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Bjoern Peters
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA;
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Julie G Burel
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA;
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24
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Mysore V, Cullere X, Settles ML, Ji X, Kattan MW, Desjardins M, Durbin-Johnson B, Gilboa T, Baden LR, Walt DR, Lichtman A, Jehi L, Mayadas TN. Protective heterologous T cell immunity in COVID-19 induced by MMR and Tdap vaccine antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.03.441323. [PMID: 33972940 PMCID: PMC8109200 DOI: 10.1101/2021.05.03.441323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells are critical for control of viral infection and effective vaccination. We investigated whether prior Measles-Mumps-Rubella (MMR) or Tetanus-Diphtheria-pertussis (Tdap) vaccination elicit cross-reactive T cells that mitigate COVID-19. Using co-cultures of antigen presenting cells (APC) loaded with antigens and autologous T cells, we found a high correlation between responses to SARS-CoV-2 (Spike-S1 and Nucleocapsid) and MMR and Tdap vaccine proteins in both SARS-CoV-2 infected individuals and individuals immunized with mRNA-based SARS-CoV-2 vaccines. The overlapping T cell population contained effector memory T cells (TEMRA) previously implicated in anti-viral immunity and their activation required APC-derived IL-15. TCR- and scRNA-sequencing detected cross-reactive clones with TEMRA features among the cells recognizing SARS-CoV-2, MMR and Tdap epitopes. A propensity-weighted analysis of 73,582 COVID-19 patients revealed that severe disease outcomes (hospitalization and transfer to intensive care unit or death) were reduced in MMR or Tdap vaccinated individuals by 38-32% and 23-20% respectively. In summary, SARS-CoV-2 re-activates memory T cells generated by Tdap and MMR vaccines, which may reduce disease severity.
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25
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Thiel BA, Worodria W, Nalukwago S, Nsereko M, Sanyu I, Rejani L, Zawedde J, Canaday DH, Stein CM, Chervenak KA, Malone LL, Kiyemba R, Silver RF, Johnson JL, Mayanja-Kizza H, Boom WH. Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resist versus those who develop latent Mycobacterium tuberculosis infection. PLoS One 2021; 16:e0249477. [PMID: 33836031 PMCID: PMC8034721 DOI: 10.1371/journal.pone.0249477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022] Open
Abstract
Background The search for immune correlates of protection against Mycobacterium tuberculosis (MTB) infection in humans is limited by the focus on peripheral blood measures. Bronchoalveolar lavage (BAL) can safely be done and provides insight into cellular function in the lung where infection is first established. In this study, blood and lung samples were assayed to determine if heavily MTB exposed persons who resist development of latent MTB infection (RSTR) vs those who develop latent MTB infection (LTBI), differ in the make-up of resident BAL innate and adaptive immune cells. Methods Bronchoscopy was performed on 21 healthy long-term Ugandan RSTR and 25 LTBI participants. Immune cell distributions in BAL and peripheral blood were compared by differential cell counting and flow cytometry. Results The bronchoscopy procedure was well tolerated with few adverse reactions. Differential macrophage and lymphocyte frequencies in BAL differed between RSTR and LTBI. When corrected for age, this difference lost statistical significance. BAL CD4+ and CD8+ T cells were almost entirely composed of effector memory T cells in contrast to PBMC, and did not differ between RSTR and LTBI. BAL NKT, γδ T cells and NK cells also did not differ between RTSR and LTBI participants. There was a marginally significant increase (p = 0.034) in CD8 T effector memory cells re-expressing CD45RA (TEMRA) in PBMC of LTBI vs RSTR participants. Conclusion This observational case-control study comparing unstimulated BAL from RSTR vs LTBI, did not find evidence of large differences in the distribution of baseline BAL immune cells. PBMC TEMRA cell percentage was higher in LTBI relative to RSTR suggesting a role in the maintenance of latent MTB infection. Functional immune studies are required to determine if and how RSTR and LTBI BAL immune cells differ in response to MTB.
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Affiliation(s)
- Bonnie A. Thiel
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
- * E-mail:
| | - William Worodria
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Sophie Nalukwago
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Mary Nsereko
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Ingvar Sanyu
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Lalitha Rejani
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Josephine Zawedde
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - David H. Canaday
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - Catherine M. Stein
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Keith A. Chervenak
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - LaShaunda L. Malone
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Ronald Kiyemba
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Richard F. Silver
- Division of Pulmonary, Critical Care and Sleep Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center and Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John L. Johnson
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
| | - W. Henry Boom
- Tuberculosis Research Unit and Division of Infectious Diseases, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Makerere University College of Health Sciences and Mulago Hospital, Kampala, Uganda
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26
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da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, Khalil N, Qian Y, Mandava A, Scheuermann RH, Cortese M, Pulendran B, Petro CD, Gilkes AP, Purcell LA, Sette A, Peters B. A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy. JCI Insight 2021; 6:141023. [PMID: 33690224 PMCID: PMC8119213 DOI: 10.1172/jci.insight.141023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 03/03/2021] [Indexed: 01/26/2023] Open
Abstract
The increased incidence of whooping cough worldwide suggests that current vaccination against Bordetella pertussis infection has limitations in quality and duration of protection. The resurgence of infection has been linked to the introduction of acellular vaccines (aP), which have an improved safety profile compared with the previously used whole-cell (wP) vaccines. To determine immunological differences between aP and wP priming in infancy, we performed a systems approach of the immune response to booster vaccination. Transcriptomic, proteomic, cytometric, and serologic profiling revealed multiple shared immune responses with different kinetics across cohorts, including an increase of blood monocyte frequencies and strong antigen-specific IgG responses. Additionally, we found a prominent subset of aP-primed individuals (30%) with a strong differential signature, including higher levels of expression for CCL3, NFKBIA, and ICAM1. Contrary to the wP individuals, this subset displayed increased PT-specific IgE responses after boost and higher antigen-specific IgG4 and IgG3 antibodies against FHA and FIM2/3 at baseline and after boost. Overall, the results show that, while broad immune response patterns to Tdap boost overlap between aP- and wP-primed individuals, a subset of aP-primed individuals present a divergent response. These findings provide candidate targets to study the causes and correlates of waning immunity after aP vaccination.
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Affiliation(s)
- Ricardo da Silva Antunes
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Ferran Soldevila
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Mikhail Pomaznoy
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Mariana Babor
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Jason Bennett
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Natalie Khalil
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Yu Qian
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, California, USA.,University of California San Diego School of Medicine, La Jolla, California, USA
| | - Mario Cortese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Bali Pulendran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - Lisa A Purcell
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.,University of California San Diego School of Medicine, La Jolla, California, USA
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27
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Soday L, Potts M, Hunter LM, Ravenhill BJ, Houghton JW, Williamson JC, Antrobus R, Wills MR, Matheson NJ, Weekes MP. Comparative Cell Surface Proteomic Analysis of the Primary Human T Cell and Monocyte Responses to Type I Interferon. Front Immunol 2021; 12:600056. [PMID: 33628210 PMCID: PMC7897682 DOI: 10.3389/fimmu.2021.600056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/13/2021] [Indexed: 12/28/2022] Open
Abstract
The cellular response to interferon (IFN) is essential for antiviral immunity, IFN-based therapy and IFN-related disease. The plasma membrane (PM) provides a critical interface between the cell and its environment, and is the initial portal of entry for viruses. Nonetheless, the effect of IFN on PM proteins is surprisingly poorly understood, and has not been systematically investigated in primary immune cells. Here, we use multiplexed proteomics to quantify IFNα2a-stimulated PM protein changes in primary human CD14+ monocytes and CD4+ T cells from five donors, quantifying 606 and 482 PM proteins respectively. Comparison of cell surface proteomes revealed a remarkable invariance between donors in the overall composition of the cell surface from each cell type, but a marked donor-to-donor variability in the effects of IFNα2a. Furthermore, whereas only 2.7% of quantified proteins were consistently upregulated by IFNα2a at the surface of CD4+ T cells, 6.8% of proteins were consistently upregulated in primary monocytes, suggesting that the magnitude of the IFNα2a response varies according to cell type. Among these differentially regulated proteins, we found the viral target Endothelin-converting enzyme 1 (ECE1) to be an IFNα2a-stimulated protein exclusively upregulated at the surface of CD4+ T cells. We therefore provide a comprehensive map of the cell surface of IFNα2a-stimulated primary human immune cells, including previously uncharacterized interferon stimulated genes (ISGs) and candidate antiviral factors.
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Affiliation(s)
- Lior Soday
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Martin Potts
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Leah M. Hunter
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin J. Ravenhill
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Jack W. Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James C. Williamson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Mark R. Wills
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Nicholas J. Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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28
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Saeed Z, Rowan A, Greiller C, Taylor GP, Pollock KM. Enhanced T-Cell Maturation and Monocyte Aggregation Are Features of Cellular Inflammation in Human T-Lymphotropic Virus Type 1-Associated Myelopathy. Clin Infect Dis 2021; 70:1326-1335. [PMID: 31063543 DOI: 10.1093/cid/ciz369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/03/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Human T-lymphotropic virus type 1 (HTLV-1)-associated myelopathy (HAM) is an inflammatory condition characterized by severe disability and high levels of infected white blood cells. The circulating cellular inflammatory changes that distinguish this condition from asymptomatic infection are not well understood. METHODS To investigate the immune characteristics of individuals with low or high HTLV-1 proviral load (pVL), symptomatic disease, and the impact of immunosuppressive therapy, 38 women living with HTLV-1 infection, at a median age of 59 (52-68) years, were studied. Nineteen were asymptomatic carriers with low or high pVL; 19 were diagnosed with HAM, with 10 receiving anti-inflammatory therapy. Peripheral blood mononuclear cells were stained and analyzed for frequency distribution and activation of innate and adaptive immune cell subsets using multiparameter flow cytometry. RESULTS Inflation of the CD4:CD8 ratio (>2) was observed among all groups irrespective of pVL. The frequency of naive CD4+ T cells correlated inversely with HTLV-1 pVL (rs = -0.344, P = .026). Mature T effector memory TEM CD4+ T cells were expanded in patients with untreated HAM compared with asymptomatic carriers (P < .001) but less so in those on therapy. High levels of exhausted (PD-1+) and senescent (CD28null) CD4+ and CD8+ T cells were observed in all individuals, particularly in those with HAM, while monocytes showed increased aggregation and CD14+CD56- monocytes were less frequent. CONCLUSIONS CD4:CD8 ratio inflation is a feature of HTLV-1 infection, whereas enhanced CD4+ T cell maturation and monocyte aggregation are features of HAM, reflecting widespread inflammatory change, which may be detectable presymptomatically and be amenable to anti-inflammatory treatment.
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Affiliation(s)
- Zainab Saeed
- Section of Virology, Department of Medicine, Imperial College London, United Kingdom
| | - Aileen Rowan
- Section of Virology, Department of Medicine, Imperial College London, United Kingdom
| | - Claire Greiller
- Section of Virology, Department of Medicine, Imperial College London, United Kingdom
| | - Graham P Taylor
- Section of Virology, Department of Medicine, Imperial College London, United Kingdom
| | - Katrina M Pollock
- Section of Virology, Department of Medicine, Imperial College London, United Kingdom
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29
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Jensen HA, Wnek R. Analytical performance of a
25‐marker
spectral cytometry immune monitoring assay in peripheral blood. Cytometry A 2020. [DOI: 10.1002/cyto.a.24290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Holly A. Jensen
- Translational Molecular Biomarkers Merck & Co., Inc Kenilworth New Jersey USA
| | - Richard Wnek
- Translational Molecular Biomarkers Merck & Co., Inc Kenilworth New Jersey USA
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30
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Lambert C, Yanikkaya Demirel G, Keller T, Preijers F, Psarra K, Schiemann M, Özçürümez M, Sack U. Flow Cytometric Analyses of Lymphocyte Markers in Immune Oncology: A Comprehensive Guidance for Validation Practice According to Laws and Standards. Front Immunol 2020; 11:2169. [PMID: 33042129 PMCID: PMC7528430 DOI: 10.3389/fimmu.2020.02169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Many anticancer therapies such as antibody-based therapies, cellular therapeutics (e.g., genetically modified cells, regulators of cytokine signaling, and signal transduction), and other biologically tailored interventions strongly influence the immune system and require tools for research, diagnosis, and monitoring. In flow cytometry, in vitro diagnostic (IVD) test kits that have been compiled and validated by the manufacturer are not available for all requirements. Laboratories are therefore usually dependent on modifying commercially available assays or, most often, developing them to meet clinical needs. However, both variants must then undergo full validation to fulfill the IVD regulatory requirements. Flow cytometric immunophenotyping is a multiparametric analysis of parameters, some of which have to be repeatedly adjusted; that must be considered when developing specific antibody panels. Careful adjustments of general rules are required to meet legal and regulatory requirements in the analysis of these assays. Here, we describe the relevant regulatory framework for flow cytometry-based assays and describe methods for the introduction of new antibody combinations into routine work including development of performance specifications, validation, and statistical methodology for design and analysis of the experiments. The aim is to increase reliability, efficiency, and auditability after the introduction of in-house-developed flow cytometry assays.
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Affiliation(s)
- Claude Lambert
- University Hospital, Immunology Laboratory, FRE-CNRS 3312, Saint-Etienne, France
| | | | | | - Frank Preijers
- Laboratory of Hematology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Katherina Psarra
- Department of Immunology-Histocompatibility, Evangelismos Hospital, Athens, Greece
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Mustafa Özçürümez
- Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - Ulrich Sack
- Medizinische Fakultät, Institut für Klinische Immunologie, Universität Leipzig, Leipzig, Germany
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31
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Czechowska K, Lannigan J, Aghaeepour N, Back JB, Begum J, Behbehani G, Bispo C, Bitoun D, Fernández AB, Boova ST, Brinkman RR, Ciccolella CO, Cotleur B, Davies D, Dela Cruz GV, Del Rio-Guerra R, Des Lauriers-Cox AM, Douagi I, Dumrese C, Bonilla Escobar DL, Estevam J, Ewald C, Fossum A, Gaudillière B, Green C, Groves C, Hall C, Haque Y, Hedrick MN, Hogg K, Hsieh EWY, Irish J, Lederer J, Leipold M, Lewis-Tuffin LJ, Litwin V, Lopez P, Nasdala I, Nedbal J, Ohlsson-Wilhelm BM, Price KM, Rahman AH, Rayanki R, Rieger AM, Robinson JP, Shapiro H, Sun YS, Tang VA, Tesfa L, Telford WG, Walker R, Welsh JA, Wheeler P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops. Cytometry A 2020; 95:1236-1274. [PMID: 31833655 DOI: 10.1002/cyto.a.23941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia.,Flow Cytometry Core, University of Virginia, School of Medicine, Charlottesville, Virginia
| | - Nima Aghaeepour
- Department of Anesthesiology, Department of Biomedical Data Sciences, Department of Pediatrics, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Jessica B Back
- Department of Oncology, Wayne State University, Detroit, Michigan
| | - Julfa Begum
- Flow Cytometry Facility, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Greg Behbehani
- Wexner Medical Center, Ohio State University, Columbus, Ohio
| | - Cláudia Bispo
- Parnassus Flow Cytometry Core, University of California San Francisco, San Francisco, California.,ISAC SRL Emerging Leader, Arlington, Virginia
| | - Daniel Bitoun
- EMA Regional Marketing, BD Lifesciences, International Office, Belgium
| | - Alfonso Blanco Fernández
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Samuel Tony Boova
- High Burden HIV Global Markets, Beckman Coulter, Inc., Miami, Florida
| | - Ryan Remy Brinkman
- Medical Genetics, University of British Columbia and British Columbia Cancer, Vancouver, British Columbia, Canada.,Cytapex Bioinformatics Inc., Vancouver, British Columbia, Canada
| | | | | | - Derek Davies
- Science Technology Platform Training Lead, Francis Crick Institute, London, UK
| | - Gelo Victoriano Dela Cruz
- Novo Nordisk Foundation Center for Stem Cell Biology - DanStem, Flow Cytometry Platform, Copenhagen, Denmark
| | - Roxana Del Rio-Guerra
- Flow Cytometry and Cell Sorting Facility, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Claudia Dumrese
- Cytometry Facility, University of Zürich, Zürich, Switzerland
| | | | - Jose Estevam
- Center of Biomarker Innovation and Development, Takeda Pharmaceuticals, Cambridge, Massachusetts
| | - Christina Ewald
- Cytometry Facility Senior Scientist, University of Zürich, Zürich, Switzerland
| | - Anna Fossum
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Brice Gaudillière
- Anesthesiology Department, Stanford University, Stanford, California
| | - Cherie Green
- Flow Cytometry Biomarkers Development Sciences, Genentech, Inc., San Francisco, California
| | - Christopher Groves
- Cytometry/Dynamic Omics in R&D Antibody Discovery and Protein Engineering, Astra Zeneca, Gaithersburg, Maryland
| | - Christopher Hall
- ISAC SRL Emerging Leader, Arlington, Virginia.,Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, UK
| | - Yasmin Haque
- Flow Cytometry Facility, Department of Immunobiology and Infectious Diseases, King's College London, London, UK
| | | | - Karen Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, Department of Pediatrics, Division of Allergy and Immunology, School of Medicine, University of Colorado, Aurora, Colorado
| | - Jonathan Irish
- Cancer & Immunology Core and Mass Cytometry Center of Excellence, Vanderbilt University, Nashville, Tennessee
| | - James Lederer
- Department of Surgery (Immunology), Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Michael Leipold
- Human Immune Monitoring Center (HIMC), Stanford University, Stanford, California
| | - Laura J Lewis-Tuffin
- Microscopy and Flow Cytometry Shared Resource, Mayo Clinic, Jacksonville, Florida
| | - Virginia Litwin
- Caprion Biosciences, Inc., Immunology, Montreal, Quebec, Canada
| | - Peter Lopez
- Cytometry and Cell Sorting Laboratory, New York University School of Medicine, New York, New York
| | | | - Jakub Nedbal
- Physics Department, King's College London, London, UK.,ISAC Marylou Ingram Scholar, Arlington, Virginia
| | | | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York.,Dept. of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Radhika Rayanki
- Cytometry/Dynamic Omics in R&D Antibody Discovery and Protein Engineering, Astra Zeneca, Gaithersburg, Maryland
| | - Aja M Rieger
- ISAC SRL Emerging Leader, Arlington, Virginia.,University of Alberta, Flow Cytometry Facility, Faculty of Medicine and Dentistry, Alberta, Canada
| | - J Paul Robinson
- College of Veterinary Medicine and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | | | | | - Vera A Tang
- University of Ottawa, Flow Cytometry and Virometry Core Facility, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Lydia Tesfa
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - William G Telford
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Center Institute, National Institutes of Health, Bethesda, Maryland
| | - Rachael Walker
- Flow Cytometry Core Facility, Babraham Institute, Cambridge, UK
| | - Joshua A Welsh
- ISAC Marylou Ingram Scholar, Arlington, Virginia.,Laboratory of Pathology, Translational Nanobiology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul Wheeler
- Flow Cytometry, Luminex Corporation, Peterborough, UK
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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32
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Quantification and characterization of granulocyte macrophage colony-stimulating factor activated human peripheral blood mononuclear cells by fluorine-19 cellular MRI in an immunocompromised mouse model. Diagn Interv Imaging 2020; 101:577-588. [DOI: 10.1016/j.diii.2020.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
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33
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Dhanwani R, Pham J, Premlal ALR, Frazier A, Kumar A, Pero ME, Bartolini F, Dutra JR, Marder KS, Peters B, Sulzer D, Sette A, Lindestam Arlehamn CS. T Cell Responses to Neural Autoantigens Are Similar in Alzheimer's Disease Patients and Age-Matched Healthy Controls. Front Neurosci 2020; 14:874. [PMID: 32982670 PMCID: PMC7481378 DOI: 10.3389/fnins.2020.00874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
Alzheimer's disease (AD), a chronic multifactorial and complex neurodegenerative disorder is a leading cause of dementia. Recently, neuroinflammation has been hypothesized as a contributing factor to AD pathogenesis. The role of adaptive immune responses against neuronal antigens, which can either confer protection or induce damage in AD, has not been fully characterized. Here, we measured T cell responses to several potential antigens of neural origin including amyloid precursor protein (APP), amyloid beta (Aβ), tau, α-synuclein, and transactive response DNA binding protein (TDP-43) in patients with AD and age-matched healthy controls (HC). Antigen-specific T cell reactivity was detected for all tested antigens, and response to tau-derived epitopes was particularly strong, but no significant differences between individuals with AD and age-matched HC were identified. We also did not observe any correlation between the antigen-specific T cell responses and clinical variables including age, gender, years since diagnosis and cognitive score. Additionally, further characterization did not reveal any differences in the relative frequency of major Peripheral Blood Mononuclear Cells (PBMC) subsets, or in the expression of genes between AD patients and HC. These observations have not identified a key role of neuronal antigen-specific T cell responses in AD.
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Affiliation(s)
- Rekha Dhanwani
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Atul Kumar
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Maria Elena Pero
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States.,Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Juliana Rezende Dutra
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Karen S Marder
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - David Sulzer
- Department of Neurology, New York State Psychiatric Institute, Columbia University, New York, NY, United States.,Department of Psychiatry and Pharmacology, New York State Psychiatric Institute, Columbia University, New York, NY, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
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Kiseleva I, Isakova-Sivak I, Stukova M, Erofeeva M, Donina S, Larionova N, Krutikova E, Bazhenova E, Stepanova E, Vasilyev K, Matyushenko V, Krylova M, Galatonova J, Ershov A, Lioznov D, Sparrow EG, Torelli G, Rudenko L. A Phase 1 Randomized Placebo-Controlled Study to Assess the Safety, Immunogenicity and Genetic Stability of a New Potential Pandemic H7N9 Live Attenuated Influenza Vaccine in Healthy Adults. Vaccines (Basel) 2020; 8:vaccines8020296. [PMID: 32532097 PMCID: PMC7350028 DOI: 10.3390/vaccines8020296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 01/06/2023] Open
Abstract
This study describes a double-blind randomized placebo-controlled phase I clinical trial in healthy adults of a new potential pandemic H7N9 live attenuated influenza vaccine (LAIV) based on the human influenza virus of Yangtze River Delta hemagglutinin lineage (ClinicalTrials.gov Identifier: NCT03739229). Two doses of H7N9 LAIV or placebo were administered intranasally to 30 and 10 subjects, respectively. The vaccine was well-tolerated and not associated with increased rates of adverse events or with any serious adverse events. Vaccine virus was detected in nasal swabs during the 6 days after vaccination or revaccination. A lower frequency of shedding was observed after the second vaccination. Twenty-five clinical viral isolates obtained after the first and second doses of vaccine retained the temperature-sensitive and cold-adapted phenotypic characteristics of LAIV. There was no confirmed transmission of the vaccine strain from vaccinees to placebo recipients. After the two H7N9 LAIV doses, an immune response was observed in 96.6% of subjects in at least one of the assays conducted.
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Affiliation(s)
- Irina Kiseleva
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
- Correspondence: ; Tel.: +7-(812)-2346-860
| | - Irina Isakova-Sivak
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Marina Stukova
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Marianna Erofeeva
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Svetlana Donina
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Natalie Larionova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Elena Krutikova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Ekaterina Bazhenova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Ekaterina Stepanova
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Kirill Vasilyev
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | - Victoria Matyushenko
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
| | - Marina Krylova
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Julia Galatonova
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Aleksey Ershov
- The Federal State Unitary Enterprise “Scientific and Production Association for Immunological Preparations “Microgen”, Ministry of Health of Russian Federation, 127473 Moscow, Russia; (M.K.); (J.G.); (A.E.)
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 St Petersburg, Russia; (M.S.); (M.E.); (K.V.); (D.L.)
| | | | - Guido Torelli
- World Health Organization, 1211 Geneva, Switzerland; (E.G.S.); (G.T.)
| | - Larisa Rudenko
- Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (I.I.-S.); (S.D.); (N.L.); (E.K.); (E.B.); (E.S.); (V.M.); (L.R.)
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Pomaznoy M, Kuan R, Lindvall M, Burel JG, Seumois G, Vijayanand P, Taplitz R, Gilman RH, Saito M, Lewinsohn DM, Sette A, Peters B, Lindestam Arlehamn CS. Quantitative and Qualitative Perturbations of CD8 + MAITs in Healthy Mycobacterium tuberculosis-Infected Individuals. Immunohorizons 2020; 4:292-307. [PMID: 32499216 PMCID: PMC7543048 DOI: 10.4049/immunohorizons.2000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
CD8 T cells are considered important contributors to the immune response against Mycobacterium tuberculosis, yet limited information is currently known regarding their specific immune signature and phenotype. In this study, we applied a cell population transcriptomics strategy to define immune signatures of human latent tuberculosis infection (LTBI) in memory CD8 T cells. We found a 41-gene signature that discriminates between memory CD8 T cells from healthy LTBI subjects and uninfected controls. The gene signature was dominated by genes associated with mucosal-associated invariant T cells (MAITs) and reflected the lower frequency of MAITs observed in individuals with LTBI. There was no evidence for a conventional CD8 T cell–specific signature between the two cohorts. We, therefore, investigated MAITs in more detail based on Vα7.2 and CD161 expression and staining with an MHC-related protein 1 (MR1) tetramer. This revealed two distinct populations of CD8+Vα7.2+CD161+ MAITs: MR1 tetramer+ and MR1 tetramer−, which both had distinct gene expression compared with memory CD8 T cells. Transcriptomic analysis of LTBI versus noninfected individuals did not reveal significant differences for MR1 tetramer+ MAITs. However, gene expression of MR1 tetramer− MAITs showed large interindividual diversity and a tuberculosis-specific signature. This was further strengthened by a more diverse TCR-α and -β repertoire of MR1 tetramer− cells as compared with MR1 tetramer+. Thus, circulating memory CD8 T cells in subjects with latent tuberculosis have a reduced number of conventional MR1 tetramer+ MAITs as well as a difference in phenotype in the rare population of MR1 tetramer− MAITs compared with uninfected controls.
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Affiliation(s)
- Mikhail Pomaznoy
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Rebecca Kuan
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Mikaela Lindvall
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Julie G Burel
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Grégory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | | | - Randy Taplitz
- Division of Infectious Diseases, University of California San Diego, La Jolla, CA 92093
| | - Robert H Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Universidad Peruana Caytano Hereida, Lima 15102, Peru
| | - Mayuko Saito
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Department of Virology, Tohuku University Graduate School of Medicine, Sendai 9808575, Japan
| | - David M Lewinsohn
- Department of Medicine, VA Portland Health Care System, Portland, OR 97239.,Pulmonary and Critical Care Medicine, Department of Medicine, Oregon Health & Science University, Portland, OR 97239; and
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
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36
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Multicentre Harmonisation of a Six-Colour Flow Cytometry Panel for Naïve/Memory T Cell Immunomonitoring. J Immunol Res 2020; 2020:1938704. [PMID: 32322591 PMCID: PMC7153001 DOI: 10.1155/2020/1938704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 01/17/2023] Open
Abstract
Background Personalised medicine in oncology needs standardised immunological assays. Flow cytometry (FCM) methods represent an essential tool for immunomonitoring, and their harmonisation is crucial to obtain comparable data in multicentre clinical trials. The objective of this study was to design a harmonisation workflow able to address the most effective issues contributing to intra- and interoperator variabilities in a multicentre project. Methods The Italian National Institute of Health (Istituto Superiore di Sanità, ISS) managed a multiparametric flow cytometric panel harmonisation among thirteen operators belonging to five clinical and research centres of Lazio region (Italy). The panel was based on a backbone mixture of dried antibodies (anti-CD3, anti-CD4, anti-CD8, anti-CD45RA, and anti-CCR7) to detect naïve/memory T cells, recognised as potential prognostic/predictive immunological biomarkers in cancer immunotherapies. The coordinating centre distributed frozen peripheral blood mononuclear cells (PBMCs) and fresh whole blood (WB) samples from healthy donors, reagents, and Standard Operating Procedures (SOPs) to participants who performed experiments by their own equipment, in order to mimic a real-life scenario. Operators returned raw and locally analysed data to ISS for central analysis and statistical elaboration. Results Harmonised and reproducible results were obtained by sharing experimental set-up and procedures along with centralising data analysis, leading to a reduction of cross-centre variability for naïve/memory subset frequencies particularly in the whole blood setting. Conclusion Our experimental and analytical working process proved to be suitable for the harmonisation of FCM assays in a multicentre setting, where high-quality data are required to evaluate potential immunological markers, which may contribute to select better therapeutic options.
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High throughput pSTAT signaling profiling by fluorescent cell barcoding and computational analysis. J Immunol Methods 2019; 477:112667. [PMID: 31726053 DOI: 10.1016/j.jim.2019.112667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/08/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022]
Abstract
Fluorescent cell barcoding (FCB) is a multiplexing technique for high-throughput flow cytometry (FCM). Although powerful in minimizing staining variability, it remains a subjective FCM technique because of inter-operator variability and differences in data analysis. FCB was implemented by combining two-dye barcoding (DyLight 350 plus Pacific Orange) with five-color surface marker antibody and intracellular staining for phosphoprotein signaling analysis. We proposed a robust method to measure intra- and inter-assay variability of FCB in T/B cells and monocytes by combining range and ratio of variability to standard statistical analyses. Data analysis was carried out by conventional and semi-automated workflows and built with R software. Results obtained from both analyses were compared to assess feasibility and reproducibility of FCB data analysis by machine-learning methods. Our results showed efficient FCB using DyLight 350 and Pacific Orange at concentrations of 0, 15 or 30, and 250 μg/mL, and a high reproducibility of FCB in combination with surface marker and intracellular antibodies. Inter-operator variability was minimized by adding an internal control bridged across matrices used as rejection criterion if significant differences were present between runs. Computational workflows showed comparable results to conventional gating strategies. FCB can be used to study phosphoprotein signaling in T/B cells and monocytes with high reproducibility across operators, and the addition of bridge internal controls can further minimize inter-operator variability. This FCB protocol, which has high throughput analysis and low intra- and inter-assay variability, can be a powerful tool for clinical trial studies. Moreover, FCB data can be reliably analyzed using computational software.
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38
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Cossarizza A, Chang HD, Radbruch A, Acs A, Adam D, Adam-Klages S, Agace WW, Aghaeepour N, Akdis M, Allez M, Almeida LN, Alvisi G, Anderson G, Andrä I, Annunziato F, Anselmo A, Bacher P, Baldari CT, Bari S, Barnaba V, Barros-Martins J, Battistini L, Bauer W, Baumgart S, Baumgarth N, Baumjohann D, Baying B, Bebawy M, Becher B, Beisker W, Benes V, Beyaert R, Blanco A, Boardman DA, Bogdan C, Borger JG, Borsellino G, Boulais PE, Bradford JA, Brenner D, Brinkman RR, Brooks AES, Busch DH, Büscher M, Bushnell TP, Calzetti F, Cameron G, Cammarata I, Cao X, Cardell SL, Casola S, Cassatella MA, Cavani A, Celada A, Chatenoud L, Chattopadhyay PK, Chow S, Christakou E, Čičin-Šain L, Clerici M, Colombo FS, Cook L, Cooke A, Cooper AM, Corbett AJ, Cosma A, Cosmi L, Coulie PG, Cumano A, Cvetkovic L, Dang VD, Dang-Heine C, Davey MS, Davies D, De Biasi S, Del Zotto G, Cruz GVD, Delacher M, Bella SD, Dellabona P, Deniz G, Dessing M, Di Santo JP, Diefenbach A, Dieli F, Dolf A, Dörner T, Dress RJ, Dudziak D, Dustin M, Dutertre CA, Ebner F, Eckle SBG, Edinger M, Eede P, Ehrhardt GR, Eich M, Engel P, Engelhardt B, Erdei A, Esser C, Everts B, Evrard M, Falk CS, Fehniger TA, Felipo-Benavent M, Ferry H, Feuerer M, Filby A, Filkor K, Fillatreau S, Follo M, Förster I, Foster J, Foulds GA, Frehse B, Frenette PS, Frischbutter S, Fritzsche W, Galbraith DW, Gangaev A, Garbi N, Gaudilliere B, Gazzinelli RT, Geginat J, Gerner W, Gherardin NA, Ghoreschi K, Gibellini L, Ginhoux F, Goda K, Godfrey DI, Goettlinger C, González-Navajas JM, Goodyear CS, Gori A, Grogan JL, Grummitt D, Grützkau A, Haftmann C, Hahn J, Hammad H, Hämmerling G, Hansmann L, Hansson G, Harpur CM, Hartmann S, Hauser A, Hauser AE, Haviland DL, Hedley D, Hernández DC, Herrera G, Herrmann M, Hess C, Höfer T, Hoffmann P, Hogquist K, Holland T, Höllt T, Holmdahl R, Hombrink P, Houston JP, Hoyer BF, Huang B, Huang FP, Huber JE, Huehn J, Hundemer M, Hunter CA, Hwang WYK, Iannone A, Ingelfinger F, Ivison SM, Jäck HM, Jani PK, Jávega B, Jonjic S, Kaiser T, Kalina T, Kamradt T, Kaufmann SHE, Keller B, Ketelaars SLC, Khalilnezhad A, Khan S, Kisielow J, Klenerman P, Knopf J, Koay HF, Kobow K, Kolls JK, Kong WT, Kopf M, Korn T, Kriegsmann K, Kristyanto H, Kroneis T, Krueger A, Kühne J, Kukat C, Kunkel D, Kunze-Schumacher H, Kurosaki T, Kurts C, Kvistborg P, Kwok I, Landry J, Lantz O, Lanuti P, LaRosa F, Lehuen A, LeibundGut-Landmann S, Leipold MD, Leung LY, Levings MK, Lino AC, Liotta F, Litwin V, Liu Y, Ljunggren HG, Lohoff M, Lombardi G, Lopez L, López-Botet M, Lovett-Racke AE, Lubberts E, Luche H, Ludewig B, Lugli E, Lunemann S, Maecker HT, Maggi L, Maguire O, Mair F, Mair KH, Mantovani A, Manz RA, Marshall AJ, Martínez-Romero A, Martrus G, Marventano I, Maslinski W, Matarese G, Mattioli AV, Maueröder C, Mazzoni A, McCluskey J, McGrath M, McGuire HM, McInnes IB, Mei HE, Melchers F, Melzer S, Mielenz D, Miller SD, Mills KH, Minderman H, Mjösberg J, Moore J, Moran B, Moretta L, Mosmann TR, Müller S, Multhoff G, Muñoz LE, Münz C, Nakayama T, Nasi M, Neumann K, Ng LG, Niedobitek A, Nourshargh S, Núñez G, O’Connor JE, Ochel A, Oja A, Ordonez D, Orfao A, Orlowski-Oliver E, Ouyang W, Oxenius A, Palankar R, Panse I, Pattanapanyasat K, Paulsen M, Pavlinic D, Penter L, Peterson P, Peth C, Petriz J, Piancone F, Pickl WF, Piconese S, Pinti M, Pockley AG, Podolska MJ, Poon Z, Pracht K, Prinz I, Pucillo CEM, Quataert SA, Quatrini L, Quinn KM, Radbruch H, Radstake TRDJ, Rahmig S, Rahn HP, Rajwa B, Ravichandran G, Raz Y, Rebhahn JA, Recktenwald D, Reimer D, e Sousa CR, Remmerswaal EB, Richter L, Rico LG, Riddell A, Rieger AM, Robinson JP, Romagnani C, Rubartelli A, Ruland J, Saalmüller A, Saeys Y, Saito T, Sakaguchi S, de-Oyanguren FS, Samstag Y, Sanderson S, Sandrock I, Santoni A, Sanz RB, Saresella M, Sautes-Fridman C, Sawitzki B, Schadt L, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schimisky E, Schlitzer A, Schlosser J, Schmid S, Schmitt S, Schober K, Schraivogel D, Schuh W, Schüler T, Schulte R, Schulz AR, Schulz SR, Scottá C, Scott-Algara D, Sester DP, Shankey TV, Silva-Santos B, Simon AK, Sitnik KM, Sozzani S, Speiser DE, Spidlen J, Stahlberg A, Stall AM, Stanley N, Stark R, Stehle C, Steinmetz T, Stockinger H, Takahama Y, Takeda K, Tan L, Tárnok A, Tiegs G, Toldi G, Tornack J, Traggiai E, Trebak M, Tree TI, Trotter J, Trowsdale J, Tsoumakidou M, Ulrich H, Urbanczyk S, van de Veen W, van den Broek M, van der Pol E, Van Gassen S, Van Isterdael G, van Lier RA, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk HD, von Borstel A, von Volkmann K, Waisman A, Walker RV, Wallace PK, Wang SA, Wang XM, Ward MD, Ward-Hartstonge KA, Warnatz K, Warnes G, Warth S, Waskow C, Watson JV, Watzl C, Wegener L, Weisenburger T, Wiedemann A, Wienands J, Wilharm A, Wilkinson RJ, Willimsky G, Wing JB, Winkelmann R, Winkler TH, Wirz OF, Wong A, Wurst P, Yang JHM, Yang J, Yazdanbakhsh M, Yu L, Yue A, Zhang H, Zhao Y, Ziegler SM, Zielinski C, Zimmermann J, Zychlinsky A. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). Eur J Immunol 2019; 49:1457-1973. [PMID: 31633216 PMCID: PMC7350392 DOI: 10.1002/eji.201970107] [Citation(s) in RCA: 689] [Impact Index Per Article: 137.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
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Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, Univ. of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Andreas Acs
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Dieter Adam
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sabine Adam-Klages
- Institut für Transfusionsmedizin, Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - William W. Agace
- Mucosal Immunology group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Immunology Section, Lund University, Lund, Sweden
| | - Nima Aghaeepour
- Departments of Anesthesiology, Pain and Perioperative Medicine; Biomedical Data Sciences; and Pediatrics, Stanford University, Stanford, CA, USA
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Matthieu Allez
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U1160, and Gastroenterology Department, Hôpital Saint-Louis – APHP, Paris, France
| | | | - Giorgia Alvisi
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Rozzano, Italy
| | | | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Achille Anselmo
- Flow Cytometry Core, Humanitas Clinical and Research Center, Milan, Italy
| | - Petra Bacher
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Institut für Klinische Molekularbiologie, Christian-Albrechts Universität zu Kiel, Germany
| | | | - Sudipto Bari
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | | | | | - Wolfgang Bauer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sabine Baumgart
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Nicole Baumgarth
- Center for Comparative Medicine & Dept. Pathology, Microbiology & Immunology, University of California, Davis, CA, USA
| | - Dirk Baumjohann
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Bianka Baying
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mary Bebawy
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney, Sydney, NSW, Australia
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Wolfgang Beisker
- Flow Cytometry Laboratory, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Center for Inflammation Research, Ghent University - VIB, Ghent, Belgium
| | - Alfonso Blanco
- Flow Cytometry Core Technologies, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Dominic A. Boardman
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Christian Bogdan
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Erlangen, Germany
- Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Medical Immunology Campus Erlangen, Erlangen, Germany
| | - Jessica G. Borger
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Giovanna Borsellino
- Neuroimmunology and Flow Cytometry Units, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Philip E. Boulais
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, New York, USA
| | | | - Dirk Brenner
- Luxembourg Institute of Health, Department of Infection and Immunity, Experimental and Molecular Immunology, Esch-sur-Alzette, Luxembourg
- Odense University Hospital, Odense Research Center for Anaphylaxis, University of Southern Denmark, Department of Dermatology and Allergy Center, Odense, Denmark
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Ryan R. Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
| | - Anna E. S. Brooks
- University of Auckland, School of Biological Sciences, Maurice Wilkins Center, Auckland, New Zealand
| | - Dirk H. Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Martin Büscher
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Timothy P. Bushnell
- Department of Pediatrics and Shared Resource Laboratories, University of Rochester Medical Center, Rochester, NY, USA
| | - Federica Calzetti
- University of Verona, Department of Medicine, Section of General Pathology, Verona, Italy
| | - Garth Cameron
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Xuetao Cao
- National Key Laboratory of Medical Immunology, Nankai University, Tianjin, China
| | - Susanna L. Cardell
- Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - Stefano Casola
- The FIRC Institute of Molecular Oncology (FOM), Milan, Italy
| | - Marco A. Cassatella
- University of Verona, Department of Medicine, Section of General Pathology, Verona, Italy
| | - Andrea Cavani
- National Institute for Health, Migration and Poverty (INMP), Rome, Italy
| | - Antonio Celada
- Macrophage Biology Group, School of Biology, University of Barcelona, Barcelona, Spain
| | - Lucienne Chatenoud
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | | | - Sue Chow
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Eleni Christakou
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | - Luka Čičin-Šain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mario Clerici
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Department of Physiopathology and Transplants, University of Milan, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | | | - Laura Cook
- BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Anne Cooke
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrea M. Cooper
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health, Department of Infection and Immunity, Esch-sur-Alzette, Luxembourg
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pierre G. Coulie
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Ana Cumano
- Unit Lymphopoiesis, Department of Immunology, Institut Pasteur, Paris, France
| | - Ljiljana Cvetkovic
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Van Duc Dang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Chantip Dang-Heine
- Clinical Research Unit, Berlin Institute of Health (BIH), Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Martin S. Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Derek Davies
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Sara De Biasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | | | - Gelo Victoriano Dela Cruz
- Novo Nordisk Foundation Center for Stem Cell Biology – DanStem, University of Copenhagen, Copenhagen, Denmark
| | - Michael Delacher
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Germany
| | - Silvia Della Bella
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Paolo Dellabona
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Günnur Deniz
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Immunology, Istanbul, Turkey
| | | | - James P. Di Santo
- Innate Immunty Unit, Department of Immunology, Institut Pasteur, Paris, France
- Institut Pasteur, Inserm U1223, Paris, France
| | - Andreas Diefenbach
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Francesco Dieli
- University of Palermo, Central Laboratory of Advanced Diagnosis and Biomedical Research, Department of Biomedicine, Neurosciences and Advanced Diagnostics, Palermo, Italy
| | - Andreas Dolf
- Flow Cytometry Core Facility, Institute of Experimental Immunology, University of Bonn, Bonn, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Regine J. Dress
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Diana Dudziak
- Department of Dermatology, Laboratory of Dendritic Cell Biology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Michael Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Charles-Antoine Dutertre
- Program in Emerging Infectious Disease, Duke-NUS Medical School, Singapore
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Friederike Ebner
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Matthias Edinger
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Pascale Eede
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Germany
| | | | - Marcus Eich
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Pablo Engel
- University of Barcelona, Faculty of Medicine and Health Sciences, Department of Biomedical Sciences, Barcelona, Spain
| | | | - Anna Erdei
- Department of Immunology, University L. Eotvos, Budapest, Hungary
| | - Charlotte Esser
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Christine S. Falk
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Todd A. Fehniger
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mar Felipo-Benavent
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Principe Felipe Research Center, Valencia, Spain
| | - Helen Ferry
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Markus Feuerer
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Germany
| | - Andrew Filby
- The Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Simon Fillatreau
- Institut Necker-Enfants Malades, Université Paris Descartes Sorbonne Paris Cité, Faculté de Médecine, AP-HP, Hôpital Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Universitaetsklinikum FreiburgLighthouse Core Facility, Zentrum für Translationale Zellforschung, Klinik für Innere Medizin I, Freiburg, Germany
| | - Irmgard Förster
- Immunology and Environment, LIMES Institute, University of Bonn, Bonn, Germany
| | | | - Gemma A. Foulds
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
| | - Britta Frehse
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Paul S. Frenette
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Stefan Frischbutter
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Dermatology, Venereology and Allergology
| | - Wolfgang Fritzsche
- Nanobiophotonics Department, Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - David W. Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, USA
- Honorary Dean of Life Sciences, Henan University, Kaifeng, China
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalio Garbi
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Brice Gaudilliere
- Stanford Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, CA, USA
| | - Ricardo T. Gazzinelli
- Fundação Oswaldo Cruz - Minas, Laboratory of Immunopatology, Belo Horizonte, MG, Brazil
- Department of Mecicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jens Geginat
- INGM - Fondazione Istituto Nazionale di Genetica Molecolare “Ronmeo ed Enrica Invernizzi”, Milan, Italy
| | - Wilhelm Gerner
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
- Christian Doppler Laboratory for Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Kamran Ghoreschi
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Gibellini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Keisuke Goda
- Department of Bioengineering, University of California, Los Angeles, California, USA
- Department of Chemistry, University of Tokyo, Tokyo, Japan
- Institute of Technological Sciences, Wuhan University, Wuhan, China
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | | | - Jose M. González-Navajas
- Alicante Institute for Health and Biomedical Research (ISABIAL), Alicante, Spain
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Carl S. Goodyear
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow, UK
| | - Andrea Gori
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, University of Milan
| | - Jane L. Grogan
- Cancer Immunology Research, Genentech, South San Francisco, CA, USA
| | | | - Andreas Grützkau
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jonas Hahn
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Hamida Hammad
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Zwijnaarde, Belgium
| | | | - Leo Hansmann
- Berlin Institute of Health (BIH), Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Goran Hansson
- Department of Medicine and Center for Molecular Medicine at Karolinska University Hospital, Solna, Sweden
| | | | - Susanne Hartmann
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Andrea Hauser
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Anja E. Hauser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin
- Department of Rheumatology and Clinical Immunology, Berlin Institute of Health, Berlin, Germany
| | - David L. Haviland
- Flow Cytometry, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - David Hedley
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Daniela C. Hernández
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Guadalupe Herrera
- Cytometry Service, Incliva Foundation. Clinic Hospital and Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Christoph Hess
- Immunobiology Laboratory, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Thomas Höfer
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, Heidelberg, Germany
| | - Petra Hoffmann
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Germany
| | - Kristin Hogquist
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Tristan Holland
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Computer Graphics and Visualization, Department of Intelligent Systems, TU Delft, Delft, The Netherlands
| | | | - Pleun Hombrink
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jessica P. Houston
- Department of Chemical & Materials Engineering, New Mexico State University, Las Cruces, NM, USA
| | - Bimba F. Hoyer
- Rheumatologie/Klinische Immunologie, Klinik für Innere Medizin I und Exzellenzzentrum Entzündungsmedizin, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Bo Huang
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Fang-Ping Huang
- Institute for Advanced Study (IAS), Shenzhen University, Shenzhen, China
| | - Johanna E. Huber
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Christopher A. Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William Y. K. Hwang
- Department of Hematology, Singapore General Hospital, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore
- Executive Offices, National Cancer Centre Singapore, Singapore
| | - Anna Iannone
- Department of Diagnostic Medicine, Clinical and Public Health, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Florian Ingelfinger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sabine M Ivison
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Peter K. Jani
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Beatriz Jávega
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Stipan Jonjic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Toralf Kaiser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Thomas Kamradt
- Jena University Hospital, Institute of Immunology, Jena, Germany
| | | | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven L. C. Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ahad Khalilnezhad
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Srijit Khan
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jan Kisielow
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Paul Klenerman
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jasmin Knopf
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Germany
| | - Jay K. Kolls
- John W Deming Endowed Chair in Internal Medicine, Center for Translational Research in Infection and Inflammation Tulane School of Medicine, New Orleans, LA, USA
| | - Wan Ting Kong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Thomas Korn
- Department of Neurology, Technical University of Munich, Munich, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Hendy Kristyanto
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Kroneis
- Division of Cell Biology, Histology & Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jenny Kühne
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Désirée Kunkel
- Flow & Mass Cytometry Core Facility, Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Berlin, Germany
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Tomohiro Kurosaki
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Christian Kurts
- Institute of Experimental Immunology, University of Bonn, Germany
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jonathan Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olivier Lantz
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, Centre on Aging Sciences and Translational Medicine (Ce.S.I.-Me.T.), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Francesca LaRosa
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Agnès Lehuen
- Institut Cochin, CNRS8104, INSERM1016, Department of Endocrinology, Metabolism and Diabetes, Université de Paris, Paris, France
| | | | - Michael D. Leipold
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, CA, USA
| | - Leslie Y.T. Leung
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Megan K. Levings
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Andreia C. Lino
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Michael Lohoff
- Inst. f. Med. Mikrobiology and Hospital Hygiene, University of Marburg, Germany
| | - Giovanna Lombardi
- King’s College London, “Peter Gorer” Department of Immunobiology, London, UK
| | | | - Miguel López-Botet
- IMIM(Hospital de Mar Medical Research Institute), University Pompeu Fabra, Barcelona, Spain
| | - Amy E. Lovett-Racke
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Erik Lubberts
- Department of Rheumatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Herve Luche
- Centre d’Immunophénomique - CIPHE (PHENOMIN), Aix Marseille Université (UMS3367), Inserm (US012), CNRS (UMS3367), Marseille, France
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Rozzano, Italy
- Flow Cytometry Core, Humanitas Clinical and Research Center, Milan, Italy
| | - Sebastian Lunemann
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Holden T. Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Orla Maguire
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Florian Mair
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Kerstin H. Mair
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
- Christian Doppler Laboratory for Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Alberto Mantovani
- Istituto Clinico Humanitas IRCCS and Humanitas University, Pieve Emanuele, Milan, Italy
- William Harvey Research Institute, Queen Mary University, London, United Kingdom
| | - Rudolf A. Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Aaron J. Marshall
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Glòria Martrus
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Ivana Marventano
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Wlodzimierz Maslinski
- National Institute of Geriatrics, Rheumatology and Rehabilitation, Department of Pathophysiology and Immunology, Warsaw, Poland
| | - Giuseppe Matarese
- Treg Cell Lab, Dipartimento di Medicina Molecolare e Biotecologie Mediche, Università di Napoli Federico II and Istituto per l’Endocrinologia e l’Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli, Italy
| | - Anna Vittoria Mattioli
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
- Lab of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Christian Maueröder
- Cell Clearance in Health and Disease Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Mairi McGrath
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Helen M. McGuire
- Ramaciotti Facility for Human Systems Biology, and Discipline of Pathology, The University of Sydney, Camperdown, Australia
| | - Iain B. McInnes
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow, UK
| | - Henrik E. Mei
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Fritz Melchers
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, University Leipzig, Leipzig, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Stephen D. Miller
- Interdepartmental Immunobiology Center, Dept. of Microbiology-Immunology, Northwestern Univ. Medical School, Chicago, IL, USA
| | - Kingston H.G. Mills
- Trinity College Dublin, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Hans Minderman
- Flow and Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, ANA Futura, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical and Experimental Medine, Linköping University, Linköping, Sweden
| | - Jonni Moore
- Abramson Cancer Center Flow Cytometry and Cell Sorting Shared Resource, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Barry Moran
- Trinity College Dublin, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesu Children’s Hospital, Rome, Italy
| | - Tim R. Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Susann Müller
- Centre for Environmental Research - UFZ, Department Environmental Microbiology, Leipzig, Germany
| | - Gabriele Multhoff
- Institute for Innovative Radiotherapy (iRT), Experimental Immune Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Radiation Immuno-Oncology Group, Center for Translational Cancer Research Technische Universität München (TranslaTUM), Klinikum rechts der Isar, Munich, Germany
| | - Luis Enrique Muñoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Christian Münz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba city, Chiba, Japan
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Discipline of Dermatology, University of Sydney, Sydney, New South Wales, Australia
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Antonia Niedobitek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Sussan Nourshargh
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, the University of Michigan, Ann Arbor, Michigan, USA
| | - José-Enrique O’Connor
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Aaron Ochel
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Oja
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana Ordonez
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alberto Orfao
- Department of Medicine, Cancer Research Centre (IBMCC-CSIC/USAL), Cytometry Service, University of Salamanca, CIBERONC and Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Eva Orlowski-Oliver
- Burnet Institute, AMREP Flow Cytometry Core Facility, Melbourne, Victoria, Australia
| | - Wenjun Ouyang
- Inflammation and Oncology, Research, Amgen Inc, South San Francisco, USA
| | | | - Raghavendra Palankar
- Department of Transfusion Medicine, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Isabel Panse
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Kovit Pattanapanyasat
- Center of Excellence for Flow Cytometry, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Malte Paulsen
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Dinko Pavlinic
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Livius Penter
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Christian Peth
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Jordi Petriz
- Functional Cytomics Group, Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain
| | - Federica Piancone
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Winfried F. Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Silvia Piconese
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A. Graham Pockley
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
- Chromocyte Limited, Electric Works, Sheffield, UK
| | - Malgorzata Justyna Podolska
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
- Department for Internal Medicine 3, Institute for Rheumatology and Immunology, AG Munoz, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Zhiyong Poon
- Department of Hematology, Singapore General Hospital, Singapore
| | - Katharina Pracht
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Sally A. Quataert
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Linda Quatrini
- Department of Immunology, IRCCS Bambino Gesu Children’s Hospital, Rome, Italy
| | - Kylie M. Quinn
- School of Biomedical and Health Sciences, RMIT University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Helena Radbruch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Germany
| | - Tim R. D. J. Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Susann Rahmig
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Hans-Peter Rahn
- Preparative Flow Cytometry, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Bartek Rajwa
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, USA
| | - Gevitha Ravichandran
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yotam Raz
- Department of Internal Medicine, Groene Hart Hospital, Gouda, The Netherlands
| | - Jonathan A. Rebhahn
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Dorothea Reimer
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Ester B.M. Remmerswaal
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Renal Transplant Unit, Division of Internal Medicine, Academic Medical Centre, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisa Richter
- Core Facility Flow Cytometry, Biomedical Center, Ludwig-Maximilians-University Munich, Germany
| | - Laura G. Rico
- Functional Cytomics Group, Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, UAB, Badalona, Spain
| | - Andy Riddell
- Flow Cytometry Scientific Technology Platform, The Francis Crick Institute, London, UK
| | - Aja M. Rieger
- Department of Medical Microbiology and Immunology, University of Alberta, Alberta, Canada
| | - J. Paul Robinson
- Purdue University Cytometry Laboratories, Purdue University, West Lafayette, IN, USA
| | - Chiara Romagnani
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Anna Rubartelli
- Cell Biology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Jürgen Ruland
- Institut für Klinische Chemie und Pathobiochemie, Fakultät für Medizin, Technische Universität München, München, Germany
| | - Armin Saalmüller
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Takashi Saito
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shimon Sakaguchi
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Francisco Sala de-Oyanguren
- Flow Cytometry Facility, Ludwig Cancer Institute, Faculty of Medicine and Biology, University of Lausanne, Epalinges, Switzerland
| | - Yvonne Samstag
- Heidelberg University, Institute of Immunology, Section of Molecular Immunology, Heidelberg, Germany
| | - Sharon Sanderson
- Translational Immunology Laboratory, NIHR BRC, University of Oxford, Kennedy Institute of Rheumatology, Oxford, UK
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Angela Santoni
- Department of Molecular Medicine, Sapienza University of Rome, IRCCS, Neuromed, Pozzilli, Italy
| | - Ramon Bellmàs Sanz
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Marina Saresella
- IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
- Milan Center for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | | | - Birgit Sawitzki
- Charité – Universitätsmedizin Berlin, and Berlin Institute of Health, Institute of Medical Immunology, Berlin, Germany
| | - Linda Schadt
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Alexander Scheffold
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hans U. Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schiemann
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Frank A. Schildberg
- Clinic for Orthopedics and Trauma Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Andreas Schlitzer
- Quantitative Systems Biology, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Josephine Schlosser
- Institute of Immunology, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Germany
| | - Stephan Schmid
- Internal Medicine I, University Hospital Regensburg, Germany
| | - Steffen Schmitt
- Flow Cytometry Core Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Daniel Schraivogel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Reiner Schulte
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
| | - Axel Ronald Schulz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Cristiano Scottá
- King’s College London, “Peter Gorer” Department of Immunobiology, London, UK
| | - Daniel Scott-Algara
- Institut Pasteur, Cellular Lymphocytes Biology, Immunology Departement, Paris, France
| | - David P. Sester
- TRI Flow Cytometry Suite (TRI.fcs), Translational Research Institute, Wooloongabba, QLD, Australia
| | | | - Bruno Silva-Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | | | - Katarzyna M. Sitnik
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Silvano Sozzani
- Dept. Molecular Translational Medicine, University of Brescia, Brescia, Italy
| | - Daniel E. Speiser
- Department of Oncology, University of Lausanne and CHUV, Epalinges, Switzerland
| | | | - Anders Stahlberg
- Lundberg Laboratory for Cancer, Department of Pathology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | | | - Natalie Stanley
- Departments of Anesthesiology, Pain and Perioperative Medicine; Biomedical Data Sciences; and Pediatrics, Stanford University, Stanford, CA, USA
| | - Regina Stark
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Christina Stehle
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Medical Department I, Division of Gastroenterology, Infectiology and Rheumatology, Berlin, Germany
| | - Tobit Steinmetz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Kiyoshi Takeda
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Attila Tárnok
- Departement for Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Department of Precision Instruments, Tsinghua University, Beijing, China
| | - Gisa Tiegs
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Julia Tornack
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- BioGenes GmbH, Berlin, Germany
| | - Elisabetta Traggiai
- Novartis Biologics Center, Mechanistic Immunology Unit, Novartis Institute for Biomedical Research, NIBR, Basel, Switzerland
| | - Mohamed Trebak
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, PA, United States
| | - Timothy I.M. Tree
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | | | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Sophia Urbanczyk
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
- Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Maries van den Broek
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Switzerland
| | - Edwin van der Pol
- Vesicle Observation Center; Biomedical Engineering & Physics; Laboratory Experimental Clinical Chemistry; Amsterdam University Medical Centers, Location AMC, The Netherlands
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | | | - René A.W. van Lier
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc Veldhoen
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | | | - Paulo Vieira
- Unit Lymphopoiesis, Department of Immunology, Institut Pasteur, Paris, France
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin and Berlin Institute of Health, Core Unit ImmunoCheck
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | | | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | - Paul K. Wallace
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, USA
| | - Sa A. Wang
- Dept of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin M. Wang
- The Scientific Platforms, the Westmead Institute for Medical Research, the Westmead Research Hub, Westmead, New South Wales, Australia
| | | | | | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gary Warnes
- Flow Cytometry Core Facility, Blizard Institute, Queen Mary London University, London, UK
| | - Sarah Warth
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | - Claudia Waskow
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging, Fritz-Lipmann-Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | | | - Carsten Watzl
- Department for Immunology, Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
| | - Leonie Wegener
- Biophysics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Thomas Weisenburger
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Annika Wiedemann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Dept. Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Jürgen Wienands
- Institute for Cellular & Molecular Immunology, University Medical Center Göttingen, Göttingen, Germany
| | - Anneke Wilharm
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Robert John Wilkinson
- Department of Infectious Disease, Imperial College London, UK
- Wellcome Centre for Infectious Diseases Research in Africa and Department of Medicine, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Republic of South Africa
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Gerald Willimsky
- Cooperation Unit for Experimental and Translational Cancer Immunology, Institute of Immunology (Charité - Universitätsmedizin Berlin) and German Cancer Research Center (DKFZ), Berlin, Germany
| | - James B. Wing
- WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Rieke Winkelmann
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Thomas H. Winkler
- Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Oliver F. Wirz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Alicia Wong
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Peter Wurst
- University Bonn, Medical Faculty, Bonn, Germany
| | - Jennie H. M. Yang
- Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institutes of Health Research Biomedical Research Centre at Guy’s and St. Thomas’ National Health Service, Foundation Trust and King’s College London, UK
| | - Juhao Yang
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Alice Yue
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Susanne Maria Ziegler
- Department of Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Christina Zielinski
- German Center for Infection Research (DZIF), Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
- TranslaTUM, Technical University of Munich, Munich, Germany
| | - Jakob Zimmermann
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
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Proportion of the CD19-Positive and CD19-Negative Lymphocytes and Monocytes within the Peripheral Blood Mononuclear Cell Set is Characteristic for Rheumatoid Arthritis. ACTA ACUST UNITED AC 2019; 55:medicina55100630. [PMID: 31554310 PMCID: PMC6843217 DOI: 10.3390/medicina55100630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 12/17/2022]
Abstract
Background and objectives: Composition of the peripheral blood (PB) cell populations and their activation state reflect the immune status of a patient. Rheumatoid arthritis (RA) is characterized by abnormal B- and T-cell functions. The objective of this study was to assess the profiles of the PB mononuclear cell (PBMC) populations in patients with rheumatoid and osteoarthritis (OA) in comparison with healthy control (HC) subjects in order to evaluate the PBMC profiles as a potential diagnostic characteristic in RA. The second aim was to assess the CCR1 and CCR2 expression on PB lymphocytes and correlate it with the plasma levels of matrix metallopeptidase 9 (MMP-9), IL-17F, TNF-α, IL-6, and IL-10. Materials and Methods: The frequency and phenotype, including CCR1 and CCR2, of the PBMC populations (monocytes, CD19+B cells, and T/NK lymphocytes) in RA (n = 15) and OA (n = 10) patients and HC (n = 12) were analyzed by five-color flow cytometry. DNA of the viruses, HHV-6, HHV-7, and B19, in the whole blood and cell-free plasma, were assessed by nested-polymerase chain reaction (PCR). Results: Active persistent or acute infections, caused by HHV-6, HHV-7, or B19, were not detected in patients of this study. Both CCR1 and CCR2 were determined on the PB B and T/NK lymphocytes in several RA and OA patients and HCs. However, in patients, the frequency of the CCR1-positive T/NK lymphocytes showed a weak negative correlation with the IL-10 level, while the frequency of the CCR2-positive B cells correlated positively with the level of IL-6. Statistically significant differences in the proportions of the CD19-positive and CD19-negative lymphocyte and monocyte subsets within the PBMC set were determined between RA and OA patients and HC adults. Conclusions: We have shown in our pilot study with rather small cohorts of patients that the PBMC-population profiles were very consistent, and statistically significantly differed between RA and OA patients and HC subjects.
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Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating. PLoS One 2019; 14:e0219892. [PMID: 31356641 PMCID: PMC6663000 DOI: 10.1371/journal.pone.0219892] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/04/2019] [Indexed: 01/22/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis is able to form endospores which have a variety of biotechnological applications. Due to this ability, B. subtilis is as well a model organism for cellular differentiation processes. Sporulating cultures of B. subtilis form sub-populations which include vegetative cells, sporulating cells and spores. In order to readily and rapidly quantify spore formation we employed flow cytometric and fluorescence activated cell sorting techniques in combination with nucleic acid fluorescent staining in order to investigate the distribution of sporulating cultures on a single cell level. Automated gating procedures using Gaussian mixture modeling (GMM) were employed to avoid subjective gating and allow for the simultaneous measurement of controls. We utilized the presented method for monitoring sporulation over time in germination deficient strains harboring different genome modifications. A decrease in the sporulation efficiency of strain Bs02018, utilized for the display of sfGFP on the spores surface was observed. On the contrary, a double knock-out mutant of the phosphatase gene encoding Spo0E and of the spore killing factor SkfA (Bs02025) exhibited the highest sporulation efficiency, as within 24 h of cultivation in sporulation medium, cultures of BS02025 already consisted of 80% spores as opposed to 18% for the control strain. We confirmed the identity of the different subpopulations formed during sporulation by employing sorting and microscopy.
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Burel JG, Pomaznoy M, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Jung Y, Babor M, Schulten V, Seumois G, Greenbaum JA, Premawansa S, Premawansa G, Wijewickrama A, Vidanagama D, Gunasena B, Tippalagama R, deSilva AD, Gilman RH, Saito M, Taplitz R, Ley K, Vijayanand P, Sette A, Peters B. Circulating T cell-monocyte complexes are markers of immune perturbations. eLife 2019; 8:46045. [PMID: 31237234 PMCID: PMC6592685 DOI: 10.7554/elife.46045] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022] Open
Abstract
Our results highlight for the first time that a significant proportion of cell doublets in flow cytometry, previously believed to be the result of technical artifacts and thus ignored in data acquisition and analysis, are the result of biological interaction between immune cells. In particular, we show that cell:cell doublets pairing a T cell and a monocyte can be directly isolated from human blood, and high resolution microscopy shows polarized distribution of LFA1/ICAM1 in many doublets, suggesting in vivo formation. Intriguingly, T cell-monocyte complex frequency and phenotype fluctuate with the onset of immune perturbations such as infection or immunization, reflecting expected polarization of immune responses. Overall these data suggest that cell doublets reflecting T cell-monocyte in vivo immune interactions can be detected in human blood and that the common approach in flow cytometry to avoid studying cell:cell complexes should be re-visited.
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Affiliation(s)
- Julie G Burel
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | - Mikhail Pomaznoy
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | | | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | | | - Yunmin Jung
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, United States
| | - Mariana Babor
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | - Veronique Schulten
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | - Gregory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States
| | - Jason A Greenbaum
- Bioinformatics core, La Jolla Institute for Immunology, La Jolla, United States
| | - Sunil Premawansa
- Department of Zoology and Environment Sciences, Science Faculty, University of Colombo, Colombo, Sri Lanka
| | | | | | | | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | | | - Aruna D deSilva
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States.,Genetech Research Institute, Colombo, Sri Lanka
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Baltimore, United States.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, United States
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, United States.,Department of Bioengineering, University of California, San Diego, La Jolla, United States
| | - Pandurangan Vijayanand
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States.,Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States.,Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, United States.,Department of Medicine, University of California, San Diego, La Jolla, United States
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Dysregulation of a specific immune-related network of genes biologically defines a subset of schizophrenia. Transl Psychiatry 2019; 9:156. [PMID: 31150013 PMCID: PMC6544656 DOI: 10.1038/s41398-019-0486-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/22/2019] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Currently, the clinical diagnosis of schizophrenia relies solely on self-reporting and clinical interview, and likely comprises heterogeneous biological subsets. Such subsets may be defined by an underlying biology leading to solid biomarkers. A transgenic rat model modestly overexpressing the full-length, non-mutant Disrupted-in-Schizophrenia 1 (DISC1) protein (tgDISC1 rat) was generated that defines such a subset, inspired by our previous identification of insoluble DISC1 protein in post mortem brains from patients with chronic mental illness. Besides specific phenotypes such as DISC1 protein pathology, abnormal dopamine homeostasis, and changes in neuroanatomy and behavior, this animal model also shows subtle disturbances in overarching signaling pathways relevant for schizophrenia. In a reverse-translational approach, assuming that both the animal model and a patient subset share common disturbed signaling pathways, we identified differentially expressed transcripts from peripheral blood mononuclear cells of tgDISC1 rats that revealed an interconnected set of dysregulated genes, led by decreased expression of regulator of G-protein signaling 1 (RGS1), chemokine (C-C) ligand 4 (CCL4), and other immune-related transcripts enriched in T-cell and macrophage signaling and converging in one module after weighted gene correlation network analysis. Testing expression of this gene network in two independent cohorts of patients with schizophrenia versus healthy controls (n = 16/50 and n = 54/45) demonstrated similar expression changes. The two top markers RGS1 and CCL4 defined a subset of 27% of patients with 97% specificity. Thus, analogous aberrant signaling pathways can be identified by a blood test in an animal model and a corresponding schizophrenia patient subset, suggesting that in this animal model tailored pharmacotherapies for this patient subset could be achieved.
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Cardoso CC, Santos-Silva MC. Eight-color panel for immune phenotype monitoring by flow cytometry. J Immunol Methods 2019; 468:40-48. [DOI: 10.1016/j.jim.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/13/2019] [Accepted: 03/22/2019] [Indexed: 12/24/2022]
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Lee H, Sun Y, Patti-Diaz L, Hedrick M, Ehrhardt AG. High-Throughput Analysis of Clinical Flow Cytometry Data by Automated Gating. Bioinform Biol Insights 2019; 13:1177932219838851. [PMID: 30983860 PMCID: PMC6448119 DOI: 10.1177/1177932219838851] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/13/2019] [Indexed: 11/30/2022] Open
Abstract
Advancements in flow cytometers with capability to measure 15 or more parameters have enabled us to characterize cell populations at unprecedented levels of detail. Beyond discovery research, there is now a growing demand to dive deeper into evaluating the immune response in clinical trials for immune modulating compounds. However, for high-volume, complex flow cytometry data generated in clinical trials, conventional manual gating remains the standard of practice. Traditional manual gating is resource intense and becomes a bottleneck and an impractical method to complete high volumes of flow cytometry data analysis. Current efforts to automate “manual gating” have shown that computational algorithms can facilitate the analysis of daunting multi-parameter data; however, a greater degree of precision in comparison with traditional manual gating is needed for wide-scale adoption of automated gating methods. In an effort to more closely follow the manual gating process, our automated gating pipeline was created to include negative controls (Fluorescence Minus One [FMO]) to enhance the reliability of gate placement. We demonstrate that use of an automated pipeline, heavily relying on FMO controls for population discrimination, can analyze multi-parameter, large-scale clinical datasets with comparable precision and accuracy to traditional manual gating.
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Affiliation(s)
- Hunjoong Lee
- Hunjoong Lee, Clinical Flow Cytometry, Translational Medicine, Bristol-Myers Squibb, Pennington, NJ 08534, USA.
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Staats J, Divekar A, McCoy JP, Maecker HT. Guidelines for Gating Flow Cytometry Data for Immunological Assays. Methods Mol Biol 2019; 2032:81-104. [PMID: 31522414 DOI: 10.1007/978-1-4939-9650-6_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
"Gating" refers to the selection of successive subpopulations of cells for analysis in flow cytometry. It is usually performed manually, based on expert knowledge of cell characteristics. However, there can be considerable disagreement in how gates should be applied, even between individuals experienced in the field. While clinical software often automates gating, and some guidelines do exist (especially for clinical assays), there are no comprehensive guidelines across the various types of immunological assays performed using flow cytometry. Here we attempt to provide such guidelines, focused on the most general and pervasive types of gates, why they are important, and what recommendations can be made regarding their use. We do so through the display of example data, collected by academic, government, and industry representatives. These guidelines should be of value to both novice and experienced flow cytometrists analyzing a wide variety of immunological assays.
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Affiliation(s)
- Janet Staats
- Duke Immune Profiling Core, Duke University Medical Center, Durham, NC, USA
| | - Anagha Divekar
- Department for Cellular Analysis, Biolegend, San Diego, CA, USA
| | | | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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Conrad VK, Dubay CJ, Malek M, Brinkman RR, Koguchi Y, Redmond WL. Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling. Cytometry A 2018; 95:183-191. [DOI: 10.1002/cyto.a.23664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Valerie K. Conrad
- Earle A. Chiles Research InstituteProvidence Portland Medical Center Portland Oregon
| | - Christopher J. Dubay
- Earle A. Chiles Research InstituteProvidence Portland Medical Center Portland Oregon
| | - Mehrnoush Malek
- Terry Fox LaboratoryBC Cancer Agency Vancouver British Columbia
| | - Ryan R. Brinkman
- Terry Fox LaboratoryBC Cancer Agency Vancouver British Columbia
- Department of Medical GeneticsUniversity of British Columbia Vancouver British Columbia
| | - Yoshinobu Koguchi
- Earle A. Chiles Research InstituteProvidence Portland Medical Center Portland Oregon
| | - William L. Redmond
- Earle A. Chiles Research InstituteProvidence Portland Medical Center Portland Oregon
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Cell-intrinsic regulation of peripheral memory-phenotype T cell frequencies. PLoS One 2018; 13:e0200227. [PMID: 30557341 PMCID: PMC6296671 DOI: 10.1371/journal.pone.0200227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/29/2018] [Indexed: 11/19/2022] Open
Abstract
Memory T and B lymphocyte numbers are thought to be regulated by recent and cumulative microbial exposures. We report here that memory-phenotype lymphocyte frequencies in B, CD4 and CD8 T-cells in 3-monthly serial bleeds from healthy young adult humans were relatively stable over a 1-year period, while Plasmablast frequencies were not, suggesting that recent environmental exposures affected steady state levels of recently activated but not of memory lymphocyte subsets. Frequencies of memory B and CD4 T cells were not correlated, suggesting that variation in them was unlikely to be determined by cumulative antigenic exposures. Immunophenotyping of adult siblings showed high concordance in memory, but not of recently activated lymphocyte subsets. To explore the possibility of cell-intrinsic regulation of T cell memory, we screened effector memory-phenotype T cell (TEM) frequencies in common independent inbred mice strains. Using two pairs from these strains that differed predominantly in either CD4 TEM and/or CD8 TEM frequencies, we constructed bi-parental bone marrow chimeras in F1 recipient mice, and found that memory T cell frequencies in recipient mice were determined by donor genotypes. Together, these data suggest cell-autonomous determination of memory T niche size, and suggest mechanisms maintaining immune variability.
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Tian Y, da Silva Antunes R, Sidney J, Lindestam Arlehamn CS, Grifoni A, Dhanda SK, Paul S, Peters B, Weiskopf D, Sette A. A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis. Front Immunol 2018; 9:2778. [PMID: 30555469 PMCID: PMC6281829 DOI: 10.3389/fimmu.2018.02778] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023] Open
Abstract
In the present review, we summarize work from our as well as other groups related to the characterization of bacterial T cell epitopes, with a specific focus on two important pathogens, namely, Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), and Bordetella pertussis (BP), the bacterium that causes whooping cough. Both bacteria and their associated diseases are of large societal significance. Although vaccines exist for both pathogens, their efficacy is incomplete. It is widely thought that defects and/or alteration in T cell compartments are associated with limited vaccine effectiveness. As discussed below, a full genome-wide map was performed in the case of Mtb. For BP, our focus has thus far been on the antigens contained in the acellular vaccine; a full genome-wide screen is in the planning stage. Nevertheless, the sum-total of the results in the two different bacterial systems allows us to exemplify approaches and techniques that we believe are generally applicable to the mapping and characterization of human immune responses to bacterial pathogens. Finally, we add, as a disclaimer, that this review by design is focused on the work produced by our laboratory as an illustration of approaches to the study of T cell responses to Mtb and BP, and is not meant to be comprehensive, nor to detract from the excellent work performed by many other groups.
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Affiliation(s)
- Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
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Olsen LR, Leipold MD, Pedersen CB, Maecker HT. The anatomy of single cell mass cytometry data. Cytometry A 2018; 95:156-172. [DOI: 10.1002/cyto.a.23621] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lars R. Olsen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Michael D. Leipold
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
| | - Christina B. Pedersen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
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Tompa A, Nilsson-Bowers A, Faresjö M. Subsets of CD4+, CD8+, and CD25hi Lymphocytes Are in General Not Influenced by Isolation and Long-Term Cryopreservation. THE JOURNAL OF IMMUNOLOGY 2018; 201:1799-1809. [DOI: 10.4049/jimmunol.1701409] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
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