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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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2
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Malviya M, Aretz Z, Molvi Z, Lee J, Pierre S, Wallisch P, Dao T, Scheinberg DA. Challenges and solutions for therapeutic TCR-based agents. Immunol Rev 2023; 320:58-82. [PMID: 37455333 PMCID: PMC11141734 DOI: 10.1111/imr.13233] [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: 05/30/2023] [Accepted: 06/18/2023] [Indexed: 07/18/2023]
Abstract
Recent development of methods to discover and engineer therapeutic T-cell receptors (TCRs) or antibody mimics of TCRs, and to understand their immunology and pharmacology, lag two decades behind therapeutic antibodies. Yet we have every expectation that TCR-based agents will be similarly important contributors to the treatment of a variety of medical conditions, especially cancers. TCR engineered cells, soluble TCRs and their derivatives, TCR-mimic antibodies, and TCR-based CAR T cells promise the possibility of highly specific drugs that can expand the scope of immunologic agents to recognize intracellular targets, including mutated proteins and undruggable transcription factors, not accessible by traditional antibodies. Hurdles exist regarding discovery, specificity, pharmacokinetics, and best modality of use that will need to be overcome before the full potential of TCR-based agents is achieved. HLA restriction may limit each agent to patient subpopulations and off-target reactivities remain important barriers to widespread development and use of these new agents. In this review we discuss the unique opportunities for these new classes of drugs, describe their unique antigenic targets, compare them to traditional antibody therapeutics and CAR T cells, and review the various obstacles that must be overcome before full application of these drugs can be realized.
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Affiliation(s)
- Manish Malviya
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Zita Aretz
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Zaki Molvi
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Jayop Lee
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Stephanie Pierre
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Tri-Institutional Medical Scientist Program, 1300 York Avenue, New York, NY 10021
| | - Patrick Wallisch
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
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3
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Zhang B, Upadhyay R, Hao Y, Samanovic MI, Herati RS, Blair JD, Axelrad J, Mulligan MJ, Littman DR, Satija R. Multimodal single-cell datasets characterize antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. Nat Immunol 2023; 24:1725-1734. [PMID: 37735591 PMCID: PMC10522491 DOI: 10.1038/s41590-023-01608-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023]
Abstract
The immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we used multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after immunization with the mRNA vaccine BNT162b2. Our data indicated distinct subpopulations of CD8+ T cells, which reliably appeared 28 days after prime vaccination. Using a suite of cross-modality integration tools, we defined their transcriptome, accessible chromatin landscape and immunophenotype, and we identified unique biomarkers within each modality. We further showed that this vaccine-induced population was SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we identified these CD8+ T cell populations in scRNA-seq datasets from COVID-19 patients and found that their relative frequency and differentiation outcomes were predictive of subsequent clinical outcomes.
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Affiliation(s)
- Bingjie Zhang
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Rabi Upadhyay
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Yuhan Hao
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - Ramin S Herati
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - John D Blair
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jordan Axelrad
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - Dan R Littman
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA.
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Rahul Satija
- New York Genome Center, New York, NY, USA.
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
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4
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Mun DG, Bhat FA, Ding H, Madden BJ, Natesampillai S, Badley AD, Johnson KL, Kelly RT, Pandey A. Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst 2023; 148:3466-3475. [PMID: 37395315 PMCID: PMC10370902 DOI: 10.1039/d3an00080j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/10/2023] [Indexed: 07/04/2023]
Abstract
Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Furthermore, trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated in data-dependent acquisition mode (DDA-PASEF) allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating the ion flux in TIMS affects the overall performance of proteome profiling. However, the effect of TIMS settings on the analysis of low-input samples has been less investigated. Thus, we sought to optimize the conditions of TIMS with regard to ion accumulation/ramp times and ion mobility range for low-input samples. We observed that an ion accumulation time of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 V s cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We used these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1116, and 1651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from a low number of cells was sufficient to delineate several essential metabolic pathways and the T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that such an approach could be applied to label-free analysis of single cells obtained from clinically relevant samples.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Firdous A Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | | | | | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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5
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Zhu Y, Yu X, Cheng G. Human skin bacterial microbiota homeostasis: A delicate balance between health and disease. MLIFE 2023; 2:107-120. [PMID: 38817619 PMCID: PMC10989898 DOI: 10.1002/mlf2.12064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/30/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2024]
Abstract
As the largest organ of the body, the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria. Furthermore, the skin bacterial microbiota plays a vital role in health and disease. Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases. In this review, we first provide an overview of research on skin bacterial microbiota and human health, including the composition of skin bacteria in a healthy state, as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens. We then discuss the diseases that result from skin microbial dysbiosis, including atopic dermatitis, common acne, chronic wounds, psoriasis, viral transmission, cutaneous lupus, cutaneous lymphoma, and hidradenitis suppurativa. Finally, we highlight the progress that utilizes skin microorganisms for disease therapeutics, such as bacteriotherapy and skin microbiome transplantation. A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.
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Affiliation(s)
- Yibin Zhu
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
| | - Xi Yu
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
| | - Gong Cheng
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
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6
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Yin H, Chu Y, Wang W, Zhang Z, Meng Z, Min Q. Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules. NANOSCALE 2023; 15:2529-2540. [PMID: 36688447 DOI: 10.1039/d2nr06020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.
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Affiliation(s)
- Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yanxin Chu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhen Meng
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
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7
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Zhang B, Upadhyay R, Hao Y, Samanovic MI, Herati RS, Blair J, Axelrad J, Mulligan MJ, Littman DR, Satija R. Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525203. [PMID: 36747786 PMCID: PMC9900816 DOI: 10.1101/2023.01.24.525203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The human immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we utilize multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after BNT162b2 immunization. Our data reveal distinct subpopulations of CD8 + T cells which reliably appear 28 days after prime vaccination (7 days post boost). Using a suite of cross-modality integration tools, we define their transcriptome, accessible chromatin landscape, and immunophenotype, and identify unique biomarkers within each modality. By leveraging DNA-oligo-tagged peptide-MHC multimers and T cell receptor sequencing, we demonstrate that this vaccine-induced population is SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we also identify these CD8 + populations in scRNA-seq datasets from COVID-19 patients and find that their relative frequency and differentiation outcomes are predictive of subsequent clinical outcomes. Our work contributes to our understanding of T cell immunity, and highlights the potential for integrative and multimodal analysis to characterize rare cell populations.
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Affiliation(s)
- Bingjie Zhang
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Cell Biology and Regenerative Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Rabi Upadhyay
- Department of Cell Biology and Regenerative Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Yuhan Hao
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Marie I. Samanovic
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - Ramin S. Herati
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - John Blair
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Jordan Axelrad
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Mark J. Mulligan
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
- New York University Langone Vaccine Center, New York, NY, USA
| | - Dan R. Littman
- Department of Cell Biology and Regenerative Medicine, New York University Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
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Lewis SA, Peters B. T-cell epitope discovery and single-cell technologies to advance food allergy research. J Allergy Clin Immunol 2023; 151:15-20. [PMID: 36411114 PMCID: PMC9825656 DOI: 10.1016/j.jaci.2022.10.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/13/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022]
Abstract
There is good evidence for a role of T cells in food allergy, but there is a lack of mechanistic understanding and phenotypic markers of the specific T cells contributing to pathology. Recent technologic advancements have allowed for a new experimental paradigm where we can find and pull out rare antigen-specific T cells and characterize them at the single-cell level. However, studies in infectious disease and broader allergy have shown that these techniques benefit greatly from precisely defined T-cell epitopes. Food allergens have fewer epitopes currently available, but it is growing and promises to overcome this gap. With growing use of this experimental design, it will be important to unbiasedly map T-cell phenotypes across food allergy and look for commonalities and contrasts to other allergic and infectious diseases. Once a pathologic phenotype for T cells has been established, the frequencies of these cells can be monitored with simpler techniques that could be applied to the clinic and used in diagnosis, prediction of treatment responsiveness, and discovery of targets for new treatments.
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Affiliation(s)
- Sloan A Lewis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, Calif
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, Calif; Department of Medicine, University of California San Diego, La Jolla, Calif.
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9
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Zhi Y, Li M, Lv G. Into the multi-omics era: Progress of T cells profiling in the context of solid organ transplantation. Front Immunol 2023; 14:1058296. [PMID: 36798139 PMCID: PMC9927650 DOI: 10.3389/fimmu.2023.1058296] [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: 09/30/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
T cells are the common type of lymphocyte to mediate allograft rejection, remaining long-term allograft survival impeditive. However, the heterogeneity of T cells, in terms of differentiation and activation status, the effector function, and highly diverse T cell receptors (TCRs) have thus precluded us from tracking these T cells and thereby comprehending their fate in recipients due to the limitations of traditional detection approaches. Recently, with the widespread development of single-cell techniques, the identification and characterization of T cells have been performed at single-cell resolution, which has contributed to a deeper comprehension of T cell heterogeneity by relevant detections in a single cell - such as gene expression, DNA methylation, chromatin accessibility, surface proteins, and TCR. Although these approaches can provide valuable insights into an individual cell independently, a comprehensive understanding can be obtained when applied joint analysis. Multi-omics techniques have been implemented in characterizing T cells in health and disease, including transplantation. This review focuses on the thesis, challenges, and advances in these technologies and highlights their application to the study of alloreactive T cells to improve the understanding of T cell heterogeneity in solid organ transplantation.
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Affiliation(s)
- Yao Zhi
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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Pan M, Li B. T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies. eLife 2022; 11:e81952. [PMID: 36350695 PMCID: PMC9683788 DOI: 10.7554/elife.81952] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022] Open
Abstract
T cells are potent at eliminating pathogens and playing a crucial role in the adaptive immune response. T cell receptor (TCR) convergence describes T cells that share identical TCRs with the same amino acid sequences but have different DNA sequences due to codon degeneracy. We conducted a systematic investigation of TCR convergence using single-cell immune profiling and bulk TCRβ-sequence (TCR-seq) data obtained from both mouse and human samples and uncovered a strong link between antigen-specificity and convergence. This association was stronger than T cell expansion, a putative indicator of antigen-specific T cells. By using flow-sorted tetramer+ single T cell data, we discovered that convergent T cells were enriched for a neoantigen-specific CD8+ effector phenotype in the tumor microenvironment. Moreover, TCR convergence demonstrated better prediction accuracy for immunotherapy response than the existing TCR repertoire indexes. In conclusion, convergent T cells are likely to be antigen-specific and might be a novel prognostic biomarker for anti-cancer immunotherapy.
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Affiliation(s)
- Mingyao Pan
- Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical CenterDallasUnited States
| | - Bo Li
- Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical CenterDallasUnited States
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11
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Suliman S, Kjer-Nielsen L, Iwany SK, Lopez Tamara K, Loh L, Grzelak L, Kedzierska K, Ocampo TA, Corbett AJ, McCluskey J, Rossjohn J, León SR, Calderon R, Lecca-Garcia L, Murray MB, Moody DB, Van Rhijn I. Dual TCR-α Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1389-1395. [PMID: 35246495 PMCID: PMC9359468 DOI: 10.4049/jimmunol.2100275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 01/12/2022] [Indexed: 05/20/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRα-chain that uses T cell receptor α-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), we performed bulk TCRα- and TCRβ-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRα-chains also coexpressed an invariant MAIT TCRα-chain. Transfection of each non-TRAV1-2 TCRα-chain with the TCRβ-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα-chain expression in human T cells and competition for the endogenous β-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity.
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Affiliation(s)
- Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, CA
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sarah K Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Kattya Lopez Tamara
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Socios en Salud Sucursal Perú, Lima, Peru
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tonatiuh A Ocampo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- 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
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; and
| | - D Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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12
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Fahad AS, Chung CY, Lopez Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour Jr HH, Price DA, DeKosky BJ. Immortalization and functional screening of natively paired human T cell receptor repertoires. Protein Eng Des Sel 2022; 35:gzab034. [PMID: 35174859 PMCID: PMC9005053 DOI: 10.1093/protein/gzab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale, and to exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of disease-relevant antigen interactions with human TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Cheng-Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sheila N Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry H Balfour Jr
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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13
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Cossarizza A, Chang HD, Radbruch A, Abrignani S, Addo R, Akdis M, Andrä I, Andreata F, Annunziato F, Arranz E, Bacher P, Bari S, Barnaba V, Barros-Martins J, Baumjohann D, Beccaria CG, Bernardo D, Boardman DA, Borger J, Böttcher C, Brockmann L, Burns M, Busch DH, Cameron G, Cammarata I, Cassotta A, Chang Y, Chirdo FG, Christakou E, Čičin-Šain L, Cook L, Corbett AJ, Cornelis R, Cosmi L, Davey MS, De Biasi S, De Simone G, del Zotto G, Delacher M, Di Rosa F, Di Santo J, Diefenbach A, Dong J, Dörner T, Dress RJ, Dutertre CA, Eckle SBG, Eede P, Evrard M, Falk CS, Feuerer M, Fillatreau S, Fiz-Lopez A, Follo M, Foulds GA, Fröbel J, Gagliani N, Galletti G, Gangaev A, Garbi N, Garrote JA, Geginat J, Gherardin NA, Gibellini L, Ginhoux F, Godfrey DI, Gruarin P, Haftmann C, Hansmann L, Harpur CM, Hayday AC, Heine G, Hernández DC, Herrmann M, Hoelsken O, Huang Q, Huber S, Huber JE, Huehn J, Hundemer M, Hwang WYK, Iannacone M, Ivison SM, Jäck HM, Jani PK, Keller B, Kessler N, Ketelaars S, Knop L, Knopf J, Koay HF, Kobow K, Kriegsmann K, Kristyanto H, Krueger A, Kuehne JF, Kunze-Schumacher H, Kvistborg P, Kwok I, Latorre D, Lenz D, Levings MK, Lino AC, Liotta F, Long HM, Lugli E, MacDonald KN, Maggi L, Maini MK, Mair F, Manta C, Manz RA, Mashreghi MF, Mazzoni A, McCluskey J, Mei HE, Melchers F, Melzer S, Mielenz D, Monin L, Moretta L, Multhoff G, Muñoz LE, Muñoz-Ruiz M, Muscate F, Natalini A, Neumann K, Ng LG, Niedobitek A, Niemz J, Almeida LN, Notarbartolo S, Ostendorf L, Pallett LJ, Patel AA, Percin GI, Peruzzi G, Pinti M, Pockley AG, Pracht K, Prinz I, Pujol-Autonell I, Pulvirenti N, Quatrini L, Quinn KM, Radbruch H, Rhys H, Rodrigo MB, Romagnani C, Saggau C, Sakaguchi S, Sallusto F, Sanderink L, Sandrock I, Schauer C, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schober K, Schoen J, Schuh W, Schüler T, Schulz AR, Schulz S, Schulze J, Simonetti S, Singh J, Sitnik KM, Stark R, Starossom S, Stehle C, Szelinski F, Tan L, Tarnok A, Tornack J, Tree TIM, van Beek JJP, van de Veen W, van Gisbergen K, Vasco C, Verheyden NA, von Borstel A, Ward-Hartstonge KA, Warnatz K, Waskow C, Wiedemann A, Wilharm A, Wing J, Wirz O, Wittner J, Yang JHM, Yang J. Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). Eur J Immunol 2021; 51:2708-3145. [PMID: 34910301 PMCID: PMC11115438 DOI: 10.1002/eji.202170126] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers.
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Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Institute for Biotechnology, Technische Universität, Berlin, Germany
| | - Andreas Radbruch
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sergio Abrignani
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Richard Addo
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Eduardo Arranz
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Sudipto Bari
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | | | - Dirk Baumjohann
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Cristian G. Beccaria
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - David Bernardo
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Dominic A. Boardman
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Jessica Borger
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Chotima Böttcher
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leonie Brockmann
- Department of Microbiology & Immunology, Columbia University, New York City, USA
| | - Marie Burns
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Dirk H. Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Garth Cameron
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Yinshui Chang
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fernando Gabriel Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos - IIFP (UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Eleni Christakou
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Laura Cook
- BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Cornelis
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Martin S. Davey
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Gabriele De Simone
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Michael Delacher
- Institute for Immunology, University Medical Center Mainz, Mainz, Germany
- Research Centre for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - James Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France
- Inserm U1223, Paris, France
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Jun Dong
- Cell Biology, German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
| | - Thomas Dörner
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Regine J. Dress
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charles-Antoine Dutertre
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Pascale Eede
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Christine S. Falk
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Markus Feuerer
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Simon Fillatreau
- Institut Necker Enfants Malades, INSERM U1151-CNRS, UMR8253, Paris, France
- Université de Paris, Paris Descartes, Faculté de Médecine, Paris, France
- AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - Aida Fiz-Lopez
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Marie Follo
- Department of Medicine I, Lighthouse Core Facility, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gemma A. Foulds
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Julia Fröbel
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Nicola Gagliani
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Germany
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalio Garbi
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - José Antonio Garrote
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Laboratory of Molecular Genetics, Servicio de Análisis Clínicos, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Jens Geginat
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Paola Gruarin
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Leo Hansmann
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin (CVK), Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
| | - Christopher M. Harpur
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Adrian C. Hayday
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Guido Heine
- Division of Allergy, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniela Carolina Hernández
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Oliver Hoelsken
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Qing Huang
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Samuel Huber
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johanna E. Huber
- Institute for Immunology, Biomedical Center, Faculty of Medicine, 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
| | - William Y. K. Hwang
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
- Executive Offices, National Cancer Centre Singapore, Singapore
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - 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, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Peter K. Jani
- German Rheumatism Research Center Berlin (DRFZ), Berlin, 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
| | - Nina Kessler
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Steven Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Laura Knop
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Jasmin Knopf
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - H. Kristyanto
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jenny F. Kuehne
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Daniel Lenz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - 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
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Heather M. Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Katherine N. MacDonald
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, Canada
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mala K. Maini
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Calin Manta
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Rudolf Armin Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | | | - 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, Melbourne, Victoria, Australia
| | - Henrik E. Mei
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Fritz Melchers
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, Leipzig University, Härtelstr.16, −18, Leipzig, 04107, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Leticia Monin
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Gabriele Multhoff
- Radiation Immuno-Oncology Group, Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
- Department of Radiation Oncology, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | - Luis Enrique Muñoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Muscate
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lai Guan Ng
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Jana Niemz
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Samuele Notarbartolo
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Lennard Ostendorf
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura J. Pallett
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Amit A. Patel
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Gulce Itir Percin
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Giovanna Peruzzi
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), 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, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Katharina Pracht
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irma Pujol-Autonell
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Peter Gorer Department of Immunobiology, King’s College London, London, UK
| | - Nadia Pulvirenti
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Linda Quatrini
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Kylie M. Quinn
- School of Biomedical and Health Sciences, RMIT University, Bundorra, 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, Berlin, Germany
| | - Hefin Rhys
- Flow Cytometry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Maria B. Rodrigo
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Chiara Romagnani
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Lieke Sanderink
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Christine Schauer
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, 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
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Germany
| | - Janina Schoen
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Axel R. Schulz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Schulze
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sonia Simonetti
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Jeeshan Singh
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Katarzyna M. Sitnik
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Regina Stark
- Charité Universitätsmedizin Berlin – BIH Center for Regenerative Therapies, Berlin, Germany
- Sanquin Research – Adaptive Immunity, Amsterdam, The Netherlands
| | - Sarah Starossom
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina Stehle
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Franziska Szelinski
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Leonard Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Attila Tarnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Department of Precision Instrument, Tsinghua University, Beijing, China
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Julia Tornack
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Timothy I. M. Tree
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Jasper J. P. van Beek
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | | | - Chiara Vasco
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Nikita A. Verheyden
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anouk von Borstel
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kirsten A. Ward-Hartstonge
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - 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
| | - Claudia Waskow
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Medicine III, Technical University Dresden, Dresden, Germany
| | - Annika Wiedemann
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anneke Wilharm
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - James Wing
- Immunology Frontier Research Center, Osaka University, Japan
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jens Wittner
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Jennie H. M. Yang
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Juhao Yang
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Fu J, Khosravi-Maharlooei M, Sykes M. High Throughput Human T Cell Receptor Sequencing: A New Window Into Repertoire Establishment and Alloreactivity. Front Immunol 2021; 12:777756. [PMID: 34804070 PMCID: PMC8604183 DOI: 10.3389/fimmu.2021.777756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high throughput sequencing (HTS) of T cell receptors (TCRs) and in transcriptomic analysis, particularly at the single cell level, have opened the door to a new level of understanding of human immunology and immune-related diseases. In this article, we discuss the use of HTS of TCRs to discern the factors controlling human T cell repertoire development and how this approach can be used in combination with human immune system (HIS) mouse models to understand human repertoire selection in an unprecedented manner. An exceptionally high proportion of human T cells has alloreactive potential, which can best be understood as a consequence of the processes governing thymic selection. High throughput TCR sequencing has allowed assessment of the development, magnitude and nature of the human alloresponse at a new level and has provided a tool for tracking the fate of pre-transplant-defined donor- and host-reactive TCRs following transplantation. New insights into human allograft rejection and tolerance obtained with this method in combination with single cell transcriptional analyses are reviewed here.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
- Department of Surgery, Columbia University, New York, NY, United States
- Department of Microbiology & Immunology, Columbia University, New York, NY, United States
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15
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Sun Q, Melino G, Amelio I, Jiang J, Wang Y, Shi Y. Recent advances in cancer immunotherapy. Discov Oncol 2021; 12:27. [PMID: 35201440 PMCID: PMC8777500 DOI: 10.1007/s12672-021-00422-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022] Open
Abstract
Cancer immunotherapy represents a major advance in the cure of cancer following the dramatic advancements in the development and refinement of chemotherapies and radiotherapies. In the recent decades, together with the development of early diagnostic techniques, immunotherapy has significantly contributed to improving the survival of cancer patients. The immune-checkpoint blockade agents have been proven effective in a significant fraction of standard therapy refractory patients. Importantly, recent advances are providing alternative immunotherapeutic tools that could help overcome their limitations. In this mini review, we provide an overview on the main steps of the discovery of classic immune-checkpoint blockade agents and summarise the most recent development of novel immunotherapeutic strategies, such as tumour antigens, bispecific antibodies and TCR-engineered T cells.
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Affiliation(s)
- Qiang Sun
- Laboratory of Cell Engineering, Institute of Biotechnology, Beijing, China
- Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, Beijing, China
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
- DZNE German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Jingting Jiang
- The Third Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, 199 Renai Road, Suzhou, 215123 Jiangsu China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031 China
| | - Yufang Shi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
- The Third Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, 199 Renai Road, Suzhou, 215123 Jiangsu China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031 China
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16
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Lentiviral Vectors for T Cell Engineering: Clinical Applications, Bioprocessing and Future Perspectives. Viruses 2021; 13:v13081528. [PMID: 34452392 PMCID: PMC8402758 DOI: 10.3390/v13081528] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
Lentiviral vectors have played a critical role in the emergence of gene-modified cell therapies, specifically T cell therapies. Tisagenlecleucel (Kymriah), axicabtagene ciloleucel (Yescarta) and most recently brexucabtagene autoleucel (Tecartus) are examples of T cell therapies which are now commercially available for distribution after successfully obtaining EMA and FDA approval for the treatment of blood cancers. All three therapies rely on retroviral vectors to transduce the therapeutic chimeric antigen receptor (CAR) into T lymphocytes. Although these innovations represent promising new therapeutic avenues, major obstacles remain in making them readily available tools for medical care. This article reviews the biological principles as well as the bioprocessing of lentiviral (LV) vectors and adoptive T cell therapy. Clinical and engineering successes, shortcomings and future opportunities are also discussed. The development of Good Manufacturing Practice (GMP)-compliant instruments, technologies and protocols will play an essential role in the development of LV-engineered T cell therapies.
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Liu R, Jiang W, Mellins ED. Yeast display of MHC-II enables rapid identification of peptide ligands from protein antigens (RIPPA). Cell Mol Immunol 2021; 18:1847-1860. [PMID: 34117370 PMCID: PMC8193015 DOI: 10.1038/s41423-021-00717-5] [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: 11/24/2020] [Accepted: 05/25/2021] [Indexed: 11/12/2022] Open
Abstract
CD4+ T cells orchestrate adaptive immune responses via binding of antigens to their receptors through specific peptide/MHC-II complexes. To study these responses, it is essential to identify protein-derived MHC-II peptide ligands that constitute epitopes for T cell recognition. However, generating cells expressing single MHC-II alleles and isolating these proteins for use in peptide elution or binding studies is time consuming. Here, we express human MHC alleles (HLA-DR4 and HLA-DQ6) as native, noncovalent αβ dimers on yeast cells for direct flow cytometry-based screening of peptide ligands from selected antigens. We demonstrate rapid, accurate identification of DQ6 ligands from pre-pro-hypocretin, a narcolepsy-related immunogenic target. We also identify 20 DR4-binding SARS-CoV-2 spike peptides homologous to SARS-CoV-1 epitopes, and one spike peptide overlapping with the reported SARS-CoV-2 epitope recognized by CD4+ T cells from unexposed individuals carrying DR4 subtypes. Our method is optimized for immediate application upon the emergence of novel pathogens.
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Affiliation(s)
- Rongzeng Liu
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Immunology, Henan University of Science and Technology School of Medicine, Luoyang, China
| | - Wei Jiang
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Elizabeth D Mellins
- Department of Pediatrics-Human Gene Therapy, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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18
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High-throughput and single-cell T cell receptor sequencing technologies. Nat Methods 2021; 18:881-892. [PMID: 34282327 PMCID: PMC9345561 DOI: 10.1038/s41592-021-01201-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)-antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity.
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Weider T, Richardson SJ, Morgan NG, Paulsen TH, Dahl-Jørgensen K, Hammerstad SS. HLA Class I Upregulation and Antiviral Immune Responses in Graves Disease. J Clin Endocrinol Metab 2021; 106:e1763-e1774. [PMID: 33367784 PMCID: PMC7993595 DOI: 10.1210/clinem/dgaa958] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/25/2022]
Abstract
CONTEXT The origin of Graves disease (GD) remains elusive. However, evidence of an association between GD and viral infections is emerging. Human leukocyte antigen (HLA) class I presents viral antigens to circulating immune cells and plays a crucial role in the defense against viral infections. OBJECTIVE This work aimed to investigate HLA class I expression, enterovirus presence, and the viral immune response proteins signal transducer and activation of transcription 1 (STAT1) and protein kinase R (PKR) in thyroid tissue from GD patients. METHODS We collected thyroid tissue from core needle biopsies or surgical specimens from 48 GD patients and 24 controls. Standard immunohistochemistry was used to detect HLA class I and enteroviral capsid protein 1 (VP1) on formalin-fixed and paraffin-embedded tissue. STAT1 and PKR were examined by combined immunofluorescence staining. HLA class I expression score was the main outcome measure. RESULTS The HLA class I expression score, which takes both proportion and intensity of immunostaining into account, was significantly higher in GD patients (3.1 ± 3.3) than in controls (0.5 ± 0.9) (P < .001). Significantly more VP1 positive thyroid cells were found GD samples (50.1 ± 30.5%) than in controls (14.9 ± 10.5%) (P < .001). STAT1 and HLA class I were found within the same thyroid cells and PKR and VP1 were also colocalized within thyroid cells. CONCLUSION HLA class I is upregulated in GD and enterovirus protein is prevalent in thyroid tissue. The colocalization of HLA class I with STAT1 and VP1 with PKR indicates an antiviral tissue response. These findings support the concept of a link between viral infections and GD.
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Affiliation(s)
- Therese Weider
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- The University of Oslo, Faculty of Medicine, Oslo, Norway
- Correspondence: Therese Weider, MD, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, P.O. Box 4950 Nydalen, 0424 Oslo, Norway.
| | - Sarah J Richardson
- Islet Biology Exeter, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, UK
| | - Noel G Morgan
- Islet Biology Exeter, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, UK
| | - Trond H Paulsen
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Oslo, Norway
| | - Knut Dahl-Jørgensen
- The University of Oslo, Faculty of Medicine, Oslo, Norway
- Department of Pediatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Sara Salehi Hammerstad
- Department of Pediatric Medicine, Oslo University Hospital, Oslo, Norway
- The Specialist Center Pilestredet Park, Oslo, Norway
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ApoB-Specific CD4 + T Cells in Mouse and Human Atherosclerosis. Cells 2021; 10:cells10020446. [PMID: 33669769 PMCID: PMC7922692 DOI: 10.3390/cells10020446] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/11/2022] Open
Abstract
Atherosclerosis is a chronic inflammatory condition of the arterial wall that leads to the formation of vessel-occluding plaques within the subintimal space of middle-sized and larger arteries. While traditionally understood as a myeloid-driven lipid-storage disease, growing evidence suggests that the accumulation of low-density lipoprotein cholesterol (LDL-C) ignites an autoimmune response with CD4+ T-helper (TH) cells that recognize self-peptides from Apolipoprotein B (ApoB), the core protein of LDL-C. These autoreactive CD4+ T cells home to the atherosclerotic plaque, clonally expand, instruct other cells in the plaque, and induce clinical plaque instability. Recent developments in detecting antigen-specific cells at the single cell level have demonstrated that ApoB-reactive CD4+ T cells exist in humans and mice. Their phenotypes and functions deviate from classical immunological concepts of distinct and terminally differentiated TH immunity. Instead, ApoB-specific CD4+ T cells have a highly plastic phenotype, can acquire several, partially opposing and mixed transcriptional programs simultaneously, and transit from one TH subset into another over time. In this review, we highlight adaptive immune mechanisms in atherosclerosis with a focus on CD4+ T cells, introduce novel technologies to detect ApoB-specific CD4+ T cells at the single cell level, and discuss the potential impact of ApoB-driven autoimmunity in atherosclerosis.
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21
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The Potential of T Cell Factor 1 in Sustaining CD8 + T Lymphocyte-Directed Anti-Tumor Immunity. Cancers (Basel) 2021; 13:cancers13030515. [PMID: 33572793 PMCID: PMC7866257 DOI: 10.3390/cancers13030515] [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: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The transcription factor T cell factor 1 (TCF1), encoded by the TCF7 gene, is a key regulator of T-cell fate, which is known to promote T cell proliferation and establish T cell stemness. Importantly, increasing evidence has demonstrated that TCF1 is a critical determinant of the success of anti-tumor immunotherapy, implicating that TCF1 is a promising biomarker and therapeutic target in cancer. In recent years, new findings have emerged to provide a clearer view of TCF1 and its role in T cell biology. In this review, we aim to provide a comprehensive outline of the most recent literature on the role of TCF1 in T cell development and to discuss the potential of TCF1 in sustaining CD8+ T lymphocyte-directed anti-tumor immunity. Abstract T cell factor 1 (TCF1) is a transcription factor that has been highlighted to play a critical role in the promotion of T cell proliferation and maintenance of cell stemness in the embryonic and CD8+ T cell populations. The regulatory nature of TCF1 in CD8+ T cells is of great significance, especially within the context of T cell exhaustion, which is linked to the tumor and viral escape in pathological contexts. Indeed, inhibitory signals, such as programmed cell death 1 (PD-1) and cytotoxic-T-lymphocyte-associated protein 4 (CTLA-4), expressed on exhausted T lymphocytes (TEX), have become major therapeutic targets in immune checkpoint blockade (ICB) therapy. The significance of TCF1 in the sustenance of CTL-mediated immunity against pathogens and tumors, as well as its recently observed necessity for an effective anti-tumor immune response in ICB therapy, presents TCF1 as a potentially significant biomarker and/or therapeutic target for overcoming CD8+ T cell exhaustion and resistance to ICB therapy. In this review, we aim to outline the recent findings on the role of TCF1 in T cell development and discuss its implications in anti-tumor immunity.
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Bousbaine D, Ploegh HL. Antigen discovery tools for adaptive immune receptor repertoire research. ACTA ACUST UNITED AC 2020; 24:64-70. [PMID: 33195881 DOI: 10.1016/j.coisb.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adaptive immune system has evolved to recognize with incredible precision a large diversity of molecules. Innovations in high-throughput sequencing and bioinformatics have accelerated large-scale immune repertoire analyses and given us important insights into the behavior of the adaptive immune system. However, establishing a connection between receptor sequence and its antigen-specificity remains a challenge despite its central role in determining T and B cell fate. We discuss recent large-scale antigen discovery technologies which can be combined with adaptive immune receptor repertoire (AIRR) studies. We highlight important discoveries made using repertoire analyses in the field of host-microbe interactions.
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Affiliation(s)
- Djenet Bousbaine
- Department of Bioengineering and ChEM-H, Stanford University, Stanford CA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston MA, USA
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23
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The immune signatures of multiple sclerosis: Lessons from twin studies. Proc Natl Acad Sci U S A 2020; 117:24013-24015. [PMID: 32929024 DOI: 10.1073/pnas.2016711117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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24
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Hickey JW, Isser A, Salathe SF, Gee KM, Hsiao MH, Shaikh W, Uzoukwu NC, Bieler JG, Mao HQ, Schneck JP. Adaptive Nanoparticle Platforms for High Throughput Expansion and Detection of Antigen-Specific T cells. NANO LETTERS 2020; 20:6289-6298. [PMID: 32594746 PMCID: PMC8008984 DOI: 10.1021/acs.nanolett.0c01511] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
T cells are critical players in disease; yet, their antigen-specificity has been difficult to identify, as current techniques are limited in terms of sensitivity, throughput, or ease of use. To address these challenges, we increased the throughput and translatability of magnetic nanoparticle-based artificial antigen presenting cells (aAPCs) to enrich and expand (E+E) murine or human antigen-specific T cells. We streamlined enrichment, expansion, and aAPC production processes by enriching CD8+ T cells directly from unpurified immune cells, increasing parallel processing capacity of aAPCs in a 96-well plate format, and designing an adaptive aAPC that enables multiplexed aAPC construction for E+E and detection. We applied these adaptive platforms to process and detect CD8+ T cells specific for rare cancer neoantigens, commensal bacterial cross-reactive epitopes, and human viral and melanoma antigens. These innovations dramatically increase the multiplexing ability and decrease the barrier to adopt for investigating antigen-specific T cell responses.
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Affiliation(s)
- John W. Hickey
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Ariel Isser
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Sebastian F. Salathe
- Department of Biology, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Kayla M. Gee
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Meng-Hsuan Hsiao
- Department of Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Wasamah Shaikh
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nkechi C. Uzoukwu
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Joanie Glick Bieler
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Hai-Quan Mao
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan P. Schneck
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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Ni Q, Zhang J, Zheng Z, Chen G, Christian L, Grönholm J, Yu H, Zhou D, Zhuang Y, Li QJ, Wan Y. VisTCR: An Interactive Software for T Cell Repertoire Sequencing Data Analysis. Front Genet 2020; 11:771. [PMID: 32849789 PMCID: PMC7416706 DOI: 10.3389/fgene.2020.00771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Recent progress in high throughput sequencing technologies has provided an opportunity to probe T cell receptor (TCR) repertoire, bringing about an explosion of TCR sequencing data and analysis tools. For easier and more heuristic analysis TCR sequencing data, we developed a client-based HTML program (VisTCR). It has a data storage module and a data analysis module that integrate multiple cutting-edge analysis algorithms in a hierarchical fashion. Researchers can group and re-group samples for different analysis purposes by customized "Experiment Design File." Moreover, the VisTCR provides a user-friendly interactive interface, by all the TCR analysis methods and visualization results can be accessed and saved as tables or graphs in the process of analysis. The source code is freely available at https://github.com/qingshanni/VisTCR.
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Affiliation(s)
- Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Jianyang Zhang
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | | | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Laura Christian
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Juha Grönholm
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Daxue Zhou
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Qi-Jing Li
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
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Abstract
Tumor immunology is undergoing a renaissance due to the recent profound clinical successes of tumor immunotherapy. These advances have coincided with an exponential growth in the development of -omics technologies. Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature and consequences of interactions between tumors and the immune system. Such interactions are inherently multivariate, spanning multiple time and size scales, cell types, and organ systems, rendering systems biology approaches particularly amenable to their interrogation. While in its infancy, the field of 'Cancer Systems Immunology' has already influenced our understanding of tumor immunology and immunotherapy. As the field matures, studies will move beyond descriptive characterizations toward functional investigations of the emergent behavior that govern tumor-immune responses. Thus, Cancer Systems Immunology holds incredible promise to advance our ability to fight this disease.
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Affiliation(s)
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of MedicineStanfordUnited States
- Stanford Cancer Institute, Stanford UniversityStanfordUnited States
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Gerber HP, Sibener LV, Lee LJ, Gee MH. Identification of Antigenic Targets. Trends Cancer 2020; 6:299-318. [PMID: 32209445 DOI: 10.1016/j.trecan.2020.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 01/06/2020] [Indexed: 12/31/2022]
Abstract
The ideal cancer target antigen (Ag) is expressed at high copy numbers on neoplastic cells, absent on normal tissues, and contributes to the survival of cancer cells. Despite significant investments in the identification of cell surface Ags, there is a paucity of targets that meet such ideal cancer target criteria. Recent clinical trials in patients with cancer treated with immune checkpoint inhibitors (ICIs) indicate that cluster of differentiation (CD)8+ T cells, by means of their T cell receptors (TCRs) recognizing intracellular targets presented as peptides in the context of human leukocyte antigen (peptide-human leukocyte antigen complex; pHLA) molecules on tumor cells, can mediate deep and long-lasting antitumor responses in patients with solid tumors. Therefore, pHLA-target Ags may represent the long sought-after, ideal targets for solid tumor targeting by high-potency oncology compounds.
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Affiliation(s)
| | - Leah V Sibener
- 3T Biosciences, 1455 Adams Drive, Menlo Park, CA 94025, USA
| | - Luke J Lee
- 3T Biosciences, 1455 Adams Drive, Menlo Park, CA 94025, USA
| | - Marvin H Gee
- 3T Biosciences, 1455 Adams Drive, Menlo Park, CA 94025, USA
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Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol 2020; 16:87-99. [PMID: 31892734 PMCID: PMC7232872 DOI: 10.1038/s41584-019-0338-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
The cellular complexity and functional diversity of the human immune system necessitate the use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as rheumatic diseases, as well as other autoimmune and inflammatory disorders. Proteomic technologies that use elemental (heavy metal) reporter ions, such as mass cytometry (also known as CyTOF) and analogous high-dimensional imaging approaches (including multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC)), have been developed from their low-dimensional counterparts, flow cytometry and immunohistochemistry, to meet this need. A growing number of studies have been published that use these technologies to identify functional biomarkers and therapeutic targets in rheumatic diseases, but the full potential of their application to rheumatic disease research has yet to be fulfilled. This Review introduces the underlying technologies for high-dimensional immune monitoring and discusses aspects necessary for their successful implementation, including study design principles, analytical tools and future developments for the field of rheumatology.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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29
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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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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Aschauer C, Jelencsics K, Hu K, Heinzel A, Vetter J, Fraunhofer T, Schaller S, Winkler S, Pimenov L, Gualdoni GA, Eder M, Kainz A, Regele H, Reindl-Schwaighofer R, Oberbauer R. Next generation sequencing based assessment of the alloreactive T cell receptor repertoire in kidney transplant patients during rejection: a prospective cohort study. BMC Nephrol 2019; 20:346. [PMID: 31477052 PMCID: PMC6719356 DOI: 10.1186/s12882-019-1541-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/27/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Kidney transplantation is the optimal treatment in end stage renal disease but the allograft survival is still hampered by immune reactions against the allograft. This process is driven by the recognition of allogenic antigens presented to T-cells and their unique T-cell receptor (TCR) via the major histocompatibility complex (MHC), which triggers a complex immune response potentially leading to graft injury. Although the immune system and kidney transplantation have been studied extensively, the subtlety of alloreactive immune responses has impeded sensitive detection at an early stage. Next generation sequencing of the TCR enables us to monitor alloreactive T-cell populations and might thus allow the detection of early rejection events. METHODS/DESIGN This is a prospective cohort study designed to sequentially evaluate the alloreactive T cell repertoire after kidney transplantation. The TCR repertoire of patients who developed biopsy confirmed acute T cell mediated rejection (TCMR) will be compared to patients without rejection. To track the alloreactive subsets we will perform a mixed lymphocyte reaction between kidney donor and recipient before transplantation and define the alloreactive TCR repertoire by next generation sequencing of the complementary determining region 3 (CDR3) of the T cell receptor beta chain. After initial clonotype assembly from sequencing reads, TCR repertoire diversity and clonal expansion of T cells of kidney transplant recipients in periphery and kidney biopsy will be analyzed for changes after transplantation, during, prior or after a rejection. The goal of this study is to describe changes of overall T cell repertoire diversity, clonality in kidney transplant recipients, define and track alloreactive T cells in the posttransplant course and decipher patterns of expanded alloreactive T cells in acute cellular rejection to find an alternative monitoring to invasive and delayed diagnostic procedures. DISCUSSION Changes of the T cell repertoire and tracking of alloreactive T cell clones after combined bone marrow and kidney transplant has proven to be of potential use to monitor the donor directed alloresponse. The dynamics of the donor specific T cells in regular kidney transplant recipients in rejection still rests elusive and can give further insights in human alloresponse. TRIAL REGISTRATION Clinicaltrials.gov: NCT03422224 , registered February 5th 2018.
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 13, 4232, Hagenberg im Muehlkreis, Austria
| | - Thomas Fraunhofer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 13, 4232, Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 13, 4232, Hagenberg im Muehlkreis, Austria
| | - Stephan Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 13, 4232, Hagenberg im Muehlkreis, Austria
| | - Lisabeth Pimenov
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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32
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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33
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Wang C, Liu R, Hu J, Lv Y. Ratiometric DNA Walking Machine for Accurate and Amplified Bioassay. Chemistry 2019; 25:12270-12274. [DOI: 10.1002/chem.201903034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Chaoqun Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationCollege of ChemistrySichuan University Chengdu 610064 China
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationCollege of ChemistrySichuan University Chengdu 610064 China
| | - Jianyu Hu
- Key Laboratory of Green Chemistry and Technology of Ministry of EducationCollege of ChemistrySichuan University Chengdu 610064 China
| | - Yi Lv
- Analytical & Testing CenterSichuan University Chengdu 610064 P.R. China
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34
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Tinnevelt GH, van Staveren S, Wouters K, Wijnands E, Verboven K, Folcarelli R, Koenderman L, Buydens LMC, Jansen JJ. A novel data fusion method for the effective analysis of multiple panels of flow cytometry data. Sci Rep 2019; 9:6777. [PMID: 31043667 PMCID: PMC6494873 DOI: 10.1038/s41598-019-43166-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/17/2019] [Indexed: 11/09/2022] Open
Abstract
Multicolour flow cytometry (MFC) is used to measure multiple cellular markers at the single-cell level. Cellular markers may be coloured with different panels of fluorescently-labelled antibodies to enable cell identification or the detection of activated cells in pre-defined, ‘gated’ specific cell subsets. The number of markers that can be used per measurement is technologically limited however, requiring every panel to be analysed in a separate aliquot measurement. The combined analyses of these dedicated panels may enhance the predictive ability of these measurements and could enrich the interpretation of the immunological information. Here we introduce a fusion method for MFC data, based on DAMACY (Discriminant Analysis of Multi-Aspect Cytometry data), which can combine information from complementary panels. This approach leads to both enhanced predictions and clearer interpretations in comparison with the analysis of separate measurements. We illustrate this method using two datasets: the response of neutrophils evoked by a systemic endotoxin challenge and the activated immune status of the innate cells, T cells and B cells in obese versus lean individuals. The data fusion approach was able to detect cells that do not individually show a difference between clinical phenotypes but do play a role in combination with other cells.
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Affiliation(s)
- Gerjen H Tinnevelt
- Radboud University, Institute for Molecules and Materials (Analytical Chemistry), postvak 61, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands. .,TI-COAST, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Selma van Staveren
- TI-COAST, Science Park 904, 1098 XH, Amsterdam, The Netherlands.,Department of Respiratory Medicine and laboratory of translational immunology (LTI), University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, The Netherlands
| | - Kristiaan Wouters
- Deptartment of Internal Medicine Laboratory of Metabolism and Vascular Medicine, P.O. Box 616 (UNS50/14), 6200 MD, Maastricht, The Netherlands
| | - Erwin Wijnands
- Experimental Vascular Pathology group, P.O. Box 5800, 6202 MZ, Maastricht, The Netherlands
| | - Kenneth Verboven
- REVAL - Rehabilitation Research Center, Faculty of Rehabilitation Sciences, Hasselt University, Diepenbeek, Belgium.,BIOMED - Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rita Folcarelli
- Radboud University, Institute for Molecules and Materials (Analytical Chemistry), postvak 61, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
| | - Leo Koenderman
- Department of Respiratory Medicine and laboratory of translational immunology (LTI), University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, The Netherlands
| | - Lutgarde M C Buydens
- Radboud University, Institute for Molecules and Materials (Analytical Chemistry), postvak 61, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
| | - Jeroen J Jansen
- Radboud University, Institute for Molecules and Materials (Analytical Chemistry), postvak 61, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
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35
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Wong AYW, Fric J, Zelante T. Learning to control tissue damage while fighting Aspergillus. Med Mycol 2019; 57:S189-S195. [PMID: 30816972 DOI: 10.1093/mmy/myy053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/02/2018] [Indexed: 12/13/2022] Open
Abstract
Aspergillus moulds are increasingly being recognised as significant human pathogens that can cause life-threatening infections in the context of host immune dysregulation, particularly in the lung. It is now clear that there is a close relationship between infection susceptibility and the fine regulation of pulmonary immunity and inflammation. While the contribution of IL-17/Th17 responses to both physiological and pathological lung inflammation is now well established, the cellular interactions, soluble factors, and signalling pathways that determine Th17 cell responses to fungal infection remain unclear. Here, we identify potential key mediators of fungus-DC-T cell interactions in the respiratory tract, with a focus on the DC-derived cytokines thought to exert a major influence on generation of pathological Th17 cells. We review recent data indicating a crucial role for Aspergillus-induced autophagy in lung DCs on subsequent T-cell polarization and modulation of 'stemness', which appears critical for avoiding pathological lung inflammation and promoting disease resolution.
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Affiliation(s)
- Alicia Yoke Wei Wong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jan Fric
- Center for Translational Medicine, International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Teresa Zelante
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
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36
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Hickey JW, Schneck JP. Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles. J Vis Exp 2018. [PMID: 30507913 DOI: 10.3791/58640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We have developed a tool to both enrich and expand antigen-specific T cells. This can be helpful in cases such as to A) detect the existence of antigen-specific T cells, B) probe the dynamics of antigen-specific responses, C) understand how antigen-specific responses affect disease state such as autoimmunity, D) demystify heterogeneous responses for antigen-specific T cells, or E) utilize antigen-specific cells for therapy. The tool is based on a magnetic particle that we conjugate antigen-specific and T cell co-stimulatory signals, and that we term as artificial antigen presenting cells (aAPCs). Consequently, since the technology is simple to produce, it can easily be adopted by other laboratories; thus, our purpose here is to describe in detail the fabrication and subsequent use of the aAPCs. We explain how to attach antigen-specific and co-stimulatory signals to the aAPCs, how to utilize them to enrich for antigen-specific T cells, and how to expand antigen-specific T cells. Furthermore, we will highlight engineering design considerations based on experimental and biological information of our experience with characterizing antigen-specific T cells.
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Affiliation(s)
- John W Hickey
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University; Institute for Cell Engineering, School of Medicine, Johns Hopkins University; Institute for Nanobiotechnology, Johns Hopkins University; Department of Pathology, School of Medicine, Johns Hopkins University
| | - Jonathan P Schneck
- Institute for Cell Engineering, School of Medicine, Johns Hopkins University; Department of Pathology, School of Medicine, Johns Hopkins University;
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37
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Zhang SQ, Ma KY, Schonnesen AA, Zhang M, He C, Sun E, Williams CM, Jia W, Jiang N. High-throughput determination of the antigen specificities of T cell receptors in single cells. Nat Biotechnol 2018; 36:nbt.4282. [PMID: 30418433 PMCID: PMC6728224 DOI: 10.1038/nbt.4282] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 09/26/2018] [Indexed: 01/07/2023]
Abstract
We present tetramer-associated T-cell receptor sequencing (TetTCR-seq) to link T cell receptor (TCR) sequences to their cognate antigens in single cells at high throughput. Binding is determined using a library of DNA-barcoded antigen tetramers that is rapidly generated by in vitro transcription and translation. We applied TetTCR-seq to identify patterns in TCR cross-reactivity with cancer neoantigens and to rapidly isolate neoantigen-specific TCRs with no cross-reactivity to the wild-type antigen.
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Affiliation(s)
- Shu-Qi Zhang
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ke-Yue Ma
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Mingliang Zhang
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center of Diabetes, Shanghai 200233, China
| | - Chenfeng He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric Sun
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Chad M. Williams
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, China
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center of Diabetes, Shanghai 200233, China
| | - Ning Jiang
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
- LIVESTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
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38
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Schneidman-Duhovny D, Khuri N, Dong GQ, Winter MB, Shifrut E, Friedman N, Craik CS, Pratt KP, Paz P, Aswad F, Sali A. Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS One 2018; 13:e0206654. [PMID: 30399156 PMCID: PMC6219782 DOI: 10.1371/journal.pone.0206654] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 10/17/2018] [Indexed: 12/16/2022] Open
Abstract
Accurate predictions of T-cell epitopes would be useful for designing vaccines, immunotherapies for cancer and autoimmune diseases, and improved protein therapies. The humoral immune response involves uptake of antigens by antigen presenting cells (APCs), APC processing and presentation of peptides on MHC class II (pMHCII), and T-cell receptor (TCR) recognition of pMHCII complexes. Most in silico methods predict only peptide-MHCII binding, resulting in significant over-prediction of CD4 T-cell epitopes. We present a method, ITCell, for prediction of T-cell epitopes within an input protein antigen sequence for given MHCII and TCR sequences. The method integrates information about three stages of the immune response pathway: antigen cleavage, MHCII presentation, and TCR recognition. First, antigen cleavage sites are predicted based on the cleavage profiles of cathepsins S, B, and H. Second, for each 12-mer peptide in the antigen sequence we predict whether it will bind to a given MHCII, based on the scores of modeled peptide-MHCII complexes. Third, we predict whether or not any of the top scoring peptide-MHCII complexes can bind to a given TCR, based on the scores of modeled ternary peptide-MHCII-TCR complexes and the distribution of predicted cleavage sites. Our benchmarks consist of epitope predictions generated by this algorithm, checked against 20 peptide-MHCII-TCR crystal structures, as well as epitope predictions for four peptide-MHCII-TCR complexes with known epitopes and TCR sequences but without crystal structures. ITCell successfully identified the correct epitopes as one of the 20 top scoring peptides for 22 of 24 benchmark cases. To validate the method using a clinically relevant application, we utilized five factor VIII-specific TCR sequences from hemophilia A subjects who developed an immune response to factor VIII replacement therapy. The known HLA-DR1-restricted factor VIII epitope was among the six top-scoring factor VIII peptides predicted by ITCall to bind HLA-DR1 and all five TCRs. Our integrative approach is more accurate than current single-stage epitope prediction algorithms applied to the same benchmarks. It is freely available as a web server (http://salilab.org/itcell).
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
- * E-mail: (AS); (DS); (PP); (FA)
| | - Natalia Khuri
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
- Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA, United States of America
| | - Guang Qiang Dong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | - Michael B. Winter
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
- California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, CA, United States of America
| | - Kathleen P. Pratt
- Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Pedro Paz
- Bayer HealthCare, San Francisco, CA, United States of America
- * E-mail: (AS); (DS); (PP); (FA)
| | - Fred Aswad
- Bayer HealthCare, San Francisco, CA, United States of America
- * E-mail: (AS); (DS); (PP); (FA)
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
- Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA, United States of America
- * E-mail: (AS); (DS); (PP); (FA)
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39
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Hickey JW, Isser AY, Vicente FP, Warner SB, Mao HQ, Schneck JP. Efficient magnetic enrichment of antigen-specific T cells by engineering particle properties. Biomaterials 2018; 187:105-116. [PMID: 30312851 DOI: 10.1016/j.biomaterials.2018.09.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022]
Abstract
Magnetic particles can enrich desired cell populations to aid in understanding cell-type functions and mechanisms, diagnosis, and therapy. As cells are heterogeneous in ligand type, location, expression, and density, careful consideration of magnetic particle design for positive isolation is necessary. Antigen-specific immune cells have low frequencies, which has made studying, identifying, and utilizing these cells for therapy a challenge. Here we demonstrate the importance of magnetic particle design based on the biology of T cells. We create magnetic particles which recognize rare antigen-specific T cells and quantitatively investigate important particle properties including size, concentration, ligand density, and ligand choice in enriching these rare cells. We observe competing optima among particle parameters, with 300 nm particles functionalized with a high density of antigen-specific ligand achieving the highest enrichment and recovery of target cells. In enriching and then activating an endogenous response, 300 nm aAPCs generate nearly 65% antigen-specific T cells with at least 450-fold expansion from endogenous precursors and a 5-fold increase in numbers of antigen-specific cells after only seven days. This systematic study of particle properties in magnetic enrichment provides a case study for the engineering design principles of particles for the isolation of rare cells through biological ligands.
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Affiliation(s)
- John W Hickey
- Department of Biomedical Engineering, School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, School of Medicine, Baltimore, MD, USA; Translational Tissue Engineering Center, Baltimore, MD, USA; Institute for Nanobiotechnology, Baltimore, MD, USA
| | - Ariel Y Isser
- Department of Biomedical Engineering, School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, School of Medicine, Baltimore, MD, USA
| | - Fernando P Vicente
- Department of Biomedical Engineering, School of Medicine, Baltimore, MD, USA
| | - Samuel B Warner
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Hai-Quan Mao
- Translational Tissue Engineering Center, Baltimore, MD, USA; Institute for Nanobiotechnology, Baltimore, MD, USA; Department of Materials Science and Engineering, Whiting School of Engineering, Baltimore, MD, USA
| | - Jonathan P Schneck
- Institute for Cell Engineering, School of Medicine, Baltimore, MD, USA; Department of Pathology, School of Medicine, Baltimore, MD, USA; Institute for Nanobiotechnology, Baltimore, MD, USA; Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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40
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Wu X, DeGottardi Q, Wu IC, Wu L, Yu J, Kwok WW, Chiu DT. Ratiometric Barcoding for Mass Cytometry. Anal Chem 2018; 90:10688-10694. [PMID: 30139253 DOI: 10.1021/acs.analchem.8b03201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Barcoding is of importance for high-throughput cellular and molecular analysis. A ratiometric barcoding strategy using lanthanide-coordinated polymer dots (Ln-Pdots) was developed for mass cytometric analysis. By using 3 metal isotopes and 4 ratio intensity levels, 16 barcodes were generated to code, and later decode, cell samples in mass cytometry. The ratiometric Ln-Pdot barcodes not only provided high-mass-signal intensities but also eliminated the bias caused by different concentrations of the labeling reagents/barcodes and run-to-run differences in cell labeling efficiency. The ability to distinguish clearly the 16 sets of labeled MCF-7 cells with mass cytometry demonstrated the excellent resolving power of the ratiometric Ln-Pdot barcodes. Furthermore, the results from barcoding PBMC samples via CD45-specific cellular targeting indicated that the ratiometric Ln-Pdot barcodes could facilitate mass cytometry in high-throughput and multiplexed analysis, especially with precious human samples.
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Affiliation(s)
- Xu Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute , Central South University , Changsha , Hunan 410078 , China
| | - Quinn DeGottardi
- Benaroya Research Institute at Virginia Mason , Seattle , Washington 98101 , United States
| | - I-Che Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Wu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Jiangbo Yu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason , Seattle , Washington 98101 , United States
| | - Daniel T Chiu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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41
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Kather JN, Suarez-Carmona M, Charoentong P, Weis CA, Hirsch D, Bankhead P, Horning M, Ferber D, Kel I, Herpel E, Schott S, Zörnig I, Utikal J, Marx A, Gaiser T, Brenner H, Chang-Claude J, Hoffmeister M, Jäger D, Halama N. Topography of cancer-associated immune cells in human solid tumors. eLife 2018; 7:36967. [PMID: 30179157 PMCID: PMC6133554 DOI: 10.7554/elife.36967] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/30/2018] [Indexed: 12/14/2022] Open
Abstract
Lymphoid and myeloid cells are abundant in the tumor microenvironment, can be quantified by immunohistochemistry and shape the disease course of human solid tumors. Yet, there is no comprehensive understanding of spatial immune infiltration patterns (‘topography’) across cancer entities and across various immune cell types. In this study, we systematically measure the topography of multiple immune cell types in 965 histological tissue slides from N = 177 patients in a pan-cancer cohort. We provide a definition of inflamed (‘hot’), non-inflamed (‘cold’) and immune excluded patterns and investigate how these patterns differ between immune cell types and between cancer types. In an independent cohort of N = 287 colorectal cancer patients, we show that hot, cold and excluded topographies for effector lymphocytes (CD8) and tumor-associated macrophages (CD163) alone are not prognostic, but that a bivariate classification system can stratify patients. Our study adds evidence to consider immune topographies as biomarkers for patients with solid tumors.
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Affiliation(s)
- Jakob Nikolas Kather
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany.,Division of Gastroenterology, Hepatology and Hepatobiliary Oncology, University Hospital RWTH Aachen, Aachen, Germany
| | - Meggy Suarez-Carmona
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Pornpimol Charoentong
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Cleo-Aron Weis
- Department of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniela Hirsch
- Department of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Bankhead
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Marcel Horning
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Dyke Ferber
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Ivan Kel
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Tissue Bank of the National Center for Tumor Diseases, Heidelberg, Germany
| | - Sarah Schott
- Department of Gynecology, University Hospital Heidelberg, Heidelberg, Germany
| | - Inka Zörnig
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center, Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Alexander Marx
- Department of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Department of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany
| | - Herrmann Brenner
- German Cancer Consortium, Heidelberg, Germany.,Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany.,Cancer Epidemiology Group, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium, Heidelberg, Germany.,Applied Tumor Immunity, German Cancer Research Center, Heidelberg, Germany
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42
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Sztein MB. Is a Human CD8 T-Cell Vaccine Possible, and if So, What Would It Take? CD8 T-Cell-Mediated Protective Immunity and Vaccination against Enteric Bacteria. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a029546. [PMID: 29254983 DOI: 10.1101/cshperspect.a029546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although induction of CD8+ responses is widely accepted as critical in clearing viral infections and necessary for effective vaccines against viruses, much less is known regarding the role of these cells in bacterial and other infections, particularly those that enter the host via the gastrointestinal tract. In this commentary, I discuss the likelihood that CD8+ responses are also important in protection from intestinal Gram-negative bacteria, as well as the many factors that should be taken into consideration during the development of vaccines, based on eliciting long-term protection predominantly mediated by CD8+ responses against these organisms.
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Affiliation(s)
- Marcelo B Sztein
- Center for Vaccine Development, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland 21201
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43
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Prinz JC. Human Leukocyte Antigen-Class I Alleles and the Autoreactive T Cell Response in Psoriasis Pathogenesis. Front Immunol 2018; 9:954. [PMID: 29760713 PMCID: PMC5936982 DOI: 10.3389/fimmu.2018.00954] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 01/08/2023] Open
Abstract
Psoriasis is a complex immune-mediated inflammatory skin disease characterized by T-cell-driven epidermal hyperplasia. It occurs on a strong genetic predisposition. The human leukocyte antigen (HLA)-class I allele HLA-C*06:02 on psoriasis susceptibility locus 1 (PSORS1 on 6p21.3) is the main psoriasis risk gene. Other HLA-class I alleles encoding HLA molecules presenting overlapping peptide repertoires show associations with psoriasis as well. Outside the major histocompatibility complex region, genome-wide association studies identified more than 60 psoriasis-associated common gene variants exerting only modest individual effects. They mainly refer to innate immune activation and the interleukin-23/Th/c17 pathway. Given their strong risk association, explaining the role of the HLA-risk alleles is essential for elucidating psoriasis pathogenesis. Psoriasis lesions develop upon epidermal infiltration, activation, and expansion of CD8+ T cells. The unbiased analysis of a paradigmatic Vα3S1/Vβ13S1-T-cell receptor from a pathogenic epidermal CD8+ T-cell clone of an HLA-C*06:02+ psoriasis patient had revealed that HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation, and it identified a peptide form ADAMTS-like protein 5 as an HLA-C*06:02-presented melanocyte autoantigen. These data demonstrate that psoriasis is an autoimmune disease, where the predisposing HLA-class I alleles promote organ-specific inflammation through facilitating a T-cell response against a particular skin-specific cell population. This review discusses the role of HLA-class I alleles in the pathogenic psoriatic T-cell immune response. It concludes that as a principle of T-cell driven HLA-associated inflammatory diseases proinflammatory traits promote autoimmunity in the context of certain HLA molecules that present particular autoantigens.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig-Maximilian-University of Munich, Munich, Germany
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44
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Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 2018; 24:580-590. [PMID: 29686426 PMCID: PMC5948148 DOI: 10.1038/s41591-018-0008-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/07/2018] [Indexed: 02/04/2023]
Abstract
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naresha Saligrama
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William S Serratelli
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicia N Schep
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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45
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Upadhyay AA, Kauffman RC, Wolabaugh AN, Cho A, Patel NB, Reiss SM, Havenar-Daughton C, Dawoud RA, Tharp GK, Sanz I, Pulendran B, Crotty S, Lee FEH, Wrammert J, Bosinger SE. BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. Genome Med 2018; 10:20. [PMID: 29558968 PMCID: PMC5859752 DOI: 10.1186/s13073-018-0528-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer. BALDR is available at https://github.com/BosingerLab/BALDR.
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Affiliation(s)
- Amit A Upadhyay
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Robert C Kauffman
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Amber N Wolabaugh
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Alice Cho
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Reem A Dawoud
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Gregory K Tharp
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Iñaki Sanz
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Division of Rheumatology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - F Eun-Hyung Lee
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Divisions of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA. .,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
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46
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Aljakna A, Lauer E, Lenglet S, Grabherr S, Fracasso T, Augsburger M, Sabatasso S, Thomas A. Multiplex quantitative imaging of human myocardial infarction by mass spectrometry-immunohistochemistry. Int J Legal Med 2018; 132:1675-1684. [PMID: 29556718 DOI: 10.1007/s00414-018-1813-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/22/2018] [Indexed: 02/01/2023]
Abstract
Simultaneous assessment of a panel of protein markers is becoming essential in order to enhance biomarker research and improve diagnostics. Specifically, postmortem diagnostics of early myocardial ischemia in sudden cardiac death cases could benefit from a multiplex marker assessment in the same tissue section. Current analytical antibody-based techniques (immunohistochemistry and immunofluorescence) limit multiplex analysis usually to not more than three antibodies. In this study, mass spectrometry-immunohistochemistry (MS-IHC) was performed by combining laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) with rare-metal-isotope-tagged antibodies as a technique for multiplex analysis of human postmortem myocardial tissue samples. Tissue sections with myocardial infarction were simultaneously analyzed for seven primary, rare-metal-isotope-tagged antibodies (troponin T, myoglobin, fibronectin, C5b-9, unphosphorylated connexin 43, VEGF-B, and JunB). Comparison between the MS-IHC approach and chromogenic IHC showed similar patterns in ionic and optical images. In addition, absolute quantification was performed by MS-IHC, providing a proportional relationship between the signal intensity and the local marker concentration in tissue sections. These data demonstrated that LA-ICP-MS combined with rare-metal-isotope-tagged antibodies is an efficient strategy for simultaneous testing of multiple markers and allows not only visualization of molecules within the tissue but also quantification of the signal. Such imaging approach has a great potential in both diagnostics and pathology-related research.
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Affiliation(s)
- Aleksandra Aljakna
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Estelle Lauer
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Sébastien Lenglet
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Silke Grabherr
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Tony Fracasso
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Marc Augsburger
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Sara Sabatasso
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland
| | - Aurélien Thomas
- University Center of Legal Medicine, Lausanne-Geneva, Rue Michel-Servet, 11211, Geneva, Switzerland.
- Faculty of Biology and Medicine, University of Lausanne, Vulliette 04, 1000, Lausanne 25, Switzerland.
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47
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Abstract
Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.
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Affiliation(s)
- Allyson L Byrd
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Cancer Immunology, Genentech, South San Francisco, California 94080, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,National Institute of Allergy and Infectious Diseases Microbiome Program, Department of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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48
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Rivino L, Le Bert N, Gill US, Kunasegaran K, Cheng Y, Tan DZ, Becht E, Hansi NK, Foster GR, Su TH, Tseng TC, Lim SG, Kao JH, Newell EW, Kennedy PT, Bertoletti A. Hepatitis B virus-specific T cells associate with viral control upon nucleos(t)ide-analogue therapy discontinuation. J Clin Invest 2018; 128:668-681. [PMID: 29309050 DOI: 10.1172/jci92812] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 11/07/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The clinical management of chronic hepatitis B virus (HBV) patients is based exclusively on virological parameters that cannot independently determine in which patients nucleos(t)ide-analogue (NUC) therapy can be safely discontinued. NUCs efficiently suppress viral replication, but do not eliminate HBV. Thus, therapy discontinuation can be associated with virological and biochemical relapse and, consequently, therapy in the majority is life-long. METHODS Since antiviral immunity is pivotal for HBV control, we investigated potential biomarkers for the safe discontinuation of NUCs within immune profiles of chronic HBV patients by utilizing traditional immunological assays (ELISPOT, flow cytometry) in conjunction with analyses of global non-antigen-specific immune populations (NanoString and CyTOF). Two distinct cohorts of 19 and 27 chronic HBV patients, respectively, were analyzed longitudinally prior to and after discontinuation of 2 different NUC therapy strategies. RESULTS Absence of hepatic flares following discontinuation of NUC treatment correlated with the presence, during NUC viral suppression, of HBV core and polymerase-specific T cells that were contained within the ex vivo PD-1+ population. CONCLUSIONS This study identifies the presence of functional HBV-specific T cells as a candidate immunological biomarker for safe therapy discontinuation in chronic HBV patients. Furthermore, the persistent and functional antiviral activity of PD-1+ HBV-specific T cells highlights the potential beneficial role of the expression of T cell exhaustion markers during human chronic viral infection. FUNDING This work was funded by a Singapore Translational Research Investigator Award (NMRC/STaR/013/2012), the Eradication of HBV TCR Program (NMRC/TCR/014-NUHS/2015), the Singapore Immunology Network, the Wellcome Trust (107389/Z/15/Z), and a Barts and The London Charity (723/1795) grant.
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Affiliation(s)
- Laura Rivino
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Nina Le Bert
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore.,Infection and Immunity Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Upkar S Gill
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore.,Hepatology, Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, United Kingdom (UK)
| | - Kamini Kunasegaran
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Yang Cheng
- Singapore Immunology Network, A*STAR, Singapore
| | - Damien Zm Tan
- Infection and Immunity Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Navjyot K Hansi
- Hepatology, Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, United Kingdom (UK)
| | - Graham R Foster
- Hepatology, Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, United Kingdom (UK)
| | - Tung-Hung Su
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Seng Gee Lim
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore
| | - Jia-Horng Kao
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Patrick Tf Kennedy
- Hepatology, Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (QMUL), London, United Kingdom (UK)
| | - Antonio Bertoletti
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore.,Infection and Immunity Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore.,Singapore Immunology Network, A*STAR, Singapore
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49
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Chew WL. Immunity to CRISPR Cas9 and Cas12a therapeutics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10. [PMID: 29083112 DOI: 10.1002/wsbm.1408] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/27/2022]
Abstract
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself. These host defenses include inflammation via activation of innate immunity, antibody induction in humoral immunity, and cell death by T-cell-mediated cytotoxicity. If left unchecked, these immunological reactions can curtail therapeutic benefits and potentially lead to mortality. Ways to assay and reduce the immunogenicity of Cas9 and Cas12a proteins are therefore critical for ensuring patient safety and treatment efficacy, and for bringing us closer to realizing the vision of permanent genetic cures. WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine Translational, Genomic, and Systems Medicine > Therapeutic Methods.
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Affiliation(s)
- Wei Leong Chew
- Synthetic Biology, Genome Institute of Singapore, Singapore, Singapore
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50
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Arakawa A, Vollmer S, Besgen P, Galinski A, Summer B, Kawakami Y, Wollenberg A, Dornmair K, Spannagl M, Ruzicka T, Thomas P, Prinz JC. Unopposed IL-36 Activity Promotes Clonal CD4 + T-Cell Responses with IL-17A Production in Generalized Pustular Psoriasis. J Invest Dermatol 2017; 138:1338-1347. [PMID: 29288651 DOI: 10.1016/j.jid.2017.12.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/24/2017] [Accepted: 12/07/2017] [Indexed: 12/31/2022]
Abstract
Generalized pustular psoriasis (GPP) is the most severe psoriasis variant. Mutations in the IL-36 antagonist IL36RN, in CARD14 or AP1S3 provide genetic evidence for autoinflammatory etiology but cannot explain its pathogenesis completely. Here we demonstrate that unopposed IL-36 signaling promotes antigen-driven and likely pathogenic T-helper type 17 (Th17) responses in GPP. We observed that CD4+ T cells in blood and skin lesions of GPP patients were characterized by intense hyperproliferation, production of the GPP key mediator, IL-17A, and highly restricted TCR repertoires with identical T-cell clones in blood and skin lesions, indicating antigen-driven T-cell expansions. The clonally expanded CD4+ T cells were major producers of IL-17A. IL-36 signaling substantially enhanced TCR-mediated proliferation of CD4+ T cells. Moreover, GPP patients showed preferences for HLA-DRB1∗14, HLA-DQB1∗05, and HLA-DQB1∗03. We conclude that in GPP unopposed IL-36 signaling and certain HLA-class II alleles may cooperate in promoting antigen-driven Th17 responses, which in the obvious absence of exogenous triggers may reflect autoimmune reactions. This study reveals a pathogenic pathway where innate immune dysregulation promotes T-cell-mediated inflammation in GPP.
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Affiliation(s)
- Akiko Arakawa
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany.
| | - Sigrid Vollmer
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Petra Besgen
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Adrian Galinski
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Burkhard Summer
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Yoshio Kawakami
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Andreas Wollenberg
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Michael Spannagl
- Laboratory of Immunogenetics and Molecular Diagnostics, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Thomas Ruzicka
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Peter Thomas
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany
| | - Jörg C Prinz
- Department of Dermatology and Allergology, University Hospital, Ludwig-Maximilian-University, Munich, Germany.
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