1
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Discepolo V, Kelly CP, Koning F, Schuppan D. How Future Pharmacologic Therapies for Celiac Disease Will Complement the Gluten-Free Diet. Gastroenterology 2024:S0016-5085(24)00416-5. [PMID: 38604542 DOI: 10.1053/j.gastro.2024.02.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
The only proven treatment for celiac disease is adherence to a strict, lifelong, gluten-free diet. However, complete dietary gluten avoidance is challenging and a substantial number of patients do not respond fully, clinically, or histologically, despite their best efforts. As celiac disease is common and its central pathophysiology is well elucidated, it has become attractive for drug development to address the limitations of dietary treatment. Most efforts address nonresponsive celiac disease, defined as continued symptoms and/or signs of disease activity despite a gluten-free diet, including the more severe forms of refractory celiac disease, types I and II. An increasing spectrum of therapeutic approaches target defined mechanisms in celiac disease pathogenesis and some have advanced to current phase 2 and 3 clinical studies. We discuss these approaches in terms of potential efficiency, practicability, safety, and need, as defined by patients, regulatory authorities, health care providers, and payors.
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Affiliation(s)
- Valentina Discepolo
- Department of Translational Medical Science and European Laboratory for the Investigation of Food Induced Diseases, University of Naples Federico II, Naples, Italy.
| | - Ciarán P Kelly
- Celiac Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Detlef Schuppan
- Celiac Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; Institute of Translational Immunology and Research Center for Immunotherapy, Center for Celiac Disease and Autoimmunity, Johannes-Gutenberg University, Mainz, Germany.
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2
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Ravi A, Jia L, Wu X, van der Meer AD, Gosens R, Stolk J, van der Does AM, Koning F, Hiemstra PS, Khedoe PPJS. Loss of Pulmonary Endothelial Cells in Emphysema Impairs Support of Human Alveolar Epithelial Cell Growth. Am J Respir Cell Mol Biol 2024; 70:149-152. [PMID: 38299794 DOI: 10.1165/rcmb.2023-0084le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Abilash Ravi
- Leiden University Medical Center Leiden, the Netherlands
| | - Li Jia
- Leiden University Medical Center Leiden, the Netherlands
| | - Xinhui Wu
- University of Groningen Groningen, the Netherlands
| | | | | | - Jan Stolk
- Leiden University Medical Center Leiden, the Netherlands
| | | | - Frits Koning
- Leiden University Medical Center Leiden, the Netherlands
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3
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Doytchinova I, Atanasova M, Fernandez A, Moreno FJ, Koning F, Dimitrov I. Modeling Peptide-Protein Interactions by a Logo-Based Method: Application in Peptide-HLA Binding Predictions. Molecules 2024; 29:284. [PMID: 38257197 PMCID: PMC10818588 DOI: 10.3390/molecules29020284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Peptide-protein interactions form a cornerstone in molecular biology, governing cellular signaling, structure, and enzymatic activities in living organisms. Improving computational models and experimental techniques to describe and predict these interactions remains an ongoing area of research. Here, we present a computational method for peptide-protein interactions' description and prediction based on leveraged amino acid frequencies within specific binding cores. Utilizing normalized frequencies, we construct quantitative matrices (QMs), termed 'logo models' derived from sequence logos. The method was developed to predict peptide binding to HLA-DQ2.5 and HLA-DQ8.1 proteins associated with susceptibility to celiac disease. The models were validated by more than 17,000 peptides demonstrating their efficacy in discriminating between binding and non-binding peptides. The logo method could be applied to diverse peptide-protein interactions, offering a versatile tool for predictive analysis in molecular binding studies.
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Affiliation(s)
- Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (M.A.); (I.D.)
| | - Mariyana Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (M.A.); (I.D.)
| | | | - F. Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain;
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands;
| | - Ivan Dimitrov
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (M.A.); (I.D.)
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4
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Atanasova M, Dimitrov I, Fernandez A, Moreno J, Koning F, Doytchinova I. Assessment of Novel Proteins Triggering Celiac Disease via Docking-Based Approach. Molecules 2023; 29:138. [PMID: 38202724 PMCID: PMC10780262 DOI: 10.3390/molecules29010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Human leukocyte antigens (HLAs) are pivotal in antigen processing, presenting to CD4+ T cells, and are linked to autoimmune disease susceptibility. In celiac disease, HLA-DQ2.5 and HLA-DQ8.1 bind gluten peptides on APCs, some recognized by CD4+ T cells, prompting inflammation and tissue damage. While extensively studied experimentally, these alleles lack comprehensive in silico analysis. To explore peptide-HLA preferences, we used molecular docking on peptide libraries, deriving quantitative matrices (QMs) for evaluating amino acids at nine-residue peptide binding cores. Our findings tie specific residue preferences to peptide backbone conformations. Validating QMs on known binders and non-binders showed strong predictive power (89-94% accuracy). These QMs excel in screening protein libraries, even whole proteomes, notably reducing time and costs for celiac disease risk assessment in novel proteins. This computational approach aligns with European Food Safety Authority guidance, promising efficient screening for potential celiac disease triggers.
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Affiliation(s)
- Mariyana Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (I.D.)
| | - Ivan Dimitrov
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (I.D.)
| | | | - Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid (CSIC-UAM), Campus of Interntional Excellence—CEI (UAM+CSIC), Nicolás Cabrera, 9, 28049 Madrid, Spain;
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands;
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (I.D.)
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5
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Pool ES, Kooy-Winkelaar Y, van Unen V, Falkenburg JF, Koning F, Heemskerk MHM, Tjon JML. Mass cytometric analysis unveils a disease-specific immune cell network in the bone marrow in acquired aplastic anemia. Front Immunol 2023; 14:1274116. [PMID: 38094307 PMCID: PMC10716190 DOI: 10.3389/fimmu.2023.1274116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Idiopathic acquired aplastic anemia (AA) is considered an immune-mediated syndrome of bone marrow failure since approximately 70% of patients respond to immunosuppressive therapy (IST) consisting of a course of anti-thymocyte globulin (ATG) followed by long-term use of ciclosporin. However, the immune response that underlies the pathogenesis of AA remains poorly understood. In this study, we applied high-dimensional mass cytometry on bone marrow aspirates of AA patients pre-ATG, AA patients post-ATG and healthy donors to decipher which immune cells may be implicated in the pathogenesis of AA. We show that the bone marrow of AA patients features an immune cell composition distinct from healthy donors, with significant differences in the myeloid, B-cell, CD4+ and CD8+ T-cells lineages. Specifically, we discovered that AA pre-ATG is characterized by a disease-specific immune cell network with high frequencies of CD16+ myeloid cells, CCR6++ B-cells, Th17-like CCR6+ memory CD4+ T-cells, CD45RA+CCR7+CD38+ CD8+ T-cells and KLRG1+ terminally differentiated effector memory (EMRA) CD8+ T-cells, compatible with a state of chronic inflammation. Successful treatment with IST strongly reduced the levels of CD16+ myeloid cells and showed a trend toward normalization of the frequencies of CCR6++ B-cells, CCR6+ memory CD4+ T-cells and KLRG1+EMRA CD8+ T-cells. Altogether, our study provides a unique overview of the immune landscape in bone marrow in AA at a single-cell level and proposes CCR6 as a potential new therapeutic target in AA.
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Affiliation(s)
- Emma S. Pool
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Jennifer M-L. Tjon
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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Li N, Zhu J, Chen P, Bao C, Wang J, Abdelaal T, Chen D, Zhu S, Wang W, Mao J, Scicluna BP, Koning F, Li F, Lei L. High-dimensional analysis reveals an immune atlas and novel neutrophil clusters in the lungs of model animals with Actinobacillus pleuropneumoniae-induced pneumonia. Vet Res 2023; 54:76. [PMID: 37705063 PMCID: PMC10500746 DOI: 10.1186/s13567-023-01207-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/24/2023] [Indexed: 09/15/2023] Open
Abstract
Due to the increase in bacterial resistance, improving the anti-infectious immunity of the host is rapidly becoming a new strategy for the prevention and treatment of bacterial pneumonia. However, the specific lung immune responses and key immune cell subsets involved in bacterial infection are obscure. Actinobacillus pleuropneumoniae (APP) can cause porcine pleuropneumonia, a highly contagious respiratory disease that has caused severe economic losses in the swine industry. Here, using high-dimensional mass cytometry, the major immune cell repertoire in the lungs of mice with APP infection was profiled. Various phenotypically distinct neutrophil subsets and Ly-6C+ inflammatory monocytes/macrophages accumulated post-infection. Moreover, a linear differentiation trajectory from inactivated to activated to apoptotic neutrophils corresponded with the stages of uninfected, onset, and recovery of APP infection. CD14+ neutrophils, which mainly increased in number during the recovery stage of infection, were revealed to have a stronger ability to produce cytokines, especially IL-10 and IL-21, than their CD14- counterparts. Importantly, MHC-II+ neutrophils with antigen-presenting cell features were identified, and their numbers increased in the lung after APP infection. Similar results were further confirmed in the lungs of piglets infected with APP and Klebsiella pneumoniae infection by using a single-cell RNA-seq technique. Additionally, a correlation analysis between cluster composition and the infection process yielded a dynamic and temporally associated immune landscape where key immune clusters, including previously unrecognized ones, marked various stages of infection. Thus, these results reveal the characteristics of key neutrophil clusters and provide a detailed understanding of the immune response to bacterial pneumonia.
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Affiliation(s)
- Na Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junhui Zhu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Peiru Chen
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Chuntong Bao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jun Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, The Netherlands
| | - Dexi Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Sibo Zhu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jiangnan Mao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Brendon P Scicluna
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fengyang Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.
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7
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Hendriks SH, Heidt S, Schulz AR, de Fijter JW, Reinders MEJ, Koning F, van Kooten C. Peripheral Blood Immune Cell Composition After Autologous MSC Infusion in Kidney Transplantation Recipients. Transpl Int 2023; 36:11329. [PMID: 37426430 PMCID: PMC10326287 DOI: 10.3389/ti.2023.11329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
Tacrolimus is the backbone of immunosuppressive agents to prevent transplant rejection. Paradoxically, tacrolimus is nephrotoxic, causing irreversible tubulointerstitial damage. Therefore, infusion of mesenchymal stromal cells (MSC) 6 and 7 weeks post-transplantation was assessed to facilitate withdrawal of tacrolimus in the randomized phase II TRITON trial. Here, we performed detailed analysis of the peripheral blood immune composition using mass cytometry to assess potential effects of MSC therapy on the immune system. We developed two metal-conjugated antibody panels containing 40 antibodies each. PBMC samples from 21 MSC-treated patients and 13 controls, obtained pre-transplant and at 24 and 52 weeks post-transplantation, were analyzed. In the MSC group at 24 weeks, 17 CD4+ T cell clusters were increased of which 14 Th2-like clusters and three Th1/Th2-like clusters, as well as CD4+FoxP3+ Tregs. Additionally, five B cell clusters were increased, representing either class switched memory B cells or proliferating B cells. At 52 weeks, CCR7+CD38+ mature B cells were decreased. Finally, eight Tc1 (effector) memory cytotoxic T cell clusters were increased. Our work provides a comprehensive account of the peripheral blood immune cell composition in kidney transplant recipients after MSC therapy and tacrolimus withdrawal. These results may help improving therapeutic strategies using MSCs with the aim to reduce the use of calcineurin inhibitors. Clinical Trial Registration: ClinicalTrials.gov, identifier NCT02057965.
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Affiliation(s)
- Sanne H. Hendriks
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Axel R. Schulz
- German Rheumatism Research Center (DRFZ), Berlin, Germany
| | - Johan W. de Fijter
- Department of Internal Medicine (Nephrology) and Transplant Center, Leiden University Medical Center, Leiden, Netherlands
| | - Marlies E. J. Reinders
- Department of Internal Medicine (Nephrology) and Transplant Center, Leiden University Medical Center, Leiden, Netherlands
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus University Medical Center, Leiden, Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Cees van Kooten
- Department of Internal Medicine (Nephrology) and Transplant Center, Leiden University Medical Center, Leiden, Netherlands
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Krop J, van der Meeren LE, van der Hoorn MLP, Ijsselsteijn ME, Dijkstra KL, Kapsenberg H, van der Keur C, Cornish EF, Nikkels PGJ, Koning F, Claas FHJ, Heidt S, Eikmans M, Bos M. Identification of a unique intervillous cellular signature in chronic histiocytic intervillositis. Placenta 2023; 139:34-42. [PMID: 37300938 DOI: 10.1016/j.placenta.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/15/2023] [Accepted: 05/13/2023] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Chronic histiocytic intervillositis (CHI) is a rare histopathological lesion in the placenta characterized by an infiltrate of CD68+ cells in the intervillous space. CHI is associated with adverse pregnancy outcomes such as miscarriage, fetal growth restriction, and (late) intrauterine fetal death. The adverse pregnancy outcomes and a variable recurrence rate of 25-100% underline its clinical relevance. The pathophysiologic mechanism of CHI is unclear, but it appears to be immunologically driven. The aim of this study was to obtain a better understanding of the phenotype of the cellular infiltrate in CHI. METHOD We used imaging mass cytometry to achieve in-depth visualization of the intervillous maternal immune cells and investigated their spatial orientation in situ in relation to the fetal syncytiotrophoblast. RESULTS We found three phenotypically distinct CD68+HLA-DR+CD38+ cell clusters that were unique for CHI. Additionally, syncytiotrophoblast cells in the vicinity of these CD68+HLA-DR+CD38+ cells showed decreased expression of the immunosuppressive enzyme CD39. DISCUSSION The current results provide novel insight into the phenotype of CD68+ cells in CHI. The identification of unique CD68+ cell clusters will allow more detailed analysis of their function and could result in novel therapeutic targets for CHI.
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Affiliation(s)
- Juliette Krop
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Lotte E van der Meeren
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands; Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | | | - Kyra L Dijkstra
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands
| | - H Kapsenberg
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - C van der Keur
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Emily F Cornish
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Michael Eikmans
- Department of Immunology, Leiden University Medical Centre, Leiden, the Netherlands.
| | - Manon Bos
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands; Department of Gynecology and Obstetrics, Leiden University Medical Centre, Leiden, the Netherlands
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9
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Ouboter LF, Barnhoorn MC, Verspaget HW, Plug L, Pool ES, Szuhai K, Hawinkels LJ, van Pel M, Zwaginga JJ, Roelen D, Koning F, Pascutti MF, van der Meulen-de Jong A. Local administration of mesenchymal stromal cells is safe and modulates the immune compartment in ulcerative proctitis. JCI Insight 2023; 8:167402. [PMID: 36951952 DOI: 10.1172/jci.insight.167402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/17/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Due to their immunoregulatory and tissue regenerative features, mesenchymal stromal cells (MSCs) are a promising novel tool for the management of ulcerative proctitis (UP). Here we report on a phase IIa clinical study to evaluate the impact of local MSC therapy in UP. METHODS Thirteen refractory UP patients, with endoscopic Mayo score (EMS) 2 or 3, were included. Seven patients received 20-40 x 106 allogeneic MSCs (cohort 1), while six patients received 40-80 x 106 MSCs (cohort 2). Adverse events (AEs) were assessed at baseline and week 2, 6, 12, and 24. Clinical, endoscopic, and biochemical parameters were assessed at baseline, week 2 and 6. Furthermore, we evaluated the engraftment of MSCs, presence of donor-specific human leukocyte antigen (HLA) antibodies (DSAs), and we determined the impact of MSC therapy on the local immune compartment. RESULTS No serious AEs were observed. The clinical Mayo score was significantly improved at week 2 and 6, and the EMS was significantly improved at week 6, compared to baseline. At week 6, donor MSCs were still detectable in rectum biopsies of 4/9 patients and DSAs against both HLA-class I and -class II were found. Mass cytometry showed a reduction of activated CD8+ T cells and CD16+ monocytes and an enrichment in mononuclear phagocytes and natural killer cells in biopsies after local MSC therapy. CONCLUSION Local administration of allogeneic MSCs is safe, tolerable, and feasible for treatment of refractory UP and shows encouraging signs of clinical efficacy and modulation of local immune responses. This sets the stage for larger clinical trials. TRIAL REGISTRATION clinicaltrialsregister.eu, EudraCT: 2017-003524-75, Dutch Trial register: NTR7205. FUNDING ECCO grant 2020.
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Affiliation(s)
- Laura F Ouboter
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Marieke C Barnhoorn
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Leonie Plug
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Emma S Pool
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas Jac Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Melissa van Pel
- Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Jaap Jan Zwaginga
- Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Dave Roelen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - M Fernanda Pascutti
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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10
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Guo N, Li N, Jia L, Jiang Q, Schreurs M, van Unen V, de Sousa Lopes SMC, Vloemans AA, Eggermont J, Lelieveldt B, Staal FJT, de Miranda NFCC, Pascutti MF, Koning F. Immune subset-committed proliferating cells populate the human foetal intestine throughout the second trimester of gestation. Nat Commun 2023; 14:1318. [PMID: 36899020 PMCID: PMC10006174 DOI: 10.1038/s41467-023-37052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The intestine represents the largest immune compartment in the human body, yet its development and organisation during human foetal development is largely unknown. Here we show the immune subset composition of this organ during development, by longitudinal spectral flow cytometry analysis of human foetal intestinal samples between 14 and 22 weeks of gestation. At 14 weeks, the foetal intestine is mainly populated by myeloid cells and three distinct CD3-CD7+ ILC, followed by rapid appearance of adaptive CD4+, CD8+ T and B cell subsets. Imaging mass cytometry identifies lymphoid follicles from week 16 onwards in a villus-like structure covered by epithelium and confirms the presence of Ki-67+ cells in situ within all CD3-CD7+ ILC, T, B and myeloid cell subsets. Foetal intestinal lymphoid subsets are capable of spontaneous proliferation in vitro. IL-7 mRNA is detected within both the lamina propria and the epithelium and IL-7 enhances proliferation of several subsets in vitro. Overall, these observations demonstrate the presence of immune subset-committed cells capable of local proliferation in the developing human foetal intestine, likely contributing to the development and growth of organized immune structures throughout most of the 2nd trimester, which might influence microbial colonization upon birth.
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Affiliation(s)
- Nannan Guo
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,State Key Laboratory of Zoonotic Diseases, Institute of Zoonoses, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Li Jia
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Qinyue Jiang
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Mette Schreurs
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | | | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - M Fernanda Pascutti
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
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11
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Schinkelshoek M, Mahfouz A, Huijbers M, Koning F, Fronczek R, Lammers G. Novel genes associated with hypocretin-producing neurons identified by gene expression profiling. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Dieckman T, Koning F, Bouma G. Celiac disease: New therapies on the horizon. Curr Opin Pharmacol 2022; 66:102268. [DOI: 10.1016/j.coph.2022.102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 11/03/2022]
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13
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Van De Haar J, de Vries N, Veninga V, Chalabi M, Ijsselsteijn M, van der Ploeg M, van den Bulk J, Ruano D, Haanen J, Schumacher T, Wessels L, Koning F, de Miranda N, Voest E. 733MO γδT cells are effectors of immune checkpoint blockade in mismatch repair-deficient colon cancers with antigen presentation defects. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Brouwer TP, de Vries NL, Abdelaal T, Krog RT, Li Z, Ruano D, Fariña A, Lelieveldt BPF, Morreau H, Bonsing BA, Vahrmeijer AL, Koning F, de Miranda NFCC. Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry. J Immunother Cancer 2022; 10:e004638. [PMID: 35793870 PMCID: PMC9260840 DOI: 10.1136/jitc-2022-004638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy in need of effective (immuno)therapeutic treatment strategies. For the optimal application and development of cancer immunotherapies, a comprehensive understanding of local and systemic immune profiles in patients with PDAC is required. Here, our goal was to decipher the interplay between local and systemic immune profiles in treatment-naïve patients with PDAC. METHODS The immune composition of PDAC, matched non-malignant pancreatic tissue, regional lymph nodes, spleen, portal vein blood, and peripheral blood samples (collected before and after surgery) from 11 patients with PDAC was assessed by measuring 41 immune cell markers by single-cell mass cytometry. Furthermore, the activation potential of tumor-infiltrating lymphocytes as determined by their ability to produce cytokines was investigated by flow cytometry. In addition, the spatial localization of tumor-infiltrating innate lymphocytes in the tumor microenvironment was confirmed by multispectral immunofluorescence. RESULTS We found that CD103+CD8+ T cells with cytotoxic potential are infrequent in the PDAC immune microenvironment and lack the expression of activation markers and checkpoint blockade molecule programmed cell death protein-1 (PD-1). In contrast, PDAC tissues showed a remarkable increased relative frequency of B cells and regulatory T cells as compared with non-malignant pancreatic tissues. Besides, a previously unappreciated innate lymphocyte cell (ILC) population (CD127-CD103+CD39+CD45RO+ ILC1-like) was discovered in PDAC tissues. Strikingly, the increased relative frequency of B cells and regulatory T cells in pancreatic cancer samples was reflected in matched portal vein blood samples but not in peripheral blood, suggesting a regional enrichment of immune cells that infiltrate the PDAC microenvironment. After surgery, decreased frequencies of myeloid dendritic cells were found in peripheral blood. CONCLUSIONS Our work demonstrates an immunosuppressive landscape in PDAC tissues, generally deprived of cytotoxic T cells and enriched in regulatory T cells and B cells. The antitumor potential of ILC1-like cells in PDAC may be exploited in a therapeutic setting. Importantly, immune profiles detected in blood isolated from the portal vein reflected the immune cell composition of the PDAC microenvironment, suggesting that this anatomical location could be a source of tumor-associated immune cell subsets.
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Affiliation(s)
- Thomas P Brouwer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Natasja L de Vries
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tamim Abdelaal
- Pattern recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Ricki T Krog
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zheng Li
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arantza Fariña
- Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Boudewijn P F Lelieveldt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bert A Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frits Koning
- Department of Immunology, Leiden University Medical Centre, Leiden, The Netherlands
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15
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van Unen V, Ouboter LF, Li N, Schreurs M, Abdelaal T, Kooy-Winkelaar Y, Beyrend G, Höllt T, Maljaars PWJ, Mearin ML, Mahfouz A, Witte AMC, Clemens CHM, Abraham S, Escher JC, Lelieveldt BPF, Pascutti MF, van der Meulen – de Jong AE, Koning F. Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease. Front Immunol 2022; 13:893803. [PMID: 35812429 PMCID: PMC9260579 DOI: 10.3389/fimmu.2022.893803] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/11/2022] [Indexed: 12/21/2022] Open
Abstract
Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultaneously. Therefore, we aimed to identify immune cell types associated with inflammation in IBD using high-dimensional mass cytometry. We analyzed 188 intestinal biopsies and paired blood samples of newly-diagnosed, treatment-naive patients (n=42) and controls (n=26) in two independent cohorts. We applied mass cytometry (36-antibody panel) to resolve single cells and analyzed the data with unbiased Hierarchical-SNE. In addition, imaging-mass cytometry (IMC) was performed to reveal the spatial distribution of the immune subsets in the tissue. We identified 44 distinct immune subsets. Correlation network analysis identified a network of inflammation-associated subsets, including HLA-DR+CD38+ EM CD4+ T cells, T regulatory-like cells, PD1+ EM CD8+ T cells, neutrophils, CD27+ TCRγδ cells and NK cells. All disease-associated subsets were validated in a second cohort. This network was abundant in a subset of patients, independent of IBD subtype, severity or intestinal location. Putative disease-associated CD4+ T cells were detectable in blood. Finally, imaging-mass cytometry revealed the spatial colocalization of neutrophils, memory CD4+ T cells and myeloid cells in the inflamed intestine. Our study indicates that a cellular network of both innate and adaptive immune cells colocalizes in inflamed biopsies from a subset of patients. These results contribute to dissecting disease heterogeneity and may guide the development of targeted therapeutics in IBD.
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Affiliation(s)
- Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Laura F. Ouboter
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Department of Gastroenterology, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Mette Schreurs
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Computer Graphics and Visualization, Delft University of Technology, Delft, Netherlands
| | | | - Guillaume Beyrend
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Thomas Höllt
- Computer Graphics and Visualization, Delft University of Technology, Delft, Netherlands
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - P. W. Jeroen Maljaars
- Department of Gastroenterology, Leiden University Medical Center, Leiden, Netherlands
| | - M. Luisa Mearin
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Computer Graphics and Visualization, Delft University of Technology, Delft, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Anne M. C. Witte
- Department of Gastroenterology, Alrijne Hospital, Leiden, Netherlands
| | | | - Sunje Abraham
- Department of Gastroenterology, Alrijne Hospital, Leiden, Netherlands
| | - Johanna C. Escher
- Department of Pediatric Gastroenterology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Boudewijn P. F. Lelieveldt
- Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, Netherlands
- Department of The Division of Imaging Processing (LKEB) Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Frits Koning,
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16
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Krop J, van der Zwan A, Ijsselsteijn ME, Kapsenberg H, Luk SJ, Hendriks SH, van der Keur C, Verleng LJ, Somarakis A, van der Meeren L, Haasnoot G, Bos M, de Miranda NF, Chuva de Sousa Lopes SM, van der Hoorn MLP, Koning F, Claas FH, Heidt S, Eikmans M. Imaging Mass cytometry reveals the prominent role of myeloid cells at the maternal-fetal interface. iScience 2022; 25:104648. [PMID: 35811852 PMCID: PMC9257341 DOI: 10.1016/j.isci.2022.104648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/03/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022] Open
Abstract
Although the immunological complexity of the maternal-fetal interface is well appreciated, the actual interaction of maternal immune cells and fetal trophoblasts is insufficiently understood. To comprehend the composition and spatial orientation of maternal immune cells and fetal extravillous trophoblasts, we applied imaging mass cytometry on decidua basalis of the three trimesters of healthy pregnancy. Within all trimesters, we observed considerably higher frequencies of myeloid cells in the decidua than is seen with single-cell suspension techniques. Moreover, they were the most pronounced cell type in the microenvironment of other decidual cells. In first trimester, HLA-DR- macrophages represented the most abundant myeloid subcluster and these cells were frequently observed in the vicinity of trophoblasts. At term, HLA-DR+ macrophage subclusters were abundantly present and frequently observed in the microenvironment of T cells. Taken together, our results highlight the dynamic role of myeloid cells at the human maternal-fetal interface throughout gestation. Frequency of myeloid cells is underestimated after tissue digestion Myeloid cells could support NK cells with proper trophoblast invasion Myeloid cells are dynamic in their role throughout gestation
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17
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Sollid LM, Koning F. Lack of relationship of AT1001 to zonulin and prehaptoglobin-2: clinical implications. Gut 2021; 70:2211-2212. [PMID: 33443022 DOI: 10.1136/gutjnl-2020-323829] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/08/2022]
Affiliation(s)
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
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18
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Alenius H, Sinkko H, Moitinho-Silva L, Rodriguez E, Broderick C, Alexander H, Reiger M, Hjort Hjelmsø M, Fyhrquist N, Olah P, Bryce P, Smith C, Koning F, Eyerich K, Greco D, van den Bogaard EH, Neumann AU, Traidl-Hoffmann C, Homey B, Flohr C, Bønnelykke K, Stokholm J, Weidinger S. The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases. Exp Dermatol 2021; 30:1517-1531. [PMID: 34387406 DOI: 10.1111/exd.14446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
The two most common chronic inflammatory skin diseases are atopic dermatitis (AD) and psoriasis. The underpinnings of the remarkable degree of clinical heterogeneity of AD and psoriasis are poorly understood and, as a consequence, disease onset and progression are unpredictable and the optimal type and time-point for intervention are as yet unknown. The BIOMAP project is the first IMI (Innovative Medicines Initiative) project dedicated to investigating the causes and mechanisms of AD and psoriasis and to identify potential biomarkers responsible for the variation in disease outcome. The consortium includes 7 large pharmaceutical companies and 25 non-industry partners including academia. Since there is mounting evidence supporting an important role for microbial exposures and our microbiota as factors mediating immune polarization and AD and psoriasis pathogenesis, an entire work package is dedicated to the investigation of skin and gut microbiome linked to AD or psoriasis. The large collaborative BIOMAP project will enable the integration of patient cohorts, data and knowledge in unprecedented proportions. The project has a unique opportunity with a potential to bridge and fill the gaps between current problems and solutions. This review highlights the power and potential of BIOMAP project in the investigation of microbe-host interplay in AD and psoriasis.
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Affiliation(s)
- Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Finland
| | - Hanna Sinkko
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Finland
| | - Lucas Moitinho-Silva
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Conor Broderick
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Helen Alexander
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthias Reiger
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany.,Chair of Environmental Medicine, Technical University Munich, Munich, Germany
| | - Mathis Hjort Hjelmsø
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77, Stockholm, Sweden
| | - Peter Olah
- Department of Dermatology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Department of Dermatology, Venereology and Oncodermatology, Medical Faculty, University of Pécs, Hungary
| | - Paul Bryce
- Type 2 Inflammation & Fibrosis Cluster, Immunology & Inflammation Therapeutic Area, Sanofi US, Cambridge, MA, United States of America
| | - Catherine Smith
- St John's Institute of Dermatology, Kings College London, and Guys and St Thomas' NHS Foundation Trust, 9th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK
| | - Frits Koning
- Department of Immunology, Leiden University Medical Centre (LUMC), Leiden, the Netherlands
| | - Kilian Eyerich
- Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Dario Greco
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud university medical center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Avidan U Neumann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany
| | - Claudia Traidl-Hoffmann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum München, Augsburg, Germany.,Chair of Environmental Medicine, Technical University Munich, Munich, Germany.,CK CARE, Christine Kühne Center for Allergy Research and Education, Davos, Switzerland.,ZIEL - Institute for Food & Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Bernhard Homey
- Department of Dermatology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Carsten Flohr
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
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19
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Bakker OB, Ramírez-Sánchez AD, Borek ZA, de Klein N, Li Y, Modderman R, Kooy-Winkelaar Y, Johannesen MK, Matarese F, Martens JHA, Kumar V, van Bergen J, Qiao SW, Lundin KEA, Sollid LM, Koning F, Wijmenga C, Withoff S, Jonkers IH. Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells. Sci Rep 2021; 11:9252. [PMID: 33927210 PMCID: PMC8085175 DOI: 10.1038/s41598-021-86612-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/18/2021] [Indexed: 02/08/2023] Open
Abstract
Celiac disease is an auto-immune disease in which an immune response to dietary gluten leads to inflammation and subsequent atrophy of small intestinal villi, causing severe bowel discomfort and malabsorption of nutrients. The major instigating factor for the immune response in celiac disease is the activation of gluten-specific CD4+ T cells expressing T cell receptors that recognize gluten peptides presented in the context of HLA-DQ2 and DQ8. Here we provide an in-depth characterization of 28 gluten-specific T cell clones. We assess their transcriptional and epigenetic response to T cell receptor stimulation and link this to genetic factors associated with celiac disease. Gluten-specific T cells have a distinct transcriptional profile that mostly resembles that of Th1 cells but also express cytokines characteristic of other types of T-helper cells. This transcriptional response appears not to be regulated by changes in chromatin state, but rather by early upregulation of transcription factors and non-coding RNAs that likely orchestrate the subsequent activation of genes that play a role in immune pathways. Finally, integration of chromatin and transcription factor binding profiles suggest that genes activated by T cell receptor stimulation of gluten‑specific T cells may be impacted by genetic variation at several genetic loci associated with celiac disease.
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Affiliation(s)
- Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zuzanna A Borek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rutger Modderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yvonne Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie K Johannesen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Filomena Matarese
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Jeroen van Bergen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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20
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van der Graaf A, Zorro MM, Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, Ricaño-Ponce I, Borek Z, Koning F, Kooy-Winkelaar Y, Sollid LM, Qiao SW, Kumar V, Li Y, Franke L, Withoff S, Wijmenga C, Sanna S, Jonkers I. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease. Front Genet 2021; 11:562434. [PMID: 33569077 PMCID: PMC7868554 DOI: 10.3389/fgene.2020.562434] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis.
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Affiliation(s)
- Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maria M. Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Raúl Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chan Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Joram Mooiweer
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Zuzanna Borek
- Deutsches Rheumaforschungszentrum Berlin (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 Gastroenterology, Infectious Diseases and Rheumatology, Berlin, Germany
| | - Frits Koning
- Department of Immunology, Leiden University, Leiden, Netherlands
| | | | - Ludvig M. Sollid
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Iris Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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21
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Scherf KA, Catassi C, Chirdo FG, Ciclitira PJ, Feighery CF, Gianfrani C, Koning F, Lundin KEA, Masci S, Schuppan D, Smulders MJM, Tranquet O, Troncone R, Koehler P. Statement of the Prolamin Working Group on the Determination of Gluten in Fermented Foods Containing Partially Hydrolyzed Gluten. Front Nutr 2021; 7:626712. [PMID: 33511151 PMCID: PMC7835721 DOI: 10.3389/fnut.2020.626712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina Anne Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Carlo Catassi
- Department of Pediatrics, Polytechnic University of Marche, Ancona, Italy
| | - Fernando G Chirdo
- Instituto de Estudios Inmunologicos y Fisiopatologicos, Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul J Ciclitira
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | | | - Carmen Gianfrani
- Institute of Biochemistry and Cell Biology, Italian National Council of Research, Naples, Italy
| | - Frits Koning
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Knut E A Lundin
- Stiftelsen KG Jebsen Coeliac Disease Research Centre, Department of Gastroenterology, Oslo University Hospital Rikshospitalet, University of Oslo, Oslo, Norway
| | - Stefania Masci
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Detlef Schuppan
- Institute for Translational Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Riccardo Troncone
- European Laboratory for the Investigation of Food Induced Diseases, Department of Medical Translational Sciences, University Federico II, Naples, Italy
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22
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Somarakis A, Van Unen V, Koning F, Lelieveldt B, Hollt T. ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data. IEEE Trans Vis Comput Graph 2021; 27:98-110. [PMID: 31369380 DOI: 10.1109/tvcg.2019.2931299] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tissue functionality is determined by the characteristics of tissue-resident cells and their interactions within their microenvironment. Imaging Mass Cytometry offers the opportunity to distinguish cell types with high precision and link them to their spatial location in intact tissues at sub-cellular resolution. This technology produces large amounts of spatially-resolved high-dimensional data, which constitutes a serious challenge for the data analysis. We present an interactive visual analysis workflow for the end-to-end analysis of Imaging Mass Cytometry data that was developed in close collaboration with domain expert partners. We implemented the presented workflow in an interactive visual analysis tool; ImaCytE. Our workflow is designed to allow the user to discriminate cell types according to their protein expression profiles and analyze their cellular microenvironments, aiding in the formulation or verification of hypotheses on tissue architecture and function. Finally, we show the effectiveness of our workflow and ImaCytE through a case study performed by a collaborating specialist.
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23
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van der Gracht ETI, Beyrend G, Abdelaal T, Pardieck IN, Wesselink TH, van Haften FJ, van Duikeren S, Koning F, Arens R. Memory CD8 + T cell heterogeneity is primarily driven by pathogen-specific cues and additionally shaped by the tissue environment. iScience 2020; 24:101954. [PMID: 33458613 PMCID: PMC7797528 DOI: 10.1016/j.isci.2020.101954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/06/2020] [Accepted: 12/12/2020] [Indexed: 12/15/2022] Open
Abstract
Factors that govern the complex formation of memory T cells are not completely understood. A better understanding of the development of memory T cell heterogeneity is however required to enhance vaccination and immunotherapy approaches. Here we examined the impact of pathogen- and tissue-specific cues on memory CD8+ T cell heterogeneity using high-dimensional single-cell mass cytometry and a tailored bioinformatics pipeline. We identified distinct populations of pathogen-specific CD8+ T cells that uniquely connected to a specific pathogen or associated to multiple types of acute and persistent infections. In addition, the tissue environment shaped the memory CD8+ T cell heterogeneity, albeit to a lesser extent than infection. The programming of memory CD8+ T cell differentiation during acute infection is eventually superseded by persistent infection. Thus, the plethora of distinct memory CD8+ T cell subsets that arise upon infection is dominantly sculpted by the pathogen-specific cues and further shaped by the tissue environment. Heterogeneous subsets of both circulating and tissue-resident memory CD8+ T cells exist Memory CD8+ T cell heterogeneity is profoundly sculpted by pathogen-specific cues Memory CD8+ T cell heterogeneity is additionally shaped by the tissue environment Viral persistance supersedes memory CD8+ T cell differentiation after acute infection
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Affiliation(s)
| | - Guillaume Beyrend
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, the Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Iris N Pardieck
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Thomas H Wesselink
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Floortje J van Haften
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Suzanne van Duikeren
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
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24
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van der Gracht ET, Schoonderwoerd MJ, van Duikeren S, Yilmaz AN, Behr FM, Colston JM, Lee LN, Yagita H, van Gisbergen KP, Hawinkels LJ, Koning F, Klenerman P, Arens R. Adenoviral vaccines promote protective tissue-resident memory T cell populations against cancer. J Immunother Cancer 2020; 8:e001133. [PMID: 33293355 PMCID: PMC7725098 DOI: 10.1136/jitc-2020-001133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Adenoviral vectors emerged as important platforms for cancer immunotherapy. Vaccination with adenoviral vectors is promising in this respect, however, their specific mechanisms of action are not fully understood. Here, we assessed the development and maintenance of vaccine-induced tumor-specific CD8+ T cells elicited upon immunization with adenoviral vectors. METHODS Adenoviral vaccine vectors encoding the full-length E7 protein from human papilloma virus (HPV) or the immunodominant epitope from E7 were generated, and mice were immunized intravenously with different quantities (107, 108 or 109 infectious units). The magnitude, kinetics and tumor protection capacity of the induced vaccine-specific T cell responses were evaluated. RESULTS The adenoviral vaccines elicited inflationary E7-specific memory CD8+ T cell responses in a dose-dependent manner. The magnitude of these vaccine-specific CD8+ T cells in the circulation related to the development of E7-specific CD8+ tissue-resident memory T (TRM) cells, which were maintained for months in multiple tissues after vaccination. The vaccine-specific CD8+ T cell responses conferred long-term protection against HPV-induced carcinomas in the skin and liver, and this protection required the induction and accumulation of CD8+ TRM cells. Moreover, the formation of CD8+ TRM cells could be enhanced by temporal targeting CD80/CD86 costimulatory interactions via CTLA-4 blockade early after immunization. CONCLUSIONS Together, these data show that adenoviral vector-induced CD8+ T cell inflation promotes protective TRM cell populations, and this can be enhanced by targeting CTLA-4.
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Affiliation(s)
| | - Mark Ja Schoonderwoerd
- Department of Gasteroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Suzanne van Duikeren
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ayse N Yilmaz
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Felix M Behr
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Julia M Colston
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lian N Lee
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hideo Yagita
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Klaas Pjm van Gisbergen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Lukas Jac Hawinkels
- Department of Gasteroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
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25
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van der Zwan A, van Unen V, Beyrend G, Laban S, van der Keur C, Kapsenberg HJM, Höllt T, Chuva de Sousa Lopes SM, van der Hoorn MLP, Koning F, Claas FHJ, Eikmans M, Heidt S. Visualizing Dynamic Changes at the Maternal-Fetal Interface Throughout Human Pregnancy by Mass Cytometry. Front Immunol 2020; 11:571300. [PMID: 33193353 PMCID: PMC7649376 DOI: 10.3389/fimmu.2020.571300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
During healthy pregnancy, a balanced microenvironment at the maternal-fetal interface with coordinated interaction between various immune cells is necessary to maintain immunological tolerance. While specific decidual immune cell subsets have been investigated, a system-wide unbiased approach is lacking. Here, mass cytometry was applied for data-driven, in-depth immune profiling of the total leukocyte population isolated from first, second, and third trimester decidua, as well as maternal peripheral blood at time of delivery. The maternal-fetal interface showed a unique composition of immune cells, different from peripheral blood, with significant differences between early and term pregnancy samples. Profiling revealed substantial heterogeneity in the decidual lymphoid and myeloid cell lineages that shape gestational-specific immune networks and putative differentiation trajectories over time during gestation. Uncovering the overall complexity at the maternal-fetal interface throughout pregnancy resulted in a human atlas that may serve as a foundation upon which comprehension of the immune microenvironment and alterations thereof in pregnancy complications can be built.
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Affiliation(s)
- Anita van der Zwan
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Guillaume Beyrend
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Sandra Laban
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Carin van der Keur
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | | | | | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Eikmans
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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26
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de Vries NL, Mahfouz A, Koning F, de Miranda NFCC. Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies. Front Oncol 2020; 10:1254. [PMID: 32793500 PMCID: PMC7390924 DOI: 10.3389/fonc.2020.01254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
Cancers are characterized by extensive heterogeneity that occurs intratumorally, between lesions, and across patients. To study cancer as a complex biological system, multidimensional analyses of the tumor microenvironment are paramount. Single-cell technologies such as flow cytometry, mass cytometry, or single-cell RNA-sequencing have revolutionized our ability to characterize individual cells in great detail and, with that, shed light on the complexity of cancer microenvironments. However, a key limitation of these single-cell technologies is the lack of information on spatial context and multicellular interactions. Investigating spatial contexts of cells requires the incorporation of tissue-based techniques such as multiparameter immunofluorescence, imaging mass cytometry, or in situ detection of transcripts. In this Review, we describe the rise of multidimensional single-cell technologies and provide an overview of their strengths and weaknesses. In addition, we discuss the integration of transcriptomic, genomic, epigenomic, proteomic, and spatially-resolved data in the context of human cancers. Lastly, we will deliberate on how the integration of multi-omics data will help to shed light on the complex role of cell types present within the human tumor microenvironment, and how such system-wide approaches may pave the way toward more effective therapies for the treatment of cancer.
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Affiliation(s)
- Natasja L. de Vries
- Pathology, Leiden University Medical Center, Leiden, Netherlands
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ahmed Mahfouz
- Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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27
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Guo N, van Unen V, Ijsselsteijn ME, Ouboter LF, van der Meulen AE, Chuva de Sousa Lopes SM, de Miranda NFCC, Koning F, Li N. A 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue. Front Immunol 2020; 11:1466. [PMID: 32765508 PMCID: PMC7381123 DOI: 10.3389/fimmu.2020.01466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Imaging mass cytometry (IMC) is able to quantify the expression of dozens of markers at sub-cellular resolution on a single tissue section by combining a novel laser ablation system with mass cytometry. As such, it allows us to gain spatial information and antigen quantification in situ, and can be applied to both snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissue sections. Herein, we have developed and optimized the immunodetection conditions for a 34-antibody panel for use on human snap-frozen tissue sections. For this, we tested the performance of 80 antibodies. Moreover, we compared tissue drying times, fixation procedures and antibody incubation conditions. We observed that variations in the drying times of tissue sections had little impact on the quality of the images. Fixation with methanol for 5 min at -20°C or 1% paraformaldehyde (PFA) for 5 min at room temperature followed by methanol for 5 min at -20°C were superior to fixation with acetone or PFA only. Finally, we observed that antibody incubation overnight at 4°C yielded more consistent results as compared to staining at room temperature for 5 h. Finally, we used the optimized method for staining of human fetal and adult intestinal tissue samples. We present the tissue architecture and spatial distribution of the stromal cells and immune cells in these samples visualizing blood vessels, the epithelium and lamina propria based on the expression of α-smooth muscle actin (α-SMA), E-Cadherin and Vimentin, while simultaneously revealing the colocalization of T cells, innate lymphoid cells (ILCs), and various myeloid cell subsets in the lamina propria of the human fetal intestine. We expect that this work can aid the scientific community who wish to improve IMC data quality.
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Affiliation(s)
- Nannan Guo
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, United States
| | | | - Laura F Ouboter
- Gastroenterology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.,Key Laboratory of Zoonoses Research, Ministry of Education, Institute of Zoonoses, College of Veterinary Medicine, Jilin University, Changchun, China
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28
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Abdelaal T, Höllt T, van Unen V, Lelieveldt BPF, Koning F, Reinders MJT, Mahfouz A. CyTOFmerge: integrating mass cytometry data across multiple panels. Bioinformatics 2020; 35:4063-4071. [PMID: 30874801 PMCID: PMC6792069 DOI: 10.1093/bioinformatics/btz180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/20/2019] [Accepted: 03/14/2019] [Indexed: 12/19/2022] Open
Abstract
Motivation High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore the full heterogeneity of a biological sample at the single-cell level is currently limited by the number of markers measured simultaneously on a single panel. Results To extend the number of markers per cell, we propose an in silico method to integrate CyTOF datasets measured using multiple panels that share a set of markers. Additionally, we present an approach to select the most informative markers from an existing CyTOF dataset to be used as a shared marker set between panels. We demonstrate the feasibility of our methods by evaluating the quality of clustering and neighborhood preservation of the integrated dataset, on two public CyTOF datasets. We illustrate that by computationally extending the number of markers we can further untangle the heterogeneity of mass cytometry data, including rare cell-population detection. Availability and implementation Implementation is available on GitHub (https://github.com/tabdelaal/CyTOFmerge). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, ZC Leiden, The Netherlands
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, ZC Leiden, The Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, XE Delft, The Netherlands
| | | | - Boudewijn P F Lelieveldt
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, ZC Leiden, The Netherlands.,Department of Radiology, Leiden University Medical Center, ZA Leiden, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, ZC Leiden, The Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, ZC Leiden, The Netherlands
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29
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Fernandez A, Mills ENC, Koning F, Moreno FJ. Allergenicity Assessment of Novel Food Proteins: What Should Be Improved? Trends Biotechnol 2020; 39:4-8. [PMID: 32546310 DOI: 10.1016/j.tibtech.2020.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 01/22/2023]
Abstract
Allergenicity prediction is one of the most challenging aspects in the safety assessment of foods derived from either biotechnology or novel food proteins. Here we present a bottom-up strategy that defines a priori the specific risk assessment (RA) needs based on a database appropriately built for such purposes.
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Affiliation(s)
- Antonio Fernandez
- European Food Safety Authority (EFSA), via Carlo Magno 1A, 43021 Parma, Italy.
| | - E N Clare Mills
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Manchester Institute of Biotechnology, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden 2333, ZA, The Netherlands
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), C/Nicolás Cabrera, 9, Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain
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30
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Sajic N, Oplatowska-Stachowiak M, Streppel L, Drijfhout JW, Salden M, Koning F. Performance characteristics of a new competitive DQ2.5-glia-α3 gliadin ELISA. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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de Vries NL, van Unen V, Ijsselsteijn ME, Abdelaal T, van der Breggen R, Farina Sarasqueta A, Mahfouz A, Peeters KCMJ, Höllt T, Lelieveldt BPF, Koning F, de Miranda NFCC. High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity. Gut 2020; 69:691-703. [PMID: 31270164 PMCID: PMC7063399 DOI: 10.1136/gutjnl-2019-318672] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE A comprehensive understanding of anticancer immune responses is paramount for the optimal application and development of cancer immunotherapies. We unravelled local and systemic immune profiles in patients with colorectal cancer (CRC) by high-dimensional analysis to provide an unbiased characterisation of the immune contexture of CRC. DESIGN Thirty-six immune cell markers were simultaneously assessed at the single-cell level by mass cytometry in 35 CRC tissues, 26 tumour-associated lymph nodes, 17 colorectal healthy mucosa and 19 peripheral blood samples from 31 patients with CRC. Additionally, functional, transcriptional and spatial analyses of tumour-infiltrating lymphocytes were performed by flow cytometry, single-cell RNA-sequencing and multispectral immunofluorescence. RESULTS We discovered that a previously unappreciated innate lymphocyte population (Lin-CD7+CD127-CD56+CD45RO+) was enriched in CRC tissues and displayed cytotoxic activity. This subset demonstrated a tissue-resident (CD103+CD69+) phenotype and was most abundant in immunogenic mismatch repair (MMR)-deficient CRCs. Their presence in tumours was correlated with the infiltration of tumour-resident cytotoxic, helper and γδ T cells with highly similar activated (HLA-DR+CD38+PD-1+) phenotypes. Remarkably, activated γδ T cells were almost exclusively found in MMR-deficient cancers. Non-activated counterparts of tumour-resident cytotoxic and γδ T cells were present in CRC and healthy mucosa tissues, but not in lymph nodes, with the exception of tumour-positive lymph nodes. CONCLUSION This work provides a blueprint for the understanding of the heterogeneous and intricate immune landscape of CRC, including the identification of previously unappreciated immune cell subsets. The concomitant presence of tumour-resident innate and adaptive immune cell populations suggests a multitargeted exploitation of their antitumour properties in a therapeutic setting.
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Affiliation(s)
- Natasja L de Vries
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands,TECObiosciences GmbH, Landshut, Germany
| | - Vincent van Unen
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tamim Abdelaal
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Ahmed Mahfouz
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands,Computer Graphics and Visualization, Delft University of Technology, Delft, The Netherlands
| | - Boudewijn P F Lelieveldt
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,LKEB Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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32
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Scherf KA, Catassi C, Chirdo F, Ciclitira PJ, Feighery C, Gianfrani C, Koning F, Lundin KEA, Schuppan D, Smulders MJM, Tranquet O, Troncone R, Koehler P. Recent Progress and Recommendations on Celiac Disease From the Working Group on Prolamin Analysis and Toxicity. Front Nutr 2020; 7:29. [PMID: 32258047 PMCID: PMC7090026 DOI: 10.3389/fnut.2020.00029] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Celiac disease (CD) affects a growing number of individuals worldwide. To elucidate the causes for this increase, future multidisciplinary collaboration is key to understanding the interactions between immunoreactive components in gluten-containing cereals and the human gastrointestinal tract and immune system and to devise strategies for CD prevention and treatment beyond the gluten-free diet. During the last meetings, the Working Group on Prolamin Analysis and Toxicity (Prolamin Working Group, PWG) discussed recent progress in the field together with key stakeholders from celiac disease societies, academia, industry and regulatory bodies. Based on the current state of knowledge, this perspective from the PWG members provides recommendations regarding clinical, analytical and legal aspects of CD. The selected key topics that require future multidisciplinary collaborative efforts in the clinical field are to collect robust data on the increasing prevalence of CD, to evaluate what is special about gluten-specific T cells, to study their kinetics and transcriptomics and to put some attention to the identification of the environmental agents that facilitate the breaking of tolerance to gluten. In the field of gluten analysis, the key topics are the precise assessment of gluten immunoreactive components in wheat, rye and barley to understand how these are affected by genetic and environmental factors, the comparison of different methods for compliance monitoring of gluten-free products and the development of improved reference materials for gluten analysis.
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Affiliation(s)
- Katharina A. Scherf
- Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Carlo Catassi
- Department of Pediatrics, Polytechnic University of Marche, Ancona, Italy
| | - Fernando Chirdo
- Instituto de Estudios Inmunologicos y Fisiopatologicos- IIFP (UNLP-CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul J. Ciclitira
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | | | - Carmen Gianfrani
- Institute of Biochemistry and Cell Biology, Italian National Council of Research, Naples, Italy
| | - Frits Koning
- Leiden University Medical Centre, Leiden, Netherlands
| | - Knut E. A. Lundin
- Department of Gastroenterology, Oslo University Hospital Rikshospitalet and Stiftelsen KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Detlef Schuppan
- Institute for Translational Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Riccardo Troncone
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), Department of Medical Translational Sciences, University Federico II, Naples, Italy
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de Ruiter K, Jochems SP, Tahapary DL, Stam KA, König M, van Unen V, Laban S, Höllt T, Mbow M, Lelieveldt BPF, Koning F, Sartono E, Smit JWA, Supali T, Yazdanbakhsh M. Helminth infections drive heterogeneity in human type 2 and regulatory cells. Sci Transl Med 2020; 12:12/524/eaaw3703. [DOI: 10.1126/scitranslmed.aaw3703] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 08/06/2019] [Accepted: 12/03/2019] [Indexed: 01/03/2023]
Abstract
Helminth infections induce strong type 2 and regulatory responses, but the degree of heterogeneity of such cells is not well characterized. Using mass cytometry, we profiled these cells in Europeans and Indonesians not exposed to helminths and in Indonesians residing in rural areas infected with soil-transmitted helminths. To assign immune alteration to helminth infection, the profiling was performed before and 1 year after deworming. Very distinct signatures were found in Europeans and Indonesians, showing expanded frequencies of T helper 2 cells, particularly CD161+ cells and ILC2s in helminth-infected Indonesians, which was confirmed functionally through analysis of cytokine-producing cells. Besides ILC2s and CD4+ T cells, CD8+ T cells and γδ T cells in Indonesians produced type 2 cytokines. Regulatory T cells were also expanded in Indonesians, but only those expressing CTLA-4, and some coexpressed CD38, HLA-DR, ICOS, or CD161. CD11c+ B cells were found to be the main IL-10 producers among B cells in Indonesians, a subset that was almost absent in Europeans. A number of the distinct immune profiles were driven by helminths as the profiles reverted after clearance of helminth infections. Moreover, Indonesians with no helminth infections residing in an urban area showed immune profiles that resembled Europeans rather than rural Indonesians, which excludes a major role for ethnicity. Detailed insight into the human type 2 and regulatory networks could provide opportunities to target these cells for more precise interventions.
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Affiliation(s)
- Karin de Ruiter
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Simon P. Jochems
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Dicky L. Tahapary
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
- Department of Internal Medicine, Division of Endocrinology, Dr. Cipto Mangunkusumo National General Hospital, Faculty of Medicine Universitas Indonesia, 10430 Jakarta, Indonesia
- Metabolic, Cardiovascular and Aging Cluster, The Indonesian Medical Education and Research Institute, Universitas Indonesia, 10430 Jakarta, Indonesia
| | - Koen A. Stam
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Marion König
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Sandra Laban
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, 2628 XE Delft, Netherlands
- Computational Biology Center, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Moustapha Mbow
- Department of Immunology, Cheikh Anta Diop University of Dakar (UCAD), 5005 Dakar, Senegal
| | - Boudewijn P. F. Lelieveldt
- Department of LKEB Radiology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, 2628 XE Delft, Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Erliyani Sartono
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Johannes W. A. Smit
- Department of Internal Medicine, Radboud University Medical Centre, 6525 GA Nijmegen, Netherlands
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Taniawati Supali
- Department of Parasitology, Faculty of Medicine Universitas Indonesia, 10430 Jakarta, Indonesia
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
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34
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Sollid LM, Tye-Din JA, Qiao SW, Anderson RP, Gianfrani C, Koning F. Update 2020: nomenclature and listing of celiac disease-relevant gluten epitopes recognized by CD4 + T cells. Immunogenetics 2019; 72:85-88. [PMID: 31735991 DOI: 10.1007/s00251-019-01141-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 11/26/2022]
Abstract
Celiac disease is caused by an abnormal intestinal T cell response to cereal gluten proteins. The disease has a strong human leukocyte antigen (HLA) association, and CD4+ T cells recognizing gluten epitopes presented by disease-associated HLA-DQ allotypes are considered to be drivers of the disease. This paper provides an update of the currently known HLA-DQ restricted gluten T cell epitopes with their names and sequences.
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Affiliation(s)
- Ludvig M Sollid
- KG Jebsen Coeliac Disease Research Centre and Department of Immunology, Oslo University Hospital, Rikshospitalet, University of Oslo, Oslo, Norway.
| | - Jason A Tye-Din
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Shuo-Wang Qiao
- KG Jebsen Coeliac Disease Research Centre and Department of Immunology, Oslo University Hospital, Rikshospitalet, University of Oslo, Oslo, Norway
| | - Robert P Anderson
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Carmen Gianfrani
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Naples, Italy
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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35
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Ijsselsteijn ME, van der Breggen R, Farina Sarasqueta A, Koning F, de Miranda NFCC. A 40-Marker Panel for High Dimensional Characterization of Cancer Immune Microenvironments by Imaging Mass Cytometry. Front Immunol 2019; 10:2534. [PMID: 31736961 PMCID: PMC6830340 DOI: 10.3389/fimmu.2019.02534] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/11/2019] [Indexed: 11/13/2022] Open
Abstract
Multiplex immunophenotyping technologies are indispensable for a deeper understanding of biological systems. Until recently, high-dimensional cellular analyses implied the loss of tissue context as they were mostly performed in single-cell suspensions. The advent of imaging mass cytometry introduced the possibility to simultaneously detect a multitude of cellular markers in tissue sections. This technique can be applied to various tissue sources including snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissues. However, a number of methodological challenges must be overcome when developing large antibody panels in order to preserve signal intensity and specificity of antigen detection. We report the development of a 40-marker panel for imaging mass cytometry on FFPE tissues with a particular focus on the study of cancer immune microenvironments. It comprises a variety of immune cell markers including lineage and activation markers as well as surrogates of cancer cell states and tissue-specific markers (e.g., stroma, epithelium, vessels) for cellular contextualization within the tissue. Importantly, we developed an optimized workflow for maximum antibody performance by separating antibodies into two distinct incubation steps, at different temperatures and incubation times, shown to significantly improve immunodetection. Furthermore, we provide insight into the antibody validation process and discuss why some antibodies and/or cellular markers are not compatible with the technique. This work is aimed at supporting the implementation of imaging mass cytometry in other laboratories by describing methodological procedures in detail. Furthermore, the panel described here is an excellent immune monitoring tool that can be readily applied in the context of cancer research.
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Affiliation(s)
| | | | | | - Frits Koning
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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36
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Beyrend G, van der Gracht E, Yilmaz A, van Duikeren S, Camps M, Höllt T, Vilanova A, van Unen V, Koning F, de Miranda NFCC, Arens R, Ossendorp F. PD-L1 blockade engages tumor-infiltrating lymphocytes to co-express targetable activating and inhibitory receptors. J Immunother Cancer 2019; 7:217. [PMID: 31412943 PMCID: PMC6694641 DOI: 10.1186/s40425-019-0700-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The clinical benefit of immunotherapeutic approaches against cancer has been well established although complete responses are only observed in a minority of patients. Combination immunotherapy offers an attractive avenue to develop more effective cancer therapies by improving the efficacy and duration of the tumor-specific T-cell response. Here, we aimed at deciphering the mechanisms governing the response to PD-1/PD-L1 checkpoint blockade to support the rational design of combination immunotherapy. METHODS Mice bearing subcutaneous MC-38 tumors were treated with blocking PD-L1 antibodies. To establish high-dimensional immune signatures of immunotherapy-specific responses, the tumor microenvironment was analyzed by CyTOF mass cytometry using 38 cellular markers. Findings were further examined and validated by flow cytometry and by functional in vivo experiments. Immune profiling was extended to the tumor microenvironment of colorectal cancer patients. RESULTS PD-L1 blockade induced selectively the expansion of tumor-infiltrating CD4+ and CD8+ T-cell subsets, co-expressing both activating (ICOS) and inhibitory (LAG-3, PD-1) molecules. By therapeutically co-targeting these molecules on the TAI cell subsets in vivo by agonistic and antagonist antibodies, we were able to enhance PD-L1 blockade therapy as evidenced by an increased number of TAI cells within the tumor micro-environment and improved tumor protection. Moreover, TAI cells were also found in the tumor-microenvironment of colorectal cancer patients. CONCLUSIONS This study shows the presence of T cell subsets in the tumor micro-environment expressing both activating and inhibitory receptors. These TAI cells can be targeted by combined immunotherapy leading to improved survival.
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Affiliation(s)
- Guillaume Beyrend
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Esmé van der Gracht
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Ayse Yilmaz
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Suzanne van Duikeren
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Marcel Camps
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department of Computer Graphics and Visualization Group, Delft, the Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualization Group, faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | | | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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37
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Li N, van Unen V, Guo N, Abdelaal T, Somarakis A, Eggermont J, Mahfouz A, Chuva de Sousa Lopes SM, Lelieveldt BPF, Koning F. Early-Life Compartmentalization of Immune Cells in Human Fetal Tissues Revealed by High-Dimensional Mass Cytometry. Front Immunol 2019; 10:1932. [PMID: 31474997 PMCID: PMC6703141 DOI: 10.3389/fimmu.2019.01932] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
The human fetal immune system must protect the infant against the sudden exposure to a large variety of pathogens upon birth. While it is known that the fetal immune system develops in sequential waves, relatively little is known about the composition of the innate and adaptive immune system in the tissues. Here, we applied high-dimensional mass cytometry to profile the immune system in human fetal liver, spleen, and intestine. With Hierarchical Stochastic Neighbor Embedding (HSNE) we distinguished 177 distinct immune cell clusters, including both previously identified and novel cell clusters. PCA analysis indicated substantial differences between the compositions of the immune system in the different organs. Through dual t-SNE we identified tissue-specific cell clusters, which were found both in the innate and adaptive compartment. To determine the spatial location of tissue-specific subsets we developed a 31-antibody panel to reveal both the immune compartment and surrounding stromal elements through analysis of snap-frozen tissue samples with imaging mass cytometry. Imaging mass cytometry reconstructed the tissue architecture and allowed both the characterization and determination of the location of the various immune cell clusters within the tissue context. Moreover, it further underpinned the distinctness of the immune system in the tissues. Thus, our results provide evidence for early compartmentalization of the adaptive and innate immune compartment in fetal spleen, liver, and intestine. Together, our data provide a unique and comprehensive overview of the composition and organization of the human fetal immune system in several tissues.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Nannan Guo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, Netherlands
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ahmed Mahfouz
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Boudewijn P F Lelieveldt
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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38
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Fernandez A, Mills EC, Koning F, Moreno FJ. Safety Assessment of Immune-Mediated Adverse Reactions to Novel Food Proteins. Trends Biotechnol 2019; 37:796-800. [DOI: 10.1016/j.tibtech.2019.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/06/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
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Lanzoni A, Castoldi AF, Kass GE, Terron A, De Seze G, Bal-Price A, Bois FY, Delclos KB, Doerge DR, Fritsche E, Halldorsson T, Kolossa-Gehring M, Hougaard Bennekou S, Koning F, Lampen A, Leist M, Mantus E, Rousselle C, Siegrist M, Steinberg P, Tritscher A, Van de Water B, Vineis P, Walker N, Wallace H, Whelan M, Younes M. Advancing human health risk assessment. EFSA J 2019; 17:e170712. [PMID: 32626449 PMCID: PMC7015480 DOI: 10.2903/j.efsa.2019.e170712] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The current/traditional human health risk assessment paradigm is challenged by recent scientific and technical advances, and ethical demands. The current approach is considered too resource intensive, is not always reliable, can raise issues of reproducibility, is mostly animal based and does not necessarily provide an understanding of the underlying mechanisms of toxicity. From an ethical and scientific viewpoint, a paradigm shift is required to deliver testing strategies that enable reliable, animal-free hazard and risk assessments, which are based on a mechanistic understanding of chemical toxicity and make use of exposure science and epidemiological data. This shift will require a new philosophy, new data, multidisciplinary expertise and more flexible regulations. Re-engineering of available data is also deemed necessary as data should be accessible, readable, interpretable and usable. Dedicated training to build the capacity in terms of expertise is necessary, together with practical resources allocated to education. The dialogue between risk assessors, risk managers, academia and stakeholders should be promoted further to understand scientific and societal needs. Genuine interest in taking risk assessment forward should drive the change and should be supported by flexible funding. This publication builds upon presentations made and discussions held during the break-out session 'Advancing risk assessment science - Human health' at EFSA's third Scientific Conference 'Science, Food and Society' (Parma, Italy, 18-21 September 2018).
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Affiliation(s)
| | | | | | | | | | | | - Frédéric Y Bois
- French National Institute for Industrial Environment and Risks FR
| | - K Barry Delclos
- National Center for Toxicological Research US Food and Drug Administration USA
| | - Daniel R Doerge
- National Center for Toxicological Research US Food and Drug Administration USA
| | - Ellen Fritsche
- Leibniz Research Institute for Environmental Medicine DE
| | | | | | | | | | | | | | - Ellen Mantus
- The National Academies of Sciences, Engineering, and Medicine USA
| | | | | | | | | | - Bob Van de Water
- Drug Discovery and Safety Leiden Academic Centre for Drug Research Leiden University NL
| | | | - Nigel Walker
- National Toxicology Program/National Institute of Environmental Health Sciences USA
| | - Heather Wallace
- Institute of Medical Sciences University of Aberdeen Scotland UK
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40
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Schinkelshoek MS, Fronczek R, Kooy-Winkelaar EMC, Petersen J, Reid HH, van der Heide A, Drijfhout JW, Rossjohn J, Lammers GJ, Koning F. H1N1 hemagglutinin-specific HLA-DQ6-restricted CD4+ T cells can be readily detected in narcolepsy type 1 patients and healthy controls. J Neuroimmunol 2019; 332:167-175. [PMID: 31048269 DOI: 10.1016/j.jneuroim.2019.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/15/2022]
Abstract
Following the 2009 H1N1 influenza pandemic, an increased risk of narcolepsy type 1 was observed. Homology between an H1N1 hemagglutinin and two hypocretin sequences has been reported. T cell reactivity to these peptides was assessed in 81 narcolepsy type 1 patients and 19 HLA-DQ6-matched healthy controls. HLA-DQ6-restricted H1N1 hemagglutinin-specific T cell responses were detected in 28.4% of patients and 15.8% of controls. Despite structural homology between HLA-DQ6-hypocretin and -H1N1 peptide complexes, T cell cross-reactivity was not detected. These results indicate that it is unlikely that cross-reactivity between H1N1 hemagglutinin and hypocretin peptides presented by HLA-DQ6 is involved in the development of narcolepsy.
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Affiliation(s)
- M S Schinkelshoek
- Department of Neurology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands; Sleep Wake Centre SEIN, Achterweg 5, 2103 SW Heemstede, the Netherlands.
| | - R Fronczek
- Department of Neurology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands; Sleep Wake Centre SEIN, Achterweg 5, 2103 SW Heemstede, the Netherlands
| | - E M C Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - J Petersen
- Infection and Immunity Program, The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - H H Reid
- Infection and Immunity Program, The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - A van der Heide
- Department of Neurology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - J W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - J Rossjohn
- Infection and Immunity Program, The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - G J Lammers
- Department of Neurology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands; Sleep Wake Centre SEIN, Achterweg 5, 2103 SW Heemstede, the Netherlands
| | - F Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, the Netherlands
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41
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Abdelaal T, van Unen V, Höllt T, Koning F, Reinders MJT, Mahfouz A. Predicting Cell Populations in Single Cell Mass Cytometry Data. Cytometry A 2019; 95:769-781. [PMID: 30861637 PMCID: PMC6767556 DOI: 10.1002/cyto.a.23738] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/05/2019] [Accepted: 02/11/2019] [Indexed: 11/17/2022]
Abstract
Mass cytometry by time‐of‐flight (CyTOF) is a valuable technology for high‐dimensional analysis at the single cell level. Identification of different cell populations is an important task during the data analysis. Many clustering tools can perform this task, which is essential to identify “new” cell populations in explorative experiments. However, relying on clustering is laborious since it often involves manual annotation, which significantly limits the reproducibility of identifying cell‐populations across different samples. The latter is particularly important in studies comparing different conditions, for example in cohort studies. Learning cell populations from an annotated set of cells solves these problems. However, currently available methods for automatic cell population identification are either complex, dependent on prior biological knowledge about the populations during the learning process, or can only identify canonical cell populations. We propose to use a linear discriminant analysis (LDA) classifier to automatically identify cell populations in CyTOF data. LDA outperforms two state‐of‐the‐art algorithms on four benchmark datasets. Compared to more complex classifiers, LDA has substantial advantages with respect to the interpretable performance, reproducibility, and scalability to larger datasets with deeper annotations. We apply LDA to a dataset of ~3.5 million cells representing 57 cell populations in the Human Mucosal Immune System. LDA has high performance on abundant cell populations as well as the majority of rare cell populations, and provides accurate estimates of cell population frequencies. Further incorporating a rejection option, based on the estimated posterior probabilities, allows LDA to identify previously unknown (new) cell populations that were not encountered during training. Altogether, reproducible prediction of cell population compositions using LDA opens up possibilities to analyze large cohort studies based on CyTOF data. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Tamim Abdelaal
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628 XE, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands.,Computer Graphics and Visualization, Delft University of Technology, Delft 2628 XE, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628 XE, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft 2628 XE, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
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42
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Miranda NFD, Vries NLD, Unen VV, Abdelaal T, Ijsselsteijn ME, Breggen RVD, Farina-Sarasqueta A, Peeters KC, Höllt T, Lelieveldt BP, Koning F. Abstract A063: Multidimensional cytometric analysis of colorectal cancer reveals novel and diverse mediators of antitumor immunity. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Checkpoint blockade has revived the potential of immunotherapy for cancer treatment. For optimal application and development of cancer immunotherapies, a comprehensive understanding of the antitumor immune response is required. We unraveled local and systemic immune profiles of colorectal cancer by multidimensional mass cytometric analysis of 36 immune cell markers at the single-cell level in tumor tissues, tumor-associated lymph nodes, adjacent normal mucosa, and peripheral blood samples from CRC patients. We identified 218 phenotypically distinct immune cell clusters, including a previously neglected innate lymphoid cell (CD7+CD3-CD127-CD45RO+CD56+) population with cytotoxic potential. This subset demonstrated a tissue-resident (CD69+, CD103+) phenotype, and was most abundant in the immunogenic mismatch repair deficient (MMRd) cancers. Furthermore, tumor-resident immune cell populations were identified across the adaptive (CD4+ and CD8+) and innate (gammadelta) T-cell compartments showing a highly similar activated (HLA-DR+, CD38+, PD-1+) phenotype. PD-1 intermediate and PD-1 high CD8+ T-cell subsets represented distinct states of T-cell activation that further discriminated immunogenic from non-immunogenic colorectal cancers. Remarkably, activated gammadelta T-cells were specific for MMRd cancers, and their potential role in the response to PD-1 checkpoint blockade requires further clarification. The nonactivated counterparts of the tumor-resident CD103+PD-1+ cytotoxic and gammadelta T-cells were present in both tumor and healthy colorectal tissues. We did not detect any of the aforementioned tumor-resident immune cell populations in lymph node samples, with the exception of a tumor-positive lymph node. This indicates that the critical immune cell populations with antitumor activity reside in the colorectal mucosa, and that the role of lymph nodes in the antitumor immune response should be revisited. Finally, by applying imaging mass cytometry we demonstrated that the cytotoxic anti-tumor response in colorectal cancer is highly diverse and not restricted to cytotoxic T-cells, which opens new avenues for the management of this disease.The findings presented here advance the paradigm of antitumor immunity in colorectal cancer and provide a blueprint for the detailed characterization of the involved immune cell subsets. The coordinated action of innate and adaptive immune cell populations suggests a multitargeted exploitation of their antitumor properties in a therapeutic setting.
Citation Format: Noel F. de Miranda, Natasja L. de Vries, Vincent van Unen, Tamim Abdelaal, Marieke E. Ijsselsteijn, Ruud van der Breggen, Arantza Farina-Sarasqueta, Koen C.M.J. Peeters, Thomas Höllt, Boudewijn P.F. Lelieveldt, Frits Koning. Multidimensional cytometric analysis of colorectal cancer reveals novel and diverse mediators of antitumor immunity [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A063.
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Affiliation(s)
| | | | | | - Tamim Abdelaal
- Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | - Thomas Höllt
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frits Koning
- Leiden University Medical Center, Leiden, The Netherlands
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43
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Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F. Memory CD4 + T cells are generated in the human fetal intestine. Nat Immunol 2019; 20:301-312. [PMID: 30664737 PMCID: PMC6420108 DOI: 10.1038/s41590-018-0294-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022]
Abstract
The fetus is thought to be protected from exposure to foreign antigens,
yet CD45RO+ T cells reside in the fetal intestine. Here we combined
functional assays with mass cytometry, single-cell RNA-sequencing and
high-throughput T cell antigen receptor (TCR) sequencing to characterize the
CD4+ T cell compartment in the human fetal intestine. We
identified 22 CD4+ T cell clusters, including naive-like,
regulatory-like and memory-like subpopulations, which were confirmed and further
characterized at the transcriptional level. Memory-like CD4+ T cells
had high expression of Ki-67, indicative of cell division, and CD5, a surrogate
marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway
analysis revealed a differentiation trajectory associated with cellular
activation and proinflammatory effector functions, and TCR repertoire analysis
indicated clonal expansions, distinct repertoire characteristics and
interconnections between subpopulations of memory-like CD4+ T cells.
Imaging-mass cytometry indicated that memory-like CD4+ T cells
colocalized with antigen-presenting cells. Collectively, these results provide
evidence for the generation of memory-like CD4+ T cells in the human
fetal intestine that is consistent with exposure to foreign antigens.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands
| | - Nannan Guo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, Delft, the Netherlands
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia.,Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Boudewijn P F Lelieveldt
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
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44
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Fergusson JR, Morgan MD, Bruchard M, Huitema L, Heesters BA, van Unen V, van Hamburg JP, van der Wel NN, Picavet D, Koning F, Tas SW, Anderson MS, Marioni JC, Holländer GA, Spits H. Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens. Front Immunol 2019; 9:2902. [PMID: 30692988 PMCID: PMC6340304 DOI: 10.3389/fimmu.2018.02902] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022] Open
Abstract
Expression of the Autoimmune regulator (AIRE) outside of the thymus has long been suggested in both humans and mice, but the cellular source in humans has remained undefined. Here we identify AIRE expression in human tonsils and extensively analyzed these "extra-thymic AIRE expressing cells" (eTACs) using combinations of flow cytometry, CyTOF and single cell RNA-sequencing. We identified AIRE+ cells as dendritic cells (DCs) with a mature and migratory phenotype including high levels of antigen presenting molecules and costimulatory molecules, and specific expression of CD127, CCR7, and PDL1. These cells also possessed the ability to stimulate and re-stimulate T cells and displayed reduced responses to toll-like receptor (TLR) agonists compared to conventional DCs. While expression of AIRE was enriched within CCR7+CD127+ DCs, single-cell RNA sequencing revealed expression of AIRE to be transient, rather than stable, and associated with the differentiation to a mature phenotype. The role of AIRE in central tolerance induction within the thymus is well-established, however our study shows that AIRE expression within the periphery is not associated with an enriched expression of tissue-restricted antigens (TRAs). This unexpected finding, suggestive of wider functions of AIRE, may provide an explanation for the non-autoimmune symptoms of APECED patients who lack functional AIRE.
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Affiliation(s)
- Joannah R. Fergusson
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Melanie Bruchard
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
| | - Leonie Huitema
- Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology & immunology Center (ARC), Academic Medical Center, Amsterdam, Netherlands
| | - Balthasar A. Heesters
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Jan Piet van Hamburg
- Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology & immunology Center (ARC), Academic Medical Center, Amsterdam, Netherlands
| | | | - Daisy Picavet
- EMCA, Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Frits Koning
- Leiden University Medical Center, Leiden, Netherlands
| | - Sander W. Tas
- Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology & immunology Center (ARC), Academic Medical Center, Amsterdam, Netherlands
| | - Mark S. Anderson
- UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, United States
| | - John C. Marioni
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Georg A. Holländer
- Laboratory of Developmental Immunology, Weatherall Institute of Molecular Medicine and Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Hergen Spits
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands
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45
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Vries ND, Unen VV, Abdelaal T, Herk MV, Van der Breggen R, Sarasqueta AF, Höllt T, Lelieveldt B, Koning F, Miranda ND. PO-260 Deep phenotyping of colorectal cancers by high-dimensional mass cytometry reveals tumor-specific immune landscapes. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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46
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Li N, van Unen V, Höllt T, Thompson A, van Bergen J, Pezzotti N, Eisemann E, Vilanova A, Chuva de Sousa Lopes SM, Lelieveldt BPF, Koning F. Mass cytometry reveals innate lymphoid cell differentiation pathways in the human fetal intestine. J Exp Med 2018; 215:1383-1396. [PMID: 29511064 PMCID: PMC5940268 DOI: 10.1084/jem.20171934] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/16/2018] [Accepted: 02/22/2018] [Indexed: 11/25/2022] Open
Abstract
Li et al. apply mass cytometry to delineate the fetal gut innate lymphoid cell (ILC) population and utilize a t-SNE–based approach to predict potential differentiation trajectories. They identify an int-ILC subset that differentiates into NK cells or ILC3s in vitro. Innate lymphoid cells (ILCs) are abundant in mucosal tissues and involved in tissue homeostasis and barrier function. Although several ILC subsets have been identified, it is unknown if additional heterogeneity exists, and their differentiation pathways remain largely unclear. We applied mass cytometry to analyze ILCs in the human fetal intestine and distinguished 34 distinct clusters through a t-SNE–based analysis. A lineage (Lin)−CD7+CD127−CD45RO+CD56+ population clustered between the CD127+ ILC and natural killer (NK) cell subsets, and expressed diverse levels of Eomes, T-bet, GATA3, and RORγt. By visualizing the dynamics of the t-SNE computation, we identified smooth phenotypic transitions from cells within the Lin−CD7+CD127−CD45RO+CD56+ cluster to both the NK cells and CD127+ ILCs, revealing potential differentiation trajectories. In functional differentiation assays, the Lin−CD7+CD127−CD45RO+CD56+CD8a− cells could develop into CD45RA+ NK cells and CD127+RORγt+ ILC3-like cells. Thus, we identified a previously unknown intermediate innate subset that can differentiate into ILC3 and NK cells.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands.,Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Allan Thompson
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen van Bergen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Nicola Pezzotti
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Elmar Eisemann
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualization Group, Delft University of Technology, Delft, Netherlands
| | | | - Boudewijn P F Lelieveldt
- Department of LKEB Radiology, Leiden University Medical Center, Leiden, Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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47
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Redeker A, Remmerswaal EBM, van der Gracht ETI, Welten SPM, Höllt T, Koning F, Cicin-Sain L, Nikolich-Žugich J, Ten Berge IJM, van Lier RAW, van Unen V, Arens R. The Contribution of Cytomegalovirus Infection to Immune Senescence Is Set by the Infectious Dose. Front Immunol 2018; 8:1953. [PMID: 29367854 PMCID: PMC5768196 DOI: 10.3389/fimmu.2017.01953] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/18/2017] [Indexed: 01/17/2023] Open
Abstract
The relationship between human cytomegalovirus (HCMV) infections and accelerated immune senescence is controversial. Whereas some studies reported a CMV-associated impaired capacity to control heterologous infections at old age, other studies could not confirm this. We hypothesized that these discrepancies might relate to the variability in the infectious dose of CMV occurring in real life. Here, we investigated the influence of persistent CMV infection on immune perturbations and specifically addressed the role of the infectious dose on the contribution of CMV to accelerated immune senescence. We show in experimental mouse models that the degree of mouse CMV (MCMV)-specific memory CD8+ T cell accumulation and the phenotypic T cell profile are directly influenced by the infectious dose, and data on HCMV-specific T cells indicate a similar connection. Detailed cluster analysis of the memory CD8+ T cell development showed that high-dose infection causes a differentiation pathway that progresses faster throughout the life span of the host, suggesting a virus–host balance that is influenced by aging and infectious dose. Importantly, short-term MCMV infection in adult mice is not disadvantageous for heterologous superinfection with lymphocytic choriomeningitis virus (LCMV). However, following long-term CMV infection the strength of the CD8+ T cell immunity to LCMV superinfection was affected by the initial CMV infectious dose, wherein a high infectious dose was found to be a prerequisite for impaired heterologous immunity. Altogether our results underscore the importance of stratification based on the size and differentiation of the CMV-specific memory T cell pools for the impact on immune senescence, and indicate that reduction of the latent/lytic viral load can be beneficial to diminish CMV-associated immune senescence.
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Affiliation(s)
- Anke Redeker
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ester B M Remmerswaal
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands.,Renal Transplant Unit, Division of Internal Medicine, Academic Medical Center, Amsterdam, Netherlands
| | - Esmé T I van der Gracht
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Suzanne P M Welten
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Thomas Höllt
- Delft University of Technology, Delft, Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Luka Cicin-Sain
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Janko Nikolich-Žugich
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, United States
| | - Ineke J M Ten Berge
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, Netherlands.,Renal Transplant Unit, Division of Internal Medicine, Academic Medical Center, Amsterdam, Netherlands
| | - René A W van Lier
- Sanquin Blood Supply Foundation and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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48
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Hollt T, Pezzotti N, van Unen V, Koning F, Lelieveldt BPF, Vilanova A. CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis. IEEE Trans Vis Comput Graph 2018; 24:739-748. [PMID: 28866537 DOI: 10.1109/tvcg.2017.2744318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-cell analysis through mass cytometry has become an increasingly important tool for immunologists to study the immune system in health and disease. Mass cytometry creates a high-dimensional description vector for single cells by time-of-flight measurement. Recently, t-Distributed Stochastic Neighborhood Embedding (t-SNE) has emerged as one of the state-of-the-art techniques for the visualization and exploration of single-cell data. Ever increasing amounts of data lead to the adoption of Hierarchical Stochastic Neighborhood Embedding (HSNE), enabling the hierarchical representation of the data. Here, the hierarchy is explored selectively by the analyst, who can request more and more detail in areas of interest. Such hierarchies are usually explored by visualizing disconnected plots of selections in different levels of the hierarchy. This poses problems for navigation, by imposing a high cognitive load on the analyst. In this work, we present an interactive summary-visualization to tackle this problem. CyteGuide guides the analyst through the exploration of hierarchically represented single-cell data, and provides a complete overview of the current state of the analysis. We conducted a two-phase user study with domain experts that use HSNE for data exploration. We first studied their problems with their current workflow using HSNE and the requirements to ease this workflow in a field study. These requirements have been the basis for our visual design. In the second phase, we verified our proposed solution in a user evaluation.
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49
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van Unen V, Höllt T, Pezzotti N, Li N, Reinders MJT, Eisemann E, Koning F, Vilanova A, Lelieveldt BPF. Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types. Nat Commun 2017; 8:1740. [PMID: 29170529 PMCID: PMC5700955 DOI: 10.1038/s41467-017-01689-9] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for the data analysis. In particular, dimensionality reduction-based techniques like t-SNE offer single-cell resolution but are limited in the number of cells that can be analyzed. Here we introduce Hierarchical Stochastic Neighbor Embedding (HSNE) for the analysis of mass cytometry data sets. HSNE constructs a hierarchy of non-linear similarities that can be interactively explored with a stepwise increase in detail up to the single-cell level. We apply HSNE to a study on gastrointestinal disorders and three other available mass cytometry data sets. We find that HSNE efficiently replicates previous observations and identifies rare cell populations that were previously missed due to downsampling. Thus, HSNE removes the scalability limit of conventional t-SNE analysis, a feature that makes it highly suitable for the analysis of massive high-dimensional data sets. Single cell profiling yields high dimensional data of very large numbers of cells, posing challenges of visualization and analysis. Here the authors introduce a method for analysis of mass cytometry data that can handle very large datasets and allows their intuitive and hierarchical exploration.
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Affiliation(s)
- Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands.,Computational Biology Center, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Nicola Pezzotti
- Computer Graphics and Visualization Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands
| | - Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Marcel J T Reinders
- Pattern Recognition and Bioinformatics Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands
| | - Elmar Eisemann
- Computer Graphics and Visualization Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualization Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands
| | - Boudewijn P F Lelieveldt
- Pattern Recognition and Bioinformatics Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands. .,Division of Image Processing, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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50
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de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE. A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics. J Immunol 2017; 199:3679-3690. [PMID: 29021373 DOI: 10.4049/jimmunol.1700502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022]
Abstract
In different macaque species, the MHC A2*05 gene is present in abundance, and its gene products are characterized by low cell-surface expression and a highly conserved peptide-binding cleft. We have characterized the peptide-binding motif of Mamu-A2*05:01, and elucidated the binding capacity for virus-derived peptides. The macaque A2*05 allotype prefers the basic amino acid arginine at the second position of the peptide, and hydrophobic and polar amino acids at the C-terminal end. These preferences are shared with HLA-B*27 and Mamu-B*008, molecules shown to be involved in elite control in human HIV type 1 and macaque SIV infections, respectively. In contrast, however, Mamu-A2*05 preferentially binds 8-mer peptides. Retention in the endoplasmic reticulum seems to be the cause of the lower cell-surface expression. Subsequent peptide-binding studies have illustrated that Mamu-A2*05:01 is able to bind SIV-epitopes known to evoke a strong CD8+ T cell response in the context of the Mamu-B*008 allotype in SIV-infected rhesus macaques. Thus, the macaque A2*05 gene encodes a specialized MHC class I molecule, and is most likely transported to the cell surface only when suitable peptides become available.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Christelle Vangenot
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; and
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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