151
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Fitch N, Marshall SJ, Stefura WP, Chooniedass R, Becker AB, HayGlass KT. Quantifying Human Innate Cytokine and Chemokine Responses Ex Vivo via Pattern Recognition Receptor Stimulation. Methods Mol Biol 2019; 2020:77-89. [PMID: 31177493 DOI: 10.1007/978-1-4939-9591-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Linkages between human innate immune capacity, the environment in which we live, and the development of clinical tolerance versus a spectrum of disease phenotypes are a major focus of inflammatory disease research. While extensive epidemiologic evidence indicates key roles for the microbiome and other environmental factors, the underlying mechanisms that explain how these stimuli lead to a given clinical phenotype remain speculative. Here we review strategies for characterizing human cytokine production ex vivo in response to innate immune receptor stimulation with defined ligands. Human cytokine and chemokine biomarker data provides a tool to test hypotheses on the relationship between innate immune capacity in vivo and expression of current or future clinical phenotypes. The most important limitations of experimental strategies that have been used to date are reviewed. Detailed experimental protocols are provided for characterization of pattern recognition receptor (PRR)-driven stimulation with a panel of bacterial (TLR4, TLR5) and viral (TLR3, TLR7/8, RIG-I/MDA5) ligands to assess the role played by human pro-inflammatory, anti-inflammatory, Th1-like, and Th2-like responses. The importance of characterizing human innate immune phenotypes extends beyond discovery-based research to development of improved strategies for prevention or inhibition of chronic inflammatory diseases, improved design of immunization programs, and more effective cancer immunotherapy.
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Affiliation(s)
- Natascha Fitch
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Stephanie J Marshall
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Orillia Soldiers Memorial Hospital, Orillia, ON, Canada
| | - William P Stefura
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Rishma Chooniedass
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Allan B Becker
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Kent T HayGlass
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada. .,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.
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152
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Stern L, Withers B, Avdic S, Gottlieb D, Abendroth A, Blyth E, Slobedman B. Human Cytomegalovirus Latency and Reactivation in Allogeneic Hematopoietic Stem Cell Transplant Recipients. Front Microbiol 2019; 10:1186. [PMID: 31191499 PMCID: PMC6546901 DOI: 10.3389/fmicb.2019.01186] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022] Open
Abstract
Human cytomegalovirus (HCMV) reactivation is a major infectious cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). HCMV is a ubiquitous beta-herpesvirus which asymptomatically infects immunocompetent individuals but establishes lifelong latency, with the potential to reactivate to a life-threatening productive infection when the host immune system is suppressed or compromised. Opportunistic HCMV reactivation is the most common viral complication following engraftment after HSCT and is associated with a marked increase in non-relapse mortality, which appears to be linked to complex effects on post-transplant immune recovery. This minireview explores the cellular sites of HCMV latency and reactivation in HSCT recipients and provides an overview of the risk factors for HCMV reactivation post-HSCT. The impact of HCMV in shaping post-transplant immune reconstitution and its relationship with patient outcomes such as relapse and graft-versus-host disease will be discussed. Finally, we survey current and emerging strategies to prevent and control HCMV reactivation in HSCT recipients, with recent developments including adoptive T cell therapies to accelerate HCMV-specific T cell reconstitution and new anti-HCMV drug therapy for HCMV reactivation after HSCT.
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Affiliation(s)
- Lauren Stern
- Discipline of Infectious Diseases and Immunology, Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Barbara Withers
- Department of Haematology, St Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Selmir Avdic
- Westmead Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead, NSW, Australia
| | - David Gottlieb
- Westmead Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead, NSW, Australia.,Blood and Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia
| | - Allison Abendroth
- Discipline of Infectious Diseases and Immunology, Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Westmead Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead, NSW, Australia.,Blood and Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
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153
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Hasan M. [Milieu Intérieur: understanding healthy immune system heterogeneity to move along the path towards personalized medicine]. Med Sci (Paris) 2019; 35:423-430. [PMID: 31115325 DOI: 10.1051/medsci/2019077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Milieu Intérieur project aims to define the boundaries of a healthy immune system in steady state and upon immune stimulation, and to elucidate environmental and hereditary determinants of its variability. The project is based on an in-depth immune phenotyping of 1 000 healthy donors. By correlating the cytometry measurements of peripheral blood immune cell composition in homeostasis, with the associated metadata, we have defined reference values of phenotypes related to sex and age, and found a significant impact of latent cytomegalovirus infection and smoking on measured phenotypes. In addition, we identified eleven novel Single-Nucleotide Polymorphisms (SNPs) associated with immune cell phenotypes. Immune response signatures were measured upon stimulation of fresh peripheral blood by 40 immune stimuli. Robust and standardized pipelines were established to quantify expression of 29 proteins and 572 genes and to explore genetic and non-genetic determinants of the variability of healthy immune response. The analytical approaches established by Milieu Intérieur and the collected data set represent an ideal reference for comparison studies of disease populations.
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Affiliation(s)
- Milena Hasan
- Cytométrie et Biomarqueurs (UTechS CB), Centre de recherche translationnelle (CRT), Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
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154
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Stereotypic Immune System Development in Newborn Children. Cell 2019; 174:1277-1292.e14. [PMID: 30142345 PMCID: PMC6108833 DOI: 10.1016/j.cell.2018.06.045] [Citation(s) in RCA: 415] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/18/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023]
Abstract
Epidemiological data suggest that early life exposures are key determinants of immune-mediated disease later in life. Young children are also particularly susceptible to infections, warranting more analyses of immune system development early in life. Such analyses mostly have been performed in mouse models or human cord blood samples, but these cannot account for the complex environmental exposures influencing human newborns after birth. Here, we performed longitudinal analyses in 100 newborn children, sampled up to 4 times during their first 3 months of life. From 100 μL of blood, we analyze the development of 58 immune cell populations by mass cytometry and 267 plasma proteins by immunoassays, uncovering drastic changes not predictable from cord blood measurements but following a stereotypic pattern. Preterm and term children differ at birth but converge onto a shared trajectory, seemingly driven by microbial interactions and hampered by early gut bacterial dysbiosis. Cord blood is not representative of postnatal immunity Preterm and term children differ at birth but rapidly converge thereafter Immune system development follows a stereotypic pattern early in life Dynamic parameters imply microbial interactions during early immune development
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155
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Das J, Lanier LL. Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute? J Leukoc Biol 2019; 105:1305-1317. [PMID: 31063614 DOI: 10.1002/jlb.6mr1218-505r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 12/31/2022] Open
Abstract
The use of mathematical and computational tools in investigating Natural Killer (NK) cell biology and in general the immune system has increased steadily in the last few decades. However, unlike the physical sciences, there is a persistent ambivalence, which however is increasingly diminishing, in the biology community toward appreciating the utility of quantitative tools in addressing questions of biological importance. We survey some of the recent developments in the application of quantitative approaches for investigating different problems in NK cell biology and evaluate opportunities and challenges of using quantitative methods in providing biological insights in NK cell biology.
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Affiliation(s)
- Jayajit Das
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Physics, The Ohio State University, Columbus, Ohio, USA.,Biophysics Program, The Ohio State University, Columbus, Ohio, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, California, USA
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156
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Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun 2019; 10:1906. [PMID: 31015506 PMCID: PMC6479061 DOI: 10.1038/s41467-019-09930-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Studying immune repertoire in the context of organ transplant provides important information on how adaptive immunity may contribute and modulate graft rejection. Here we characterize the peripheral blood immune repertoire of individuals before and after kidney transplant using B cell receptor sequencing in a longitudinal clinical study. Individuals who develop rejection after transplantation have a more diverse immune repertoire before transplant, suggesting a predisposition for post-transplant rejection risk. Additionally, over 2 years of follow-up, patients who develop rejection demonstrate a specific set of expanded clones that persist after the rejection. While there is an overall reduction of peripheral B cell diversity, likely due to increased general immunosuppression exposure in this cohort, the detection of specific IGHV gene usage across all rejecting patients supports that a common pool of immunogenic antigens may drive post-transplant rejection. Our findings may have clinical implications for the prediction and clinical management of kidney transplant rejection.
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MESH Headings
- Adolescent
- Adult
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Child
- Child, Preschool
- Clone Cells
- Female
- Gene Expression
- Graft Rejection/genetics
- Graft Rejection/immunology
- Graft Rejection/pathology
- Graft Survival/genetics
- Humans
- Immunocompromised Host
- Infant
- Kidney/immunology
- Kidney/pathology
- Kidney/surgery
- Kidney Transplantation
- Longitudinal Studies
- Male
- Middle Aged
- Polymorphism, Genetic/immunology
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Renal Insufficiency, Chronic/genetics
- Renal Insufficiency, Chronic/immunology
- Renal Insufficiency, Chronic/pathology
- Renal Insufficiency, Chronic/surgery
- Sequence Analysis, DNA
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Tara K Sigdel
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Juliane M Liberto
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Flavio Vincenti
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Department of Pediatrics, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
| | - Minnie M Sarwal
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
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157
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Manel N, Di Santo JP. Editorial overview: Pillars of innate immunity: constantly learning and trying to remember. Curr Opin Immunol 2019; 56:iii-vi. [PMID: 30981385 DOI: 10.1016/j.coi.2019.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Nicolas Manel
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005, Paris, France
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France
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158
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Gomes GF, Peixoto RDDF, Maciel BG, Santos KFD, Bayma LR, Feitoza Neto PA, Fernandes TN, de Abreu CC, Casseb SMM, de Lima CM, de Oliveira MA, Diniz DG, Vasconcelos PFDC, Sosthenes MCK, Diniz CWP. Differential Microglial Morphological Response, TNFα, and Viral Load in Sedentary-like and Active Murine Models After Systemic Non-neurotropic Dengue Virus Infection. J Histochem Cytochem 2019; 67:419-439. [PMID: 30924711 DOI: 10.1369/0022155419835218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peripheral inflammatory stimuli increase proinflammatory cytokines in the bloodstream and central nervous system and activate microglial cells. Here we tested the hypothesis that contrasting environments mimicking sedentary and active lives would be associated with differential microglial morphological responses, inflammatory cytokines concentration, and virus load in the peripheral blood. For this, mice were maintained either in standard (standard environment) or enriched cages (enriched environment) and then subjected to a single (DENV1) serotype infection. Blood samples from infected animals showed higher viral loads and higher tumor necrosis factor-α (TNFα) mRNA concentrations than control subjects. Using an unbiased stereological sampling approach, we selected 544 microglia from lateral septum for microscopic 3D reconstruction. Morphological complexity contributed most to cluster formation. Infected groups exhibited significant increase in the microglia morphological complexity and number, despite the absence of dengue virus antigens in the brain. Two microglial phenotypes (type I with lower and type II with higher morphological complexity) were found in both infected and control groups. However, microglia from infected mice maintained in enriched environment showed only one morphological phenotype. Two-way ANOVA revealed that environmental changes and infection influenced type-I and II microglial morphologies and number. Environmental enrichment and infection interactions may contribute to microglial morphological change to a point that type-I and II morphological phenotypes could no longer be distinguished in infected mice from enriched environment. Significant linear correlation was found between morphological complexity and TNFα peripheral blood. Our findings demonstrated that sedentary-like and active murine models exhibited differential microglial responses and peripheral inflammation to systemic non-neurotropic infections with DENV1 virus.
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Affiliation(s)
- Giovanni Freitas Gomes
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Railana Deise da Fonseca Peixoto
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Brenda Gonçalves Maciel
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Kedma Farias Dos Santos
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Lohrane Rosa Bayma
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Pedro Alves Feitoza Neto
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Taiany Nogueira Fernandes
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Cintya Castro de Abreu
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | | | - Camila Mendes de Lima
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Marcus Augusto de Oliveira
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Daniel Guerreiro Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | | | - Marcia Consentino Kronka Sosthenes
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
| | - Cristovam Wanderley Picanço Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, Brasil
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159
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A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring. Nat Med 2019; 25:487-495. [PMID: 30842675 DOI: 10.1038/s41591-019-0381-y] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/07/2019] [Indexed: 01/08/2023]
Abstract
Immune responses generally decline with age. However, the dynamics of this process at the individual level have not been characterized, hindering quantification of an individual's immune age. Here, we use multiple 'omics' technologies to capture population- and individual-level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observed high inter-individual variability in the rates of change of cellular frequencies that was dictated by their baseline values, allowing identification of steady-state levels toward which a cell subset converged and the ordered convergence of multiple cell subsets toward an older adult homeostasis. These data form a high-dimensional trajectory of immune aging (IMM-AGE) that describes a person's immune status better than chronological age. We show that the IMM-AGE score predicted all-cause mortality beyond well-established risk factors in the Framingham Heart Study, establishing its potential use in clinics for identification of patients at risk.
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160
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Human Immunology through the Lens of Evolutionary Genetics. Cell 2019; 177:184-199. [DOI: 10.1016/j.cell.2019.02.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023]
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161
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Gutierrez-Arcelus M, Teslovich N, Mola AR, Polidoro RB, Nathan A, Kim H, Hannes S, Slowikowski K, Watts GFM, Korsunsky I, Brenner MB, Raychaudhuri S, Brennan PJ. Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. Nat Commun 2019; 10:687. [PMID: 30737409 PMCID: PMC6368609 DOI: 10.1038/s41467-019-08604-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 01/21/2019] [Indexed: 02/06/2023] Open
Abstract
How innate T cells (ITC), including invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, and γδ T cells, maintain a poised effector state has been unclear. Here we address this question using low-input and single-cell RNA-seq of human lymphocyte populations. Unbiased transcriptomic analyses uncover a continuous ‘innateness gradient’, with adaptive T cells at one end, followed by MAIT, iNKT, γδ T and natural killer cells at the other end. Single-cell RNA-seq reveals four broad states of innateness, and heterogeneity within canonical innate and adaptive populations. Transcriptional and functional data show that innateness is characterized by pre-formed mRNA encoding effector functions, but impaired proliferation marked by decreased baseline expression of ribosomal genes. Together, our data shed new light on the poised state of ITC, in which innateness is defined by a transcriptionally-orchestrated trade-off between rapid cell growth and rapid effector function. Innate T cells (ITC) contain many subsets and are poised to promptly respond to antigens and pathogens, but how this poised state is maintained is still unclear. Here the authors perform single-cell RNA-seq to align the various ITC subsets along an ‘innateness gradient’ that is associated with changes in proliferation and effector functions.
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Affiliation(s)
- Maria Gutierrez-Arcelus
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nikola Teslovich
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alex R Mola
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rafael B Polidoro
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Aparna Nathan
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hyun Kim
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Susan Hannes
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kamil Slowikowski
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Gerald F M Watts
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ilya Korsunsky
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael B Brenner
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Soumya Raychaudhuri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA, 02115. .,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA. .,Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Faculty of Medical and Human Sciences, University of Manchester, Manchester, M13 9PL, UK.
| | - Patrick J Brennan
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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162
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Lim YW, Chen-Harris H, Mayba O, Lianoglou S, Wuster A, Bhangale T, Khan Z, Mariathasan S, Daemen A, Reeder J, Haverty PM, Forrest WF, Brauer M, Mellman I, Albert ML. Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration. Proc Natl Acad Sci U S A 2018; 115:E11701-E11710. [PMID: 30463956 PMCID: PMC6294879 DOI: 10.1073/pnas.1804506115] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cancer immunotherapy has emerged as an effective therapy in a variety of cancers. However, a key challenge in the field is that only a subset of patients who receive immunotherapy exhibit durable response. It has been hypothesized that host genetics influences the inherent immune profiles of patients and may underlie their differential response to immunotherapy. Herein, we systematically determined the association of common germline genetic variants with gene expression and immune cell infiltration of the tumor. We identified 64,094 expression quantitative trait loci (eQTLs) that associated with 18,210 genes (eGenes) across 24 human cancers. Overall, eGenes were enriched for their being involved in immune processes, suggesting that expression of immune genes can be shaped by hereditary genetic variants. We identified the endoplasmic reticulum aminopeptidase 2 (ERAP2) gene as a pan-cancer type eGene whose expression levels stratified overall survival in a subset of patients with bladder cancer receiving anti-PD-L1 (atezolizumab) therapy. Finally, we identified 103 gene signature QTLs (gsQTLs) that were associated with predicted immune cell abundance within the tumor microenvironment. Our findings highlight the impact of germline SNPs on cancer-immune phenotypes and response to therapy; and these analyses provide a resource for integration of germline genetics as a component of personalized cancer immunotherapy.
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Affiliation(s)
- Yoong Wearn Lim
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080
| | - Haiyin Chen-Harris
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080
| | - Oleg Mayba
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Steve Lianoglou
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Arthur Wuster
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
- Department of Human Genetics, Genentech, South San Francisco, CA 94080
| | - Tushar Bhangale
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
- Department of Human Genetics, Genentech, South San Francisco, CA 94080
| | - Zia Khan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080
| | | | - Anneleen Daemen
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Jens Reeder
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Peter M Haverty
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - William F Forrest
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Matthew Brauer
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Ira Mellman
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080
| | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080;
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163
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Kroon EE, Coussens AK, Kinnear C, Orlova M, Möller M, Seeger A, Wilkinson RJ, Hoal EG, Schurr E. Neutrophils: Innate Effectors of TB Resistance? Front Immunol 2018; 9:2637. [PMID: 30487797 PMCID: PMC6246713 DOI: 10.3389/fimmu.2018.02637] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Certain individuals are able to resist Mycobacterium tuberculosis infection despite persistent and intense exposure. These persons do not exhibit adaptive immune priming as measured by tuberculin skin test (TST) and interferon-γ (IFN-γ) release assay (IGRA) responses, nor do they develop active tuberculosis (TB). Genetic investigation of individuals who are able to resist M. tuberculosis infection shows there are likely a combination of genetic variants that contribute to the phenotype. The contribution of the innate immune system and the exact cells involved in this phenotype remain incompletely elucidated. Neutrophils are prominent candidates for possible involvement as primers for microbial clearance. Significant variability is observed in neutrophil gene expression and DNA methylation. Furthermore, inter-individual variability is seen between the mycobactericidal capacities of donor neutrophils. Clearance of M. tuberculosis infection is favored by the mycobactericidal activity of neutrophils, apoptosis, effective clearance of cells by macrophages, and resolution of inflammation. In this review we will discuss the different mechanisms neutrophils utilize to clear M. tuberculosis infection. We discuss the duality between neutrophils' ability to clear infection and how increasing numbers of neutrophils contribute to active TB severity and mortality. Further investigation into the potential role of neutrophils in innate immune-mediated M. tuberculosis infection resistance is warranted since it may reveal clinically important activities for prevention as well as vaccine and treatment development.
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Affiliation(s)
- Elouise E Kroon
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anna K Coussens
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Infection and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Division of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Craig Kinnear
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada.,Departments of Medicine and Human Genetics, McGill University, Montreal, QC, Canada
| | - Marlo Möller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Allison Seeger
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Imperial College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Eileen G Hoal
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,McGill International TB Centre, McGill University, Montreal, QC, Canada.,Departments of Medicine and Human Genetics, McGill University, Montreal, QC, Canada
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164
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Lagou V, Garcia-Perez JE, Smets I, Van Horebeek L, Vandebergh M, Chen L, Mallants K, Prezzemolo T, Hilven K, Humblet-Baron S, Moisse M, Van Damme P, Boeckxstaens G, Bowness P, Dubois B, Dooley J, Liston A, Goris A. Genetic Architecture of Adaptive Immune System Identifies Key Immune Regulators. Cell Rep 2018; 25:798-810.e6. [PMID: 30332657 PMCID: PMC6205839 DOI: 10.1016/j.celrep.2018.09.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
The immune system is highly diverse, but characterization of its genetic architecture has lagged behind the vast progress made by genome-wide association studies (GWASs) of emergent diseases. Our GWAS for 54 functionally relevant phenotypes of the adaptive immune system in 489 healthy individuals identifies eight genome-wide significant associations explaining 6%-20% of variance. Coding and splicing variants in PTPRC and COMMD10 are involved in memory T cell differentiation. Genetic variation controlling disease-relevant T helper cell subsets includes RICTOR and STON2 associated with Th2 and Th17, respectively, and the interferon-lambda locus controlling regulatory T cell proliferation. Early and memory B cell differentiation stages are associated with variation in LARP1B and SP4. Finally, the latrophilin family member ADGRL2 correlates with baseline pro-inflammatory interleukin-6 levels. Suggestive associations reveal mechanisms of autoimmune disease associations, in particular related to pro-inflammatory cytokine production. Pinpointing these key human immune regulators offers attractive therapeutic perspectives.
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Affiliation(s)
- Vasiliki Lagou
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Josselyn E Garcia-Perez
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Ide Smets
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Lies Van Horebeek
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Marijne Vandebergh
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Liye Chen
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Klara Mallants
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Teresa Prezzemolo
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Kelly Hilven
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Stephanie Humblet-Baron
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Matthieu Moisse
- Leuven Brain Institute (LBI), Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium; KU Leuven Department of Neurosciences, Experimental Neurology, 3000 Leuven, Belgium
| | - Philip Van Damme
- Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium; KU Leuven Department of Neurosciences, Experimental Neurology, 3000 Leuven, Belgium
| | - Guy Boeckxstaens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for GI Disorders (TARGID), 3000 Leuven, Belgium; Department of Gastroenterology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Bénédicte Dubois
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - James Dooley
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Adrian Liston
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium.
| | - An Goris
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium.
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165
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von Seth E, Zimmer CL, Reuterwall-Hansson M, Barakat A, Arnelo U, Bergquist A, Ivarsson MA, Björkström NK. Primary sclerosing cholangitis leads to dysfunction and loss of MAIT cells. Eur J Immunol 2018; 48:1997-2004. [PMID: 30252934 DOI: 10.1002/eji.201847608] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 02/06/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a severe chronic liver disease of the small and large bile ducts. The pathogenesis is unknown but a strong immune cell component has been suggested. Mucosal-associated invariant T (MAIT) cells are abundant in human liver and localize around bile ducts. Yet, the role of MAIT cells in PSC remains unclear. Here, we performed a detailed characterization of MAIT cells in circulation and assessed their presence in bile ducts of PSC patients as well as non-PSC controls. We observed a dramatic reduction in MAIT cell levels in PSC patients. High-dimensional phenotypical analysis using stochastic neighbor embedding revealed the MAIT cells to be activated, a phenotype shared by the investigated disease control groups. In line with the noted phenotypic alterations, MAIT cell function was reduced in response to Escherichia coli and to cytokine stimulation in PSC patients as compared to healthy controls. Using a novel sampling approach of human bile ducts, we found MAIT cells to be specifically enriched within bile ducts. Finally, distinct from the dramatic decline observed in circulation, PSC-patients had retained levels of MAIT cells within bile ducts. Altogether, our results provide a detailed insight into how the human MAIT cell compartment is affected in PSC.
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Affiliation(s)
- Erik von Seth
- Division of Hepatology, Department of Upper GI Diseases, Karolinska University Hospital, Stockholm, Sweden.,Unit of Gastroenterology and Rheumatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Christine L Zimmer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marcus Reuterwall-Hansson
- Division of Endoscopy, Department of Upper GI Diseases, Karolinska University Hospital, Stockholm, Sweden.,Division of Surgery, Department of CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Ammar Barakat
- Division of Hepatology, Department of Upper GI Diseases, Karolinska University Hospital, Stockholm, Sweden.,Unit of Gastroenterology and Rheumatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Urban Arnelo
- Division of Endoscopy, Department of Upper GI Diseases, Karolinska University Hospital, Stockholm, Sweden.,Division of Surgery, Department of CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Annika Bergquist
- Division of Hepatology, Department of Upper GI Diseases, Karolinska University Hospital, Stockholm, Sweden.,Unit of Gastroenterology and Rheumatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin A Ivarsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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166
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Ruggieri A, Gagliardi MC, Anticoli S. Sex-Dependent Outcome of Hepatitis B and C Viruses Infections: Synergy of Sex Hormones and Immune Responses? Front Immunol 2018; 9:2302. [PMID: 30349537 PMCID: PMC6186821 DOI: 10.3389/fimmu.2018.02302] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/17/2018] [Indexed: 01/19/2023] Open
Abstract
Hepatitis B virus (HBV) and hepatitis C virus (HCV) are hepatotropic viruses that differ in their genomic content, life cycle and molecular prognosis. HBV and HCV establish chronic lifespan infections that can evolve to fibrosis, cirrhosis and hepatocellular carcinoma (HCC). This malignant liver cancer affects more commonly male patients than females, with a male-to-female incidence ratio of <Capword>2</Capword>:1 up to 7:1. Sex significantly contributes to shape the immune responses, contributing to differences in the pathogenesis of infectious diseases, in males and females patients. Females usually develop more intense innate, humoral and cellular immune responses to viral infections and to vaccination compared to male subjects. Sex hormones, in turn, differentially affect the immune responses to viruses, by specific binding to the hormone receptors expressed on the immune cells. In general, estrogens have immune-stimulating effect, while androgens are immune-suppressing. However, sex hormones, such as androgen, can also directly interact with HBV genome integrated into the cell nucleus and activate transcription of HBV oncoproteins. On the other side, estradiol and estrogen receptors protect liver cells from inflammatory damage, apoptosis and oxidative stress, which contribute to fibrosis and malignant transformation preceding HCC. In HCV-associated cirrhosis and HCC the decreased expression of estrogen receptor alfa (ERα) in male patients may explain the worse outcome of HCV infection in men than in women. The synergistic action of male and female sex hormones and of immune responses, together with viral factors contribute to the mechanism of sex/gender disparity in the outcome and progression of hepatitis viruses infection.
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Affiliation(s)
- Anna Ruggieri
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Simona Anticoli
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
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167
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Wagar LE, DiFazio RM, Davis MM. Advanced model systems and tools for basic and translational human immunology. Genome Med 2018; 10:73. [PMID: 30266097 PMCID: PMC6162943 DOI: 10.1186/s13073-018-0584-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
There are fundamental differences between humans and the animals we typically use to study the immune system. We have learned much from genetically manipulated and inbred animal models, but instances in which these findings have been successfully translated to human immunity have been rare. Embracing the genetic and environmental diversity of humans can tell us about the fundamental biology of immune cell types and the elasticity of the immune system. Although people are much more immunologically diverse than conventionally housed animal models, tools and technologies are now available that permit high-throughput analysis of human samples, including both blood and tissues, which will give us deep insights into human immunity in health and disease. As we gain a more detailed picture of the human immune system, we can build more sophisticated models to better reflect this complexity, both enabling the discovery of new immunological mechanisms and facilitating translation into the clinic.
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Affiliation(s)
- Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Robert M DiFazio
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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168
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Clave E, Araujo IL, Alanio C, Patin E, Bergstedt J, Urrutia A, Lopez-Lastra S, Li Y, Charbit B, MacPherson CR, Hasan M, Melo-Lima BL, Douay C, Saut N, Germain M, Trégouët DA, Morange PE, Fontes M, Duffy D, Di Santo JP, Quintana-Murci L, Albert ML, Toubert A. Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus. Sci Transl Med 2018; 10:10/457/eaao2966. [DOI: 10.1126/scitranslmed.aao2966] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 04/11/2018] [Accepted: 07/25/2018] [Indexed: 12/12/2022]
Abstract
The thymus is the primary lymphoid organ where naïve T cells are generated; however, with the exception of age, the parameters that govern its function in healthy humans remain unknown. We characterized the variability of thymic function among 1000 age- and sex-stratified healthy adults of the Milieu Intérieur cohort, using quantification of T cell receptor excision circles (TRECs) in peripheral blood T cells as a surrogate marker of thymopoiesis. Age and sex were the only nonheritable factors identified that affect thymic function. TREC amounts decreased with age and were higher in women compared to men. In addition, a genome-wide association study revealed a common variant (rs2204985) within the T cell receptor TCRA-TCRD locus, between the DD2 and DD3 gene segments, which associated with TREC amounts. Strikingly, transplantation of human hematopoietic stem cells with the rs2204985 GG genotype into immunodeficient mice led to thymopoiesis with higher TRECs, increased thymocyte counts, and a higher TCR repertoire diversity. Our population immunology approach revealed a genetic locus that influences thymopoiesis in healthy adults, with potentially broad implications in precision medicine.
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169
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Bucciol G, Moens L, Bosch B, Bossuyt X, Casanova JL, Puel A, Meyts I. Lessons learned from the study of human inborn errors of innate immunity. J Allergy Clin Immunol 2018; 143:507-527. [PMID: 30075154 DOI: 10.1016/j.jaci.2018.07.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 07/13/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
Innate immunity contributes to host defense through all cell types and relies on their shared germline genetic background, whereas adaptive immunity operates through only 3 main cell types, αβ T cells, γδ T cells, and B cells, and relies on their somatic genetic diversification of antigen-specific responses. Human inborn errors of innate immunity often underlie infectious diseases. The range and nature of infections depend on the mutated gene, the deleteriousness of the mutation, and other ill-defined factors. Most known inborn errors of innate immunity to infection disrupt the development or function of leukocytes other than T and B cells, but a growing number of inborn errors affect cells other than circulating and tissue leukocytes. Here we review inborn errors of innate immunity that have been recently discovered or clarified. We highlight the immunologic implications of these errors.
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Affiliation(s)
- Giorgia Bucciol
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Moens
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Xavier Bossuyt
- Experimental Laboratory Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Howard Hughes Medical Institute, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Hospital for Sick Children, INSERM U1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, INSERM U1163, Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Hospital for Sick Children, INSERM U1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Isabelle Meyts
- Laboratory of Childhood Immunology, Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.
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170
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Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Murci L, Duffy D, Albert ML, Fellay J. Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines. Genome Med 2018; 10:59. [PMID: 30053915 PMCID: PMC6063007 DOI: 10.1186/s13073-018-0568-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Humoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that human genetic variation influences (i) serum immunoglobulin levels, (ii) seroconversion rates, and (iii) intensity of antigen-specific immune responses. Here, we evaluated the impact of intrinsic (age and sex), environmental, and genetic factors on the variability of humoral response to common pathogens and vaccines. METHODS We characterized the serological response to 15 antigens from common human pathogens or vaccines, in an age- and sex-stratified cohort of 1000 healthy individuals (Milieu Intérieur cohort). Using clinical-grade serological assays, we measured total IgA, IgE, IgG, and IgM levels, as well as qualitative (serostatus) and quantitative IgG responses to cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1 and 2, varicella zoster virus, Helicobacter pylori, Toxoplasma gondii, influenza A virus, measles, mumps, rubella, and hepatitis B virus. Following genome-wide genotyping of single nucleotide polymorphisms and imputation, we examined associations between ~ 5 million genetic variants and antibody responses using single marker and gene burden tests. RESULTS We identified age and sex as important determinants of humoral immunity, with older individuals and women having higher rates of seropositivity for most antigens. Genome-wide association studies revealed significant associations between variants in the human leukocyte antigen (HLA) class II region on chromosome 6 and anti-EBV and anti-rubella IgG levels. We used HLA imputation to fine map these associations to amino acid variants in the peptide-binding groove of HLA-DRβ1 and HLA-DPβ1, respectively. We also observed significant associations for total IgA levels with two loci on chromosome 2 and with specific KIR-HLA combinations. CONCLUSIONS Using extensive serological testing and genome-wide association analyses in a well-characterized cohort of healthy individuals, we demonstrated that age, sex, and specific human genetic variants contribute to inter-individual variability in humoral immunity. By highlighting genes and pathways implicated in the normal antibody response to frequently encountered antigens, these findings provide a basis to better understand disease pathogenesis. TRIALS REGISTRATION ClinicalTrials.gov , NCT01699893.
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Affiliation(s)
- Petar Scepanovic
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cécile Alanio
- Immunobiology of Dendritic Cell Unit, Institut Pasteur, Paris, France.,Center for Translational Research, Institut Pasteur, Paris, France.,Inserm U1223, Institut Pasteur, Paris, France
| | - Christian Hammer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Flavia Hodel
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacob Bergstedt
- Department of Automatic Control, Lund University, Lund, Sweden
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA 3012, Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015, Paris, France
| | - Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bruno Charbit
- Center for Translational Research, Institut Pasteur, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker branch, Inserm U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France.,St Giles laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA 3012, Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015, Paris, France
| | - Darragh Duffy
- Immunobiology of Dendritic Cell Unit, Institut Pasteur, Paris, France.,Center for Translational Research, Institut Pasteur, Paris, France.,Inserm U1223, Institut Pasteur, Paris, France
| | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA.
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland.
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171
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Duffy D. Milieu intérieur: Defining the boundaries of a healthy immune response for improved vaccination strategies. Hum Vaccin Immunother 2018; 14:2217-2221. [PMID: 29714672 PMCID: PMC6183329 DOI: 10.1080/21645515.2018.1466764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Immune responses in human populations are highly variable, with this variability presenting challenges for vaccine design. As such a better understanding of the factors that determine this variability will help in the development of precision vaccination strategies. The Milieu Interieur consortium was established to address this challenge through a definition of the normal boundaries of a healthy immune response, and the characterization of their genetic and environmental determinants. To do this we have implemented standardized tools for monitoring functional immune responses at the proteomic and transcriptional level, which have been applied to a 1,000 healthy donor cohort. This approach has recently allowed us to quantify the extent of genetic control of cellular variability and transcriptional responses to infection. Initial findings on the influence of age, sex, and genetics may already be included in considerations for improved vaccine development, and ongoing analysis will further define the factors behind inter-individual variability in diverse immune responses. This approach will help to guide the development of the next generation of vaccines that will take into account differences in populations and eventually individuals.
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Affiliation(s)
- Darragh Duffy
- a Dendritic Cell Immunobiology Unit, Department of Immunology, Institut Pasteur , Paris , France.,b INSERM U1223, Institut Pasteur , Paris , France
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172
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Floris M, Olla S, Schlessinger D, Cucca F. Genetic-Driven Druggable Target Identification and Validation. Trends Genet 2018; 34:558-570. [PMID: 29803319 PMCID: PMC6088790 DOI: 10.1016/j.tig.2018.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 12/19/2022]
Abstract
Choosing the right biological target is the critical primary decision for the development of new drugs. Systematic genetic association testing of both human diseases and quantitative traits, along with resultant findings of coincident associations between them, is becoming a powerful approach to infer drug targetable candidates and generate in vitro tests to identify compounds that can modulate them therapeutically. Here, we discuss opportunities and challenges, and infer criteria for the optimal use of genetic findings in the drug discovery pipeline.
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Affiliation(s)
- Matteo Floris
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Stefania Olla
- IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; IRGB-CNR, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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173
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Schirmer M, Kumar V, Netea MG, Xavier RJ. The causes and consequences of variation in human cytokine production in health. Curr Opin Immunol 2018; 54:50-58. [PMID: 29913309 DOI: 10.1016/j.coi.2018.05.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/19/2018] [Indexed: 02/07/2023]
Abstract
Cytokines are important cell-signaling molecules that activate and modulate immune responses. Major factors influencing cytokine variation in healthy individuals are host genetics, non-heritable factors and the microbiome. Genetic variation accounts for a significant part of heterogeneity in cytokine production by peripheral blood mononuclear cells. Variation in cytokines such as IL-6 and IL-6Ra is strongly influenced by heritability, suggesting an evolutionarily pressure for their genetic regulation that potentially contributes to differences in immune responsiveness between human populations. Non-heritable factors, including age, body weight and environmental variables such as seasonality, drive variation in baseline cytokine levels. Age further affects pathogen-induced lymphocyte-derived cytokine responses, whereas seasonality affects monocyte-derived cytokine production in response to influenza virus, Coxiella burnetti or Cryptococcus neoformans. Another influential factor that shapes the immune system is the human microbiome. Microbes and microbial products (e.g. short-chain fatty acids and tryptophan metabolites) possess strong immunomodulatory effects, induce regulatory T cells and lead to the diversification of B cells and the production of specific antibodies. In particular, differential TNFα and IFNγ production is associated with the gut microbiome. Understanding causes of variation in the healthy human immune system can reveal factors that lead to aberrant cytokine production in immune-related disorders.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vinod Kumar
- University of Groningen, University Medical Center Groningen, 9713 EX Groningen, Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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