151
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Sanz J, Randolph HE, Barreiro LB. Genetic and evolutionary determinants of human population variation in immune responses. Curr Opin Genet Dev 2018; 53:28-35. [PMID: 29960896 DOI: 10.1016/j.gde.2018.06.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
Humans display remarkable immune response variation when exposed to identical immune challenges. However, our understanding of the genetic, evolutionary, and environmental factors that impact this inter-individual and inter-population immune response heterogeneity is still in its early days. In this review, we discuss three fundamental questions concerning the recent evolution of the human immune system: the degree to which individuals from different populations vary in their innate immune responses, the genetic variants accounting for such differences, and the evolutionary mechanisms that led to the establishment of these variants in modern human populations. We also discuss how past selective events might have contributed to the uneven distribution of immune-related disorders across populations.
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Affiliation(s)
- Joaquin Sanz
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Haley E Randolph
- Department of Biochemistry, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada; Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1C5, Canada.
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152
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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: 36] [Impact Index Per Article: 6.0] [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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153
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Liefferinckx C, Franchimont D. Viewpoint: Toward the Genetic Architecture of Disease Severity in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2018; 24:1428-1439. [PMID: 29788122 DOI: 10.1093/ibd/izy109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is characterized by uneven disease courses with various clinical outcomes. A few prognostic markers of disease severity may help stratify patients and identify those who will benefit the most from early aggressive treatment. The concept of disease severity remains too broad and vague, mainly because the definition must embrace several disease mechanisms, mainly inflammation and fibrosis, with various rates of disease progression. The magnitude of inflammation is an obvious key driver of disease severity in IBD that ultimately influence disease behavior. Advances in the genetics underlying disease severity are currently emerging, but attempts to overlap the genetics of disease susceptibility and severity have until now been unsatisfactory, suggesting that the genetic architecture of disease severity may be distinct from the genetics of disease susceptibility. In this review, we report on the current knowledge on disease severity and on the main research venues to decipher the genetic architecture of disease severity.
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Affiliation(s)
| | - Denis Franchimont
- Department of Gastroenterology, Erasme Hospital, ULB, Brussels, Belgium
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154
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Saemi-Komsari M, Mousavi-Sabet H, Kratochwil CF, Sattari M, Eagderi S, Meyer A. Early developmental and allometric patterns in the electric yellow cichlid Labidochromis caeruleus. JOURNAL OF FISH BIOLOGY 2018; 92:1888-1901. [PMID: 29624691 DOI: 10.1111/jfb.13627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
The electric yellow cichlid Labidochromis caeruleus is a mouth-brooding haplochromine cichlid from Lake Malawi and one of the most popular cichlids in the ornamental fish industry. To investigate the early development of L. caeruleus from hatching until the juvenile stage, we studied its morphological development and allometric growth patterns. In newly-hatched larvae, most organs and body parts were not yet differentiated and continued to develop until 15 days post hatching (dph). The yolk sac was depleted at 13 dph. There was allometric growth, primarily in the anterior and posterior regions of the body, and inflection points when trajectories of allometric growth changed. Head and tail growth was prioritized, suggesting that body parts linked to feeding and swimming behaviour mature earlier than the rest of the body. Additionally, growth patterns revealed that development of organs related to vital functions such as branchial respiration, sensation, exogenous feeding and swimming was prioritized. Comparisons with other African and Neotropical cichlids revealed differences in ontogenetic processes and allometric growth along the anterior-posterior axis as well as variation in developmental timing. These results indicate how early morphological development and ontogenic processes might respond to the distinctive parental care observed in mouth-brooding cichlids.
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Affiliation(s)
- M Saemi-Komsari
- Department of Fisheries, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Guilan, Iran
| | - H Mousavi-Sabet
- Department of Fisheries, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Guilan, Iran
| | - C F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Constance, Germany
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Karaj, Alborz Province, Iran
| | - M Sattari
- Department of Fisheries, Faculty of Natural Resources, University of Guilan, Sowmeh Sara, Guilan, Iran
| | - S Eagderi
- Zukunftskolleg, University of Konstanz, 78457, Constance, Germany
| | - A Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Constance, Germany
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155
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Bakker OB, Aguirre-Gamboa R, Sanna S, Oosting M, Smeekens SP, Jaeger M, Zorro M, Võsa U, Withoff S, Netea-Maier RT, Koenen HJPM, Joosten I, Xavier RJ, Franke L, Joosten LAB, Kumar V, Wijmenga C, Netea MG, Li Y. Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nat Immunol 2018; 19:776-786. [PMID: 29784908 PMCID: PMC6022810 DOI: 10.1038/s41590-018-0121-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 04/12/2018] [Indexed: 01/17/2023]
Abstract
The immune response to pathogens varies substantially among people. While both genetic and non-genetic factors contribute to inter-person variation, their relative contributions and potential predictive power have remained largely unknown. By systematically correlating host factors in 534 healthy volunteers, including baseline immunological parameters and molecular profiles (genome, metabolome and gut microbiome), with cytokine-production capacity after stimulation with 20 pathogens, we identified distinct patterns of co-regulation. Among the 91 different cytokine–stimulus pairs, 11 categories of host factors together explained up to 67% of inter-individual variation in cytokine production induced by stimulation. A computational model based on genetic data predicted the genetic component of stimulus-induced cytokine-production (correlation 0.28-0.89), while non-genetic factors influenced cytokine production as well.
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Affiliation(s)
- Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raul Aguirre-Gamboa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maria Zorro
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Romana T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Department of Immunology, University of Oslo, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands. .,Department of Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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156
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Sologuren I, Martínez-Saavedra MT, Solé-Violán J, de Borges de Oliveira E, Betancor E, Casas I, Oleaga-Quintas C, Martínez-Gallo M, Zhang SY, Pestano J, Colobran R, Herrera-Ramos E, Pérez C, López-Rodríguez M, Ruiz-Hernández JJ, Franco N, Ferrer JM, Bilbao C, Andújar-Sánchez M, Álvarez Fernández M, Ciancanelli MJ, Rodríguez de Castro F, Casanova JL, Bustamante J, Rodríguez-Gallego C. Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. J Clin Immunol 2018; 38:513-526. [PMID: 29882021 PMCID: PMC6429553 DOI: 10.1007/s10875-018-0512-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/28/2018] [Indexed: 11/18/2022]
Abstract
The pathogenesis of life-threatening influenza A virus (IAV) disease remains elusive, as infection is benign in most individuals. We studied two relatives who died from influenza. We Sanger sequenced GATA2 and evaluated the mutation by gene transfer, measured serum cytokine levels, and analyzed circulating T- and B-cells. Both patients (father and son, P1 and P2) died in 2011 of H1N1pdm IAV infection at the ages of 54 and 31 years, respectively. They had not suffered from severe or moderately severe infections in the last 17 (P1) and 15 years (P2). A daughter of P1 had died at 20 years from infectious complications. Low B-cell, NK- cell, and monocyte numbers and myelodysplastic syndrome led to sequence GATA2. Patients were heterozygous for a novel, hypomorphic, R396L mutation leading to haplo-insufficiency. B- and T-cell rearrangement in peripheral blood from P1 during the influenza episode showed expansion of one major clone. No T-cell receptor excision circles were detected in P1 and P3 since they were 35 and 18 years, respectively. Both patients presented an exuberant, interferon (IFN)-γ-mediated hypercytokinemia during H1N1pdm infection. No data about patients with viremia was available. Two previously reported adult GATA2-deficient patients died from severe H1N1 IAV infection; GATA2 deficiency may predispose to life-threatening influenza in adulthood. However, a role of other genetic variants involved in immune responses cannot be ruled out. Patients with GATA2 deficiency can reach young adulthood without severe infections, including influenza, despite long-lasting complete B-cell and natural killer (NK) cell deficiency, as well as profoundly diminished T-cell thymic output.
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Affiliation(s)
- Ithaisa Sologuren
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | | | - Jordi Solé-Violán
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Edgar de Borges de Oliveira
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | - Eva Betancor
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Inmaculada Casas
- National Influenza Center-Madrid, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
| | | | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Jose Pestano
- Department of Biochemistry, Molecular Biology, Physiology, Genetics and Immunology, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Roger Colobran
- Department of Immunology, Vall d'Hebrón University Hospital, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Estefanía Herrera-Ramos
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Carmen Pérez
- Department of Microbiology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Marta López-Rodríguez
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - José Juan Ruiz-Hernández
- Department of Internal Medicine, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Nieves Franco
- Intensive Care Unit, Mostoles University Hospital, Madrid, Spain
| | - José María Ferrer
- Intensive Care Unit, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Bilbao
- Department of Hematology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Miguel Andújar-Sánchez
- Department of Pathology, Complejo Hospitalario Universitario Insular Materno Infantil, Las Palmas de Gran Canaria, Spain
| | | | - Michael J Ciancanelli
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
| | - Felipe Rodríguez de Castro
- Department of Respiratory Diseases, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Paris, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, 10065, USA
- Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Gran Canaria Dr. Negrín University Hospital, Las Palmas de Gran Canaria, Spain.
- Department of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Calle Barranco de la Ballena s/n, 35019, Las Palmas de Gran Canaria, Spain.
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157
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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158
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Khoyratty TE, Udalova IA. Diverse mechanisms of IRF5 action in inflammatory responses. Int J Biochem Cell Biol 2018; 99:38-42. [PMID: 29578052 DOI: 10.1016/j.biocel.2018.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 10/25/2022]
Abstract
Interferon regulatory factor 5 (IRF5) is a key signal-dependent transcription factor in myeloid cells. Its expression is induced by granulocyte-macrophage colony stimulating factor and interferon-gamma. IRF5 protein is further activated in response to stimulation, translocating to the nucleus where it mediates inflammatory responses. IRF5 is capable of both the up-regulation of pro-inflammatory genes and repressing anti-inflammatory mediators, thus polarising macrophages to a pro-inflammatory phenotype. We discuss IRF5 interactions with a wide range of transcriptional regulators that give rise to its diverse effects at the level of chromatin.
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Affiliation(s)
- Tariq E Khoyratty
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, United Kingdom.
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159
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Lu M, Taylor BV, Körner H. Genomic Effects of the Vitamin D Receptor: Potentially the Link between Vitamin D, Immune Cells, and Multiple Sclerosis. Front Immunol 2018; 9:477. [PMID: 29593729 PMCID: PMC5857605 DOI: 10.3389/fimmu.2018.00477] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Vitamin D has a plethora of functions that are important for the maintenance of general health and in particular, the functional integrity of the immune system, such as promoting an anti-inflammatory cytokine profile and reducing the Treg/Th17 ratio. Multiple sclerosis (MS) is a chronic, inflammatory, and neurodegenerative central nervous system (CNS) disorder of probable autoimmune origin. MS is characterized by recurring or progressive demyelination and degeneration of the CNS due in part to a misguided immune response to as yet undefined (CNS) antigens, potentially including myelin basic protein and proteolipid protein. MS has also been shown to be associated significantly with environmental factors such as the lack of vitamin D. The role of vitamin D in the pathogenesis and progression of MS is complex. Recent genetic studies have shown that various common MS-associated risk-single-nucleotide polymorphisms (SNPs) are located within or in the vicinity of genes associated with the complex metabolism of vitamin D. The functional aspects of these genetic associations may be explained either by a direct SNP-associated loss- or gain-of-function in a vitamin D-associated gene or due to a change in the regulation of gene expression in certain immune cell types. The development of new genetic tools using next-generation sequencing: e.g., chromatin immunoprecipitation sequencing (ChIP-seq) and the accompanying rapid progress of epigenomics has made it possible to recognize that the association between vitamin D and MS could be based on the extensive and characteristic genomic binding of the vitamin D receptor (VDR). Therefore, it is important to analyze comprehensively the spatiotemporal VDR binding patterns that have been identified using ChIP-seq in multiple immune cell types to reveal an integral profile of genomic VDR interaction. In summary, the aim of this review is to connect genomic effects vitamin D has on immune cells with MS and thus, to contribute to a better understanding of the influence of vitamin D on the etiology and the pathogenesis of this complex autoimmune disease.
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Affiliation(s)
- Ming Lu
- Menzies Institute for Medical Research Tasmania, Hobart, TAS, Australia
| | - Bruce V. Taylor
- Menzies Institute for Medical Research Tasmania, Hobart, TAS, Australia
| | - Heinrich Körner
- Menzies Institute for Medical Research Tasmania, Hobart, TAS, Australia
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Engineering Technology Research Center of Anti-inflammatory and Immunodrugs in Anhui Province, Hefei, China
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160
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Lea AJ, Tung J, Archie EA, Alberts SC. Developmental plasticity: Bridging research in evolution and human health. Evol Med Public Health 2018; 2017:162-175. [PMID: 29424834 PMCID: PMC5798083 DOI: 10.1093/emph/eox019] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023] Open
Abstract
Early life experiences can have profound and persistent effects on traits expressed throughout the life course, with consequences for later life behavior, disease risk, and mortality rates. The shaping of later life traits by early life environments, known as 'developmental plasticity', has been well-documented in humans and non-human animals, and has consequently captured the attention of both evolutionary biologists and researchers studying human health. Importantly, the parallel significance of developmental plasticity across multiple fields presents a timely opportunity to build a comprehensive understanding of this phenomenon. We aim to facilitate this goal by highlighting key outstanding questions shared by both evolutionary and health researchers, and by identifying theory and empirical work from both research traditions that is designed to address these questions. Specifically, we focus on: (i) evolutionary explanations for developmental plasticity, (ii) the genetics of developmental plasticity and (iii) the molecular mechanisms that mediate developmental plasticity. In each section, we emphasize the conceptual gains in human health and evolutionary biology that would follow from filling current knowledge gaps using interdisciplinary approaches. We encourage researchers interested in developmental plasticity to evaluate their own work in light of research from diverse fields, with the ultimate goal of establishing a cross-disciplinary understanding of developmental plasticity.
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Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
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161
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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Nat Genet 2018; 50:424-431. [PMID: 29379200 DOI: 10.1038/s41588-018-0046-7] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/22/2017] [Indexed: 01/25/2023]
Abstract
Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs) for chromatin accessibility and gene expression in human macrophages exposed to IFNγ, Salmonella and IFNγ plus Salmonella. We observed that ~60% of stimulus-specific expression QTLs with a detectable effect on chromatin altered the chromatin accessibility in naive cells, thus suggesting that they perturb enhancer priming. Such variants probably influence binding of cell-type-specific transcription factors, such as PU.1, which can then indirectly alter the binding of stimulus-specific transcription factors, such as NF-κB or STAT2. Thus, although chromatin accessibility assays are powerful for fine-mapping causal regulatory variants, detecting their downstream effects on gene expression will be challenging, requiring profiling of large numbers of stimulated cellular states and time points.
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162
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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2018; 36:89-94. [PMID: 29227470 PMCID: PMC5784859 DOI: 10.1038/nbt.4042] [Citation(s) in RCA: 509] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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163
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Manches O, Muniz LR, Bhardwaj N. Dendritic Cell Biology. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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164
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Dendrou CA, Cortes A, Shipman L, Evans HG, Attfield KE, Jostins L, Barber T, Kaur G, Kuttikkatte SB, Leach OA, Desel C, Faergeman SL, Cheeseman J, Neville MJ, Sawcer S, Compston A, Johnson AR, Everett C, Bell JI, Karpe F, Ultsch M, Eigenbrot C, McVean G, Fugger L. Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity. Sci Transl Med 2017; 8:363ra149. [PMID: 27807284 DOI: 10.1126/scitranslmed.aag1974] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/14/2016] [Indexed: 01/08/2023]
Abstract
Thousands of genetic variants have been identified, which contribute to the development of complex diseases, but determining how to elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders; subsequent molecular, cellular, in vivo, and structural functional follow-up; and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for certain common autoimmune disorders.
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Affiliation(s)
- Calliope A Dendrou
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Adrian Cortes
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Lydia Shipman
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hayley G Evans
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Kathrine E Attfield
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Barber
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gurman Kaur
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Subita Balaram Kuttikkatte
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Oliver A Leach
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Christiane Desel
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Soren L Faergeman
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Department of Clinical Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Jane Cheeseman
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alastair Compston
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Adam R Johnson
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Everett
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John I Bell
- University of Oxford, Richard Doll Building, Roosevelt Drive, Oxford OX3 7DG, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Churchill Hospital, Oxford OX3 7LE, UK
| | - Mark Ultsch
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Charles Eigenbrot
- Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK. .,Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Department of Clinical Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark
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165
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Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges. Proc Natl Acad Sci U S A 2017; 115:E488-E497. [PMID: 29282317 PMCID: PMC5776984 DOI: 10.1073/pnas.1714765115] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Identifying the drivers of the interindividual diversity of the human immune system is crucial to understand their consequences on immune-mediated diseases. By examining the transcriptional responses of 1,000 individuals to various microbial challenges, we show that age and sex influence the expression of many immune-related genes, but their effects are overall moderate, whereas genetic factors affect a smaller gene set but with a stronger effect. We identify numerous genetic variants that affect transcriptional variation on infection, many of which are associated with autoimmune or inflammatory disorders. These results enable additional exploration of the role of regulatory variants in the pathogenesis of immune-related diseases and improve our understanding of the respective effects of age, sex, and genetics on immune response variation. The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8+ T cells for age and CD4+ T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including a Candida albicans-specific master regulator at the CR1 locus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes.
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166
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Sweeney TE, Wong HR, Khatri P. Robust classification of bacterial and viral infections via integrated host gene expression diagnostics. Sci Transl Med 2017; 8:346ra91. [PMID: 27384347 DOI: 10.1126/scitranslmed.aaf7165] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/13/2016] [Indexed: 12/17/2022]
Abstract
Improved diagnostics for acute infections could decrease morbidity and mortality by increasing early antibiotics for patients with bacterial infections and reducing unnecessary antibiotics for patients without bacterial infections. Several groups have used gene expression microarrays to build classifiers for acute infections, but these have been hampered by the size of the gene sets, use of overfit models, or lack of independent validation. We used multicohort analysis to derive a set of seven genes for robust discrimination of bacterial and viral infections, which we then validated in 30 independent cohorts. We next used our previously published 11-gene Sepsis MetaScore together with the new bacterial/viral classifier to build an integrated antibiotics decision model. In a pooled analysis of 1057 samples from 20 cohorts (excluding infants), the integrated antibiotics decision model had a sensitivity and specificity for bacterial infections of 94.0 and 59.8%, respectively (negative likelihood ratio, 0.10). Prospective clinical validation will be needed before these findings are implemented for patient care.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH 45223, USA. Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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167
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Glinos DA, Soskic B, Trynka G. Immunogenomic approaches to understand the function of immune disease variants. Immunology 2017; 152:527-535. [PMID: 28718505 PMCID: PMC5680056 DOI: 10.1111/imm.12796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 02/07/2023] Open
Abstract
Mapping hundreds of genetic variants through genome wide association studies provided an opportunity to gain insights into the pathobiology of immune-mediated diseases. However, as most of the disease variants fall outside the gene coding sequences the functional interpretation of the exact role of the associated variants remains to be determined. The integration of disease-associated variants with large scale genomic maps of cell-type-specific gene regulation at both chromatin and transcript levels deliver examples of functionally prioritized causal variants and genes. In particular, the enrichment of disease variants with histone marks can point towards the cell types most relevant to disease development. Furthermore, chromatin contact maps that link enhancers to promoter regions in a direct way allow the identification of genes that can be regulated by the disease variants. Candidate genes implicated with such approaches can be further examined through the correlation of gene expression with genotypes. Additionally, in the context of immune-mediated diseases it is important to combine genomics with immunology approaches. Genotype correlations with the immune system as a whole, as well as with cellular responses to different stimuli, provide a valuable platform for understanding the functional impact of disease-associated variants. The intersection of immunogenomic resources with disease-associated variants paints a detailed picture of disease causal mechanisms. Here, we provide an overview of recent studies that combine these approaches to identify disease vulnerable pathways.
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Affiliation(s)
- Dafni A. Glinos
- Wellcome Trust Sanger InstituteWellcome Genome CampusHinxtonCambridgeUK
| | - Blagoje Soskic
- Wellcome Trust Sanger InstituteWellcome Genome CampusHinxtonCambridgeUK
- Open TargetsWellcome Genome CampusHinxtonCambridgeUK
| | - Gosia Trynka
- Wellcome Trust Sanger InstituteWellcome Genome CampusHinxtonCambridgeUK
- Open TargetsWellcome Genome CampusHinxtonCambridgeUK
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168
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Gosik K, Kong L, Chinchilli VM, Wu R. iFORM/eQTL: an ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts. Brief Bioinform 2017; 18:250-259. [PMID: 26944084 DOI: 10.1093/bib/bbw014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 01/03/2023] Open
Abstract
Knowledge about how changes in gene expression are encoded by expression quantitative trait loci (eQTLs) is a key to construct the genotype-phenotype map for complex traits or diseases. Traditional eQTL mapping is to associate one transcript with a single marker at a time, thereby limiting our inference about a complete picture of the genetic architecture of gene expression. Here, we implemented an ultrahigh-dimensional variable selection model to build a computing platform that can systematically scan main effects and interaction effects among all possible loci and identify a set of significant eQTLs modulating differentiation and function of gene expression. This platform, named iFORM/eQTL, was assembled by forward-selection-based procedures to tackle complex covariance structures of gene-gene interactions. iFORM/eQTL can particularly discern the role of cis-QTLs, trans-QTLs and their epistatic interactions in gene expression. Results from the reanalysis of a published genetic and genomic data set through iFORM/eQTL gain new discoveries on the genetic origin of gene expression differentiation in Caenorhabditis elegans, which could not be detected by a traditional one-locus/one-transcript analysis approach.
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Affiliation(s)
- Kirk Gosik
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Lan Kong
- Department of Public Health Sciences Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vernon M Chinchilli
- Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Rongling Wu
- Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
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169
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Abstract
Inflammatory bowel disease (IBD), including Crohn disease and ulcerative colitis, is characterized by chronic intestinal inflammation due to a complex interaction of genetic determinants, disruption of mucosal barriers, aberrant inflammatory signals, loss of tolerance, and environmental triggers. Importantly, the incidence of pediatric IBD is rising, particularly in children younger than 10 years. In this review, we discuss the clinical presentation of these patients and highlight environmental exposures that may affect disease risk, particularly among people with a background genetic risk. With regard to both children and adults, we review advancements in understanding the intestinal epithelium, the mucosal immune system, and the resident microbiota, describing how dysfunction at any level can lead to diseases like IBD. We conclude with future directions for applying advances in IBD genetics to better understand pathogenesis and develop therapeutics targeting key pathogenic nodes.
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Affiliation(s)
- Joanna M Peloquin
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Gautam Goel
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Eduardo J Villablanca
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , , .,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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170
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Lindén M, Ramírez Sepúlveda JI, James T, Thorlacius GE, Brauner S, Gómez-Cabrero D, Olsson T, Kockum I, Wahren-Herlenius M. Sex influences eQTL effects of SLE and Sjögren's syndrome-associated genetic polymorphisms. Biol Sex Differ 2017; 8:34. [PMID: 29070082 PMCID: PMC5657123 DOI: 10.1186/s13293-017-0153-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/09/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) are autoimmune disorders characterized by autoantibodies, dysregulated B cells, and notably high female-to-male incidence ratios. Genome-wide association studies have identified several susceptibility SNPs for both diseases. Many SNPs in the genome are expression quantitative trait loci (eQTLs), with context-dependent effects. Assuming that sex is a biological context, we investigated whether SLE/pSS SNPs act as eQTLs in B cells and used a disease-targeted approach to understand if they display sex-specific effects. METHODS We used genome-wide genotype and gene expression data from primary B cells from 125 males and 162 females. The MatrixEQTL R package was used to identify eQTLs within a genomic window of 2 Mb centered on each of 22 established SLE and/or pSS susceptibility SNPs. To find sex-specific eQTLs, we used a linear model with a SNP * sex interaction term. RESULTS We found ten SNPs affecting the expression of 16 different genes (FDR < 0.05). rs7574865-INPP1, rs7574865-MYO1B, rs4938573-CD3D, rs11755393-SNRPC, and rs4963128-PHRF1 were novel observations for the immune compartment and B cells. By analyzing the SNP * sex interaction terms, we identified six genes with differentially regulated expression in females compared to males, depending on the genotype of SLE/pSS-associated SNPs: SLC39A8 (BANK1 locus), CD74 (TNIP1 locus), PXK, CTSB (BLK/FAM167A locus), ARCN1 (CXCR5 locus), and DHX9 (NCF2 locus). CONCLUSIONS We identified several unknown sex-specific eQTL effects of SLE/pSS-associated genetic polymorphisms and provide novel insight into how gene-sex interactions may contribute to the sex bias in systemic autoimmune diseases.
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Affiliation(s)
- Magdalena Lindén
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jorge I Ramírez Sepúlveda
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Tojo James
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Gudny Ella Thorlacius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Brauner
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - David Gómez-Cabrero
- Unit of Computational Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.,Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, 17121, Solna, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK
| | - Tomas Olsson
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Unit of Neuroimmunology, Department of Clinical Neuroscience, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.
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171
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Reconstructing the Molecular Function of Genetic Variation in Regulatory Networks. Genetics 2017; 207:1699-1709. [PMID: 29046401 DOI: 10.1534/genetics.117.300381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/11/2017] [Indexed: 11/18/2022] Open
Abstract
Over the past decade, genetic studies have recognized hundreds of polymorphic DNA loci called response QTLs (reQTLs) as potential contributors to interindividual variation in transcriptional responses to stimulations. Such reQTLs commonly affect the transduction of signals along the regulatory network that controls gene transcription. Identifying the pathways through which reQTLs perturb the underlying network has been a major challenge. Here, we present GEVIN ("Genome-wide Embedding of Variation In Networks"), a methodology that simultaneously identifies a reQTL and the particular pathway in which the reQTL affects downstream signal transduction along the network. Using synthetic data, we show that this algorithm outperforms existing pathway identification and reQTL identification methods. We applied GEVIN to the analysis of murine and human dendritic cells in response to pathogenic components. These analyses revealed significant reQTLs together with their perturbed Toll-like receptor signaling pathways. GEVIN thus offers a powerful framework that renders a comprehensive picture of disease-related DNA loci and their molecular functions within regulatory networks.
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172
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Hen-Avivi S, Avraham R. Immune cell type 'fingerprints' at the basis of outcome diversity of human infection. Curr Opin Microbiol 2017; 42:31-39. [PMID: 29049916 DOI: 10.1016/j.mib.2017.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022]
Abstract
Despite the availability of antibiotics and immunization, infectious diseases remain a major cause of malignancy and death worldwide. Yet, it is well documented that for most infectious agents, clinical disease develops in only a small minority of infected individuals. There is, in fact, great heterogeneity in infection outcome, from complete clearance of the pathogen to severe illness. Understanding this variation remains elusive, despite its great potential to equip us with new tools for the treatment of infectious diseases. Here, we propose a novel perspective for studying this diversity in human infection outcome, one that utilizes single-cell analysis technologies. Recent advances in single-cell RNA-seq technologies allow the detection of rare subpopulations that play important roles in host-pathogen interactions. We propose that applying single-cell RNA-seq to the study of infection can provide a 'fingerprint' of the immune cell types that are associated with the ability of the host to clear a pathogen and, thereby, broaden our current understanding of variation in susceptibility to infection within the population.
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Affiliation(s)
- Shelly Hen-Avivi
- Weizmann Institute of Science, Department of Biological Regulation, Rehovot, Israel
| | - Roi Avraham
- Weizmann Institute of Science, Department of Biological Regulation, Rehovot, Israel.
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173
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Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues. Nature 2017; 550:244-248. [PMID: 29022598 PMCID: PMC5685192 DOI: 10.1038/nature24265] [Citation(s) in RCA: 611] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/28/2017] [Indexed: 12/16/2022]
Abstract
X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.
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Affiliation(s)
- Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Manuel A. Rivas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jamie L. Marshall
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Matt Aguirre
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Laura Gauthier
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark Fleharty
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Kirby
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beryl B. Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephane E. Castel
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Konrad J. Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrea Byrnes
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Abstract
PURPOSE OF REVIEW Our understanding on genetic basis of SLE has been advanced through genome-wide association studies. We review recent progress in lupus genetics with a focus on SLE-associated loci that have been functionally characterized, and discuss the potential for clinical translation of genetics data. RECENT FINDINGS Over 100 loci have been confirmed to show robust association with SLE and many share with other immune-mediated diseases. Although causative variants captured at these established loci are limited, they guide biological studies of gene targets for functional characterization which highlight the importance of aberrant recognition of self-nucleic acid, type I interferon overproduction, and defective immune cell signaling underlying the pathogenesis of SLE. Increasing examples illustrate a predictive value of genetic findings in susceptibility/prognosis prediction, clinical classification, and pharmacological implication. Genetic findings provide a foundation for better understanding of disease pathogenic mechanisms and opportunities for target selection in lupus drug development.
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175
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Jonkers IH, Wijmenga C. Context-specific effects of genetic variants associated with autoimmune disease. Hum Mol Genet 2017; 26:R185-R192. [PMID: 28977443 PMCID: PMC5886469 DOI: 10.1093/hmg/ddx254] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/22/2022] Open
Abstract
Autoimmune diseases such as rheumatoid arthritis and coeliac disease are typical examples of complex genetic diseases caused by a combination of genetic and non-genetic risk factors. Insight into the genetic risk factors (single nucleotide polymorphisms (SNPs)) has increased since genome-wide association studies (GWAS) became possible in 2007 and, for individual diseases, SNPs can now explain some 15-50% of genetic risk. GWAS have also shown that some 50% of the genetic risk factors for individual autoimmune diseases overlap between different diseases. Thus, shared risk factors may converge to pathways that, when perturbed by genetic variation, predispose to autoimmunity in general. This raises the question of what determines disease specificity, and suggests that identical risk factors may have different effects in various autoimmune diseases. Addressing this question requires translation of genetic risk factors to causal genes and then to molecular and cellular pathways. Since >90% of the genetic risk factors are found in the non-coding part of the genome (i.e. outside the exons of protein-coding genes) and can have an impact on gene regulation, there is an urgent need to better understand the non-coding part of the genome. Here, we will outline the methods being used to unravel the gene regulatory networks perturbed in autoimmune diseases and the importance of doing this in the relevant cell types. We will highlight findings in coeliac disease, which manifests in the small intestine, to demonstrate how cell type and disease context can impact on the consequences of genetic risk factors.
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Affiliation(s)
- Iris H. Jonkers
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0424 Oslo, Norway
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176
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Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas DC, Wei P, Montgomery SB. Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. Am J Epidemiol 2017; 186:771-777. [PMID: 28978191 PMCID: PMC5860556 DOI: 10.1093/aje/kwx229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/07/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022] Open
Abstract
A growing knowledge base of genetic and environmental information has greatly enabled the study of disease risk factors. However, the computational complexity and statistical burden of testing all variants by all environments has required novel study designs and hypothesis-driven approaches. We discuss how incorporating biological knowledge from model organisms, functional genomics, and integrative approaches can empower the discovery of novel gene-environment interactions and discuss specific methodological considerations with each approach. We consider specific examples where the application of these approaches has uncovered effects of gene-environment interactions relevant to drug response and immunity, and we highlight how such improvements enable a greater understanding of the pathogenesis of disease and the realization of precision medicine.
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Affiliation(s)
- Marylyn D. Ritchie
- Correspondence to Dr. Stephen B. Montgomery, Departments of Genetics and Pathology, Stanford University School of Medicine, Stanford, CA 94305 (e-mail: ); or Dr. Marylyn D. Ritchie, Geisinger Health System, 205 Hood Center for Health Research, Center Street, Danville, PA 17821(e-mail: )
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen B. Montgomery
- Correspondence to Dr. Stephen B. Montgomery, Departments of Genetics and Pathology, Stanford University School of Medicine, Stanford, CA 94305 (e-mail: ); or Dr. Marylyn D. Ritchie, Geisinger Health System, 205 Hood Center for Health Research, Center Street, Danville, PA 17821(e-mail: )
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177
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Kang K, Park SH, Chen J, Qiao Y, Giannopoulou E, Berg K, Hanidu A, Li J, Nabozny G, Kang K, Park-Min KH, Ivashkiv LB. Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF. Immunity 2017; 47:235-250.e4. [PMID: 28813657 DOI: 10.1016/j.immuni.2017.07.017] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 04/19/2017] [Accepted: 05/23/2017] [Indexed: 12/29/2022]
Abstract
Mechanisms by which interferon (IFN)-γ activates genes to promote macrophage activation are well studied, but little is known about mechanisms and functions of IFN-γ-mediated gene repression. We used an integrated transcriptomic and epigenomic approach to analyze chromatin accessibility, histone modifications, transcription-factor binding, and gene expression in IFN-γ-primed human macrophages. IFN-γ suppressed basal expression of genes corresponding to an "M2"-like homeostatic and reparative phenotype. IFN-γ repressed genes by suppressing the function of enhancers enriched for binding by transcription factor MAF. Mechanistically, IFN-γ disassembled a subset of enhancers by inducing coordinate suppression of binding by MAF, lineage-determining transcription factors, and chromatin accessibility. Genes associated with MAF-binding enhancers were suppressed in macrophages isolated from rheumatoid-arthritis patients, revealing a disease-associated signature of IFN-γ-mediated repression. These results identify enhancer inactivation and disassembly as a mechanism of IFN-γ-mediated gene repression and reveal that MAF regulates the macrophage enhancer landscape and is suppressed by IFN-γ to augment macrophage activation.
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Affiliation(s)
- Kyuho Kang
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sung Ho Park
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Janice Chen
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Yu Qiao
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Eugenia Giannopoulou
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA; Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, NY 11201, USA
| | - Karen Berg
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Adedayo Hanidu
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Jun Li
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Gerald Nabozny
- Department of Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, Chungnam 330-714, Republic of Korea
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Lionel B Ivashkiv
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA.
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178
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Duffy D, Rouilly V, Braudeau C, Corbière V, Djebali R, Ungeheuer MN, Josien R, LaBrie ST, Lantz O, Louis D, Martinez-Caceres E, Mascart F, Ruiz de Morales JG, Ottone C, Redjah L, Guen NSL, Savenay A, Schmolz M, Toubert A, Albert ML. Standardized whole blood stimulation improves immunomonitoring of induced immune responses in multi-center study. Clin Immunol 2017; 183:325-335. [PMID: 28943400 DOI: 10.1016/j.clim.2017.09.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 09/19/2017] [Indexed: 12/17/2022]
Abstract
Functional immune responses are increasingly important for clinical studies, providing in depth biomarker information to assess immunotherapy or vaccination. Incorporating functional immune assays into routine clinical practice has remained limited due to challenges in standardizing sample preparation. We recently described the use of a whole blood syringe-based system, TruCulture®, which permits point-of-care standardized immune stimulation. Here, we report on a multi-center clinical study in seven FOCIS Centers of Excellence to directly compare TruCulture to conventional PBMC methods. Whole blood and PBMCs from healthy donors were exposed to LPS, anti-CD3 anti-CD28 antibodies, or media alone. 55 protein analytes were analyzed centrally by Luminex multi-analyte profiling in a CLIA-certified laboratory. TruCulture responses showed greater reproducibility and improved the statistical power for monitoring differential immune response activation. The use of TruCulture addresses a major unmet need through a robust and flexible method for immunomonitoring that can be reproducibly applied in multi-center clinical studies. ONE SENTENCE SUMMARY A multi-center study revealed greater reproducibility from whole blood stimulation systems as compared to PBMC stimulation for studying induced immune responses.
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Affiliation(s)
- Darragh Duffy
- Center for Translational Research, Institut Pasteur, Paris, France; Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France; INSERM U1223, Institut Pasteur, Paris, France.
| | - Vincent Rouilly
- Center for Translational Research, Institut Pasteur, Paris, France
| | - Cecile Braudeau
- CHU Nantes, Laboratoire d'Immunologie, CIMNA, Nantes, France; Centre de Recherche en Transplantation et Immunologie UMR 1064, Inserm, Université de Nantes, Nantes, France
| | - Véronique Corbière
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Raouf Djebali
- Center for Translational Research, Institut Pasteur, Paris, France
| | - Marie-Noelle Ungeheuer
- Center for Translational Research, Institut Pasteur, Paris, France; ICAReB Platform, Center for Translational Research, Institut Pasteur, Paris, France
| | - Regis Josien
- CHU Nantes, Laboratoire d'Immunologie, CIMNA, Nantes, France; Centre de Recherche en Transplantation et Immunologie UMR 1064, Inserm, Université de Nantes, Nantes, France; LabEx IGO Immunotherapy Graf-Oncology, Nantes, France
| | | | - Olivier Lantz
- Laboratoire d'Immunologie clinique, CIC-4218 et Unité Inserm 932 Institut Curie, Paris, France
| | - Delphine Louis
- Laboratoire d'Immunologie clinique, CIC-4218 et Unité Inserm 932 Institut Curie, Paris, France
| | - Eva Martinez-Caceres
- Germans Trias i Pujol Hospital, Dept Cellular Biology, Physiology, Immunology, UAB, Barcelona, Spain
| | - Francoise Mascart
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (ULB), Brussels, Belgium; Immunobiology Clinic, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Catherine Ottone
- Center for Translational Research, Institut Pasteur, Paris, France; ICAReB Platform, Center for Translational Research, Institut Pasteur, Paris, France
| | - Lydia Redjah
- Laboratory of Vaccinology and Mucosal Immunity, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nina Salabert-Le Guen
- CHU Nantes, Laboratoire d'Immunologie, CIMNA, Nantes, France; Centre de Recherche en Transplantation et Immunologie UMR 1064, Inserm, Université de Nantes, Nantes, France; LabEx IGO Immunotherapy Graf-Oncology, Nantes, France
| | - Alain Savenay
- INSERM UMR1160, Université Paris Diderot, AP-HP, Hopital St Louis, Paris, France
| | | | - Antoine Toubert
- INSERM UMR1160, Université Paris Diderot, AP-HP, Hopital St Louis, Paris, France
| | - Matthew L Albert
- Center for Translational Research, Institut Pasteur, Paris, France; Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France; INSERM U1223, Institut Pasteur, Paris, France; Department of Cancer Immunology, Genentech Inc., San Francisco, CA 94080, USA.
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179
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Lu Y, Biancotto A, Cheung F, Remmers E, Shah N, McCoy JP, Tsang JS. Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations. Immunity 2017; 45:1162-1175. [PMID: 27851916 DOI: 10.1016/j.immuni.2016.10.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Cell-to-cell expression variation (CEV) is a prevalent feature of even well-defined cell populations, but its functions, particularly at the organismal level, are not well understood. Using single-cell data obtained via high-dimensional flow cytometry of T cells as a model, we introduce an analysis framework for quantifying CEV in primary cell populations and studying its functional associations in human cohorts. Analyses of 840 CEV phenotypes spanning multiple baseline measurements of 14 proteins in 28 T cell subpopulations suggest that the quantitative extent of CEV can exhibit substantial subject-to-subject differences and yet remain stable within healthy individuals over months. We linked CEV to age and disease-associated genetic polymorphisms, thus implicating CEV as a biomarker of aging and disease susceptibility and suggesting that it might play an important role in health and disease. Our dataset, interactive figures, and software for computing CEV with flow cytometry data provide a resource for exploring CEV functions.
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Affiliation(s)
- Yong Lu
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Angelique Biancotto
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA
| | - Elaine Remmers
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Naisha Shah
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - J Philip McCoy
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA; Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, MD 20892, USA.
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180
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Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol. Proc Natl Acad Sci U S A 2017; 114:E7746-E7755. [PMID: 28827342 DOI: 10.1073/pnas.1706070114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Risk, severity, and outcome of infection depend on the interplay of pathogen virulence and host susceptibility. Systematic identification of genetic susceptibility to infection is being undertaken through genome-wide association studies, but how to expeditiously move from genetic differences to functional mechanisms is unclear. Here, we use genetic association of molecular, cellular, and human disease traits and experimental validation to demonstrate that genetic variation affects expression of VAC14, a phosphoinositide-regulating protein, to influence susceptibility to Salmonella enterica serovar Typhi (S Typhi) infection. Decreased VAC14 expression increased plasma membrane cholesterol, facilitating Salmonella docking and invasion. This increased susceptibility at the cellular level manifests as increased susceptibility to typhoid fever in a Vietnamese population. Furthermore, treating zebrafish with a cholesterol-lowering agent, ezetimibe, reduced susceptibility to S Typhi. Thus, coupling multiple genetic association studies with mechanistic dissection revealed how VAC14 regulates Salmonella invasion and typhoid fever susceptibility and may open doors to new prophylactic/therapeutic approaches.
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181
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Kim-Hellmuth S, Bechheim M, Pütz B, Mohammadi P, Nédélec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel SE, Nöthen MM, Barreiro LB, Pickrell JK, Müller-Myhsok B, Lappalainen T, Schumacher J, Hornung V. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat Commun 2017; 8:266. [PMID: 28814792 PMCID: PMC5559603 DOI: 10.1038/s41467-017-00366-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022] Open
Abstract
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions. We characterize the dynamics of genetic regulation on early and late immune response and observe an enrichment of reQTLs in distal cis-regulatory elements. In addition, reQTLs are enriched for recent positive selection with an evolutionary trend towards enhanced immune response. Finally, we uncover reQTL effects in multiple GWAS loci and show a stronger enrichment for response than constant eQTLs in GWAS signals of several autoimmune diseases. This demonstrates the importance of infectious stimuli in modifying genetic predisposition to disease.Insight into the genetic influence on the immune response is important for the understanding of interindividual variability in human pathologies. Here, the authors generate transcriptome data from human blood monocytes stimulated with various immune stimuli and provide a time-resolved response eQTL map.
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Affiliation(s)
- Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, 10013, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany.
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany.
| | - Matthias Bechheim
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Benno Pütz
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Pejman Mohammadi
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Yohann Nédélec
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Canada, H3T 1C5
- Department of Biochemistry, University of Montreal, Montreal, Canada, H3C 3J7
| | - Nicholas Giangreco
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Vera Kaiser
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Esther Beier
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Clinic of RWTH Aachen, Aachen, 52074, Germany
| | - Stephane E Castel
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Canada, H3T 1C5
- Department of Pediatrics, University of Montreal, Montreal, Canada, H3T 1C5
| | - Joseph K Pickrell
- New York Genome Center, New York, NY, 10013, USA
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bertram Müller-Myhsok
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, 80804, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GL, UK
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany.
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany.
| | - Veit Hornung
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität Munich, Munich, 81377, Germany
- Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität Munich, Munich, 81377, Germany
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182
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Marigorta UM, Denson LA, Hyams JS, Mondal K, Prince J, Walters TD, Griffiths A, Noe JD, Crandall WV, Rosh JR, Mack DR, Kellermayer R, Heyman MB, Baker SS, Stephens MC, Baldassano RN, Markowitz JF, Kim MO, Dubinsky MC, Cho J, Aronow BJ, Kugathasan S, Gibson G. Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease. Nat Genet 2017; 49:1517-1521. [PMID: 28805827 PMCID: PMC5745037 DOI: 10.1038/ng.3936] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Kajari Mondal
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jarod Prince
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Joel R Rosh
- Department of Pediatrics, Goryeb Children's Hospital, Morristown, New Jersey, USA
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, Ottawa, Ontario, Canada
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, New York, USA
| | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Mi-Ok Kim
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Judy Cho
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA
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183
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Manry J, Nédélec Y, Fava VM, Cobat A, Orlova M, Thuc NV, Thai VH, Laval G, Barreiro LB, Schurr E. Deciphering the genetic control of gene expression following Mycobacterium leprae antigen stimulation. PLoS Genet 2017; 13:e1006952. [PMID: 28793313 PMCID: PMC5565194 DOI: 10.1371/journal.pgen.1006952] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/21/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022] Open
Abstract
Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation before and after stimulation with M. leprae sonicate in whole blood cells. We show that M. leprae antigen stimulation mainly triggered the upregulation of immune related genes and that a substantial proportion of the differential gene expression is genetically controlled. Indeed, using stringent criteria, we identified 318 genes displaying cis-eQTL at an FDR of 0.01, including 66 genes displaying response-eQTL (reQTL), i.e. cis-eQTL that showed significant evidence for interaction with the M. leprae stimulus. Such reQTL correspond to regulatory variations that affect the interaction between human whole blood cells and M. leprae sonicate and, thus, likely between the human host and M. leprae bacilli. We found that reQTL were significantly enriched among binding sites of transcription factors that are activated in response to infection, and that they were enriched among single nucleotide polymorphisms (SNPs) associated with susceptibility to leprosy per se and Type-I Reaction, and seven of them have been targeted by recent positive selection. Our study suggested that natural selection shaped our genomic diversity to face pathogen exposure including M. leprae infection. Each year, 200,000 new leprosy cases are reported worldwide. While there is unambiguous evidence for a role of host genetics in leprosy pathogenesis, the mechanisms by which the human host fights the infection are poorly understood. Here, we highlight the search for naturally occurring genetic variations that modulate gene expression levels following exposure to sonicate of Mycobacterium leprae, the bacterium causing the disease. Because M. leprae is not cultivable and the genuine immune cells involved in the host response during infection are still unknown, we performed a genome-wide search for such genetic variations after stimulation of whole-blood from leprosy patients with M. leprae sonicate. This design allowed to provide a general framework for the genetic control of host responses to M. leprae and outlined the contribution of host genetics to leprosy pathogenesis. Among the M. leprae-dependent genetic regulators of gene expression levels there was an enrichment of variants (i) associated with leprosy, (ii) located in transcription factor binding sites and (iii) targeted by recent positive selection.
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Affiliation(s)
- Jérémy Manry
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
- * E-mail: (ES); (JM)
| | - Yohann Nédélec
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Vinicius M. Fava
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U.1163, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Vu Hong Thai
- Hospital for Dermato-Venerology, Ho Chi Minh City, Vietnam
| | - Guillaume Laval
- Institut Pasteur, Unit of Human Evolutionary Genetics, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, URA3012, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Luis B. Barreiro
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
- * E-mail: (ES); (JM)
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184
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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185
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SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans. Nat Med 2017; 23:975-983. [PMID: 28714988 DOI: 10.1038/nm.4370] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/15/2017] [Indexed: 12/13/2022]
Abstract
Previous studies have reported associations of IFITM3 SNP rs12252 with severe influenza, but evidence of association and the mechanism by which risk is conferred remain controversial. We prioritized SNPs in IFITM3 on the basis of putative biological function and identified rs34481144 in the 5' UTR. We found evidence of a new association of rs34481144 with severe influenza in three influenza-infected cohorts characterized by different levels of influenza illness severity. We determined a role for rs34481144 as an expression quantitative trait locus (eQTL) for IFITM3, with the risk allele associated with lower mRNA expression. The risk allele was found to have decreased IRF3 binding and increased CTCF binding in promoter-binding assays, and risk allele carriage diminished transcriptional correlations among IFITM3-neighboring genes, indicative of CTCF boundary activity. Furthermore, the risk allele disrupts a CpG site that undergoes differential methylation in CD8+ T cell subsets. Carriers of the risk allele had reduced numbers of CD8+ T cells in their airways during natural influenza infection, consistent with IFITM3 promoting accumulation of CD8+ T cells in airways and indicating that a critical function for IFITM3 may be to promote immune cell persistence at mucosal sites.Our study identifies a new regulator of IFITM3 expression that associates with CD8+ T cell levels in the airways and a spectrum of clinical outcomes.
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186
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Type-I interferon pathway in neuroinflammation and neurodegeneration: focus on Alzheimer's disease. J Neural Transm (Vienna) 2017; 125:797-807. [PMID: 28676934 DOI: 10.1007/s00702-017-1745-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/09/2017] [Indexed: 12/18/2022]
Abstract
Past research in Alzheimer's disease (AD) has largely been driven by the amyloid hypothesis; the accompanying neuroinflammation seen in AD has been assumed to be consequential and not disease modifying or causative. However, recent data from both clinical and preclinical studies have established that the immune-driven neuroinflammation contributes to AD pathology. Key evidence for the involvement of neuroinflammation in AD includes enhanced microglial and astroglial activation in the brains of AD patients, increased pro-inflammatory cytokine burden in AD brains, and epidemiological evidence that chronic non-steroidal anti-inflammatory drug use prior to disease onset leads to a lower incidence of AD. Identifying critical mediators controlling this neuroinflammation will prove beneficial in developing anti-inflammatory therapies for the treatment of AD. The type-I interferons (IFNs) are pleiotropic cytokines that control pro-inflammatory cytokine secretion and are master regulators of the innate immune response that impact on disorders of the central nervous system. This review provides evidence that the type-I IFNs play a critical role in the exacerbation of neuroinflammation and actively contribute to the progression of AD.
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187
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Inflammasomes and intestinal inflammation. Mucosal Immunol 2017; 10:865-883. [PMID: 28401932 DOI: 10.1038/mi.2017.19] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
The inflammasome is a cytosolic multi-protein innate immune rheostat, sensing a variety of endogenous and environmental stimuli, and regulating homeostasis or damage control. In the gastrointestinal tract, inflammasomes orchestrate immune tolerance to microbial and potentially food-related signals or drive the initiation of inflammatory responses to invading pathogens. When inadequately regulated, intestinal inflammasome activation leads to a perpetuated inflammatory response leading to immune pathology and tissue damage. In this review, we present the main features of the predominant types of inflammasomes participating in intestinal homeostasis and inflammation. We then discuss current controversies and open questions related to their functions and implications in disease, highlighting how pathological inflammasome over-activation or impaired function impact gut homeostasis, the microbiome ecosystem, and the propensity to develop gut-associated diseases. Collectively, understanding of the molecular basis of intestinal inflammasome signaling may be translated into clinical manipulation of this fundamental pathway as a potential immune modulatory therapeutic intervention.
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188
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Renz H, Holt PG, Inouye M, Logan AC, Prescott SL, Sly PD. An exposome perspective: Early-life events and immune development in a changing world. J Allergy Clin Immunol 2017; 140:24-40. [DOI: 10.1016/j.jaci.2017.05.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 02/09/2023]
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189
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190
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Ram R, Morahan G. Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression. Genes (Basel) 2017; 8:E167. [PMID: 28635624 PMCID: PMC5485531 DOI: 10.3390/genes8060167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/17/2017] [Accepted: 06/14/2017] [Indexed: 12/12/2022] Open
Abstract
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC). These comprised four different immune cell types (Epstein-Barr virus (EBV)-transformed B cells, either basal or after stimulation; and cluster of differentiation (CD)4+ and CD8+ T cells). Many of the T1D-associated risk variants regulated expression of either neighboring (cis-) or distant (trans-) genes. In brief, 24 of the non-HLA T1D variants affected the expression of 31 nearby genes (cis) while 25 affected 38 distant genes (trans). The effects were highly significant (False Discovery Rate p < 0.001). In addition, we searched in public databases for expression effects of T1D single nucleotide polymorphisms (SNPs) in other immune cell types such as CD14+ monocytes, lipopolysaccharide (LPS) stimulated monocytes, and CD19+ B cells. In this paper, we review the (expression quantitative trait loci (eQTLs) associated with each of the 60 T1D variants and provide a summary of the genes impacted by T1D risk alleles in various immune cells. We then review the methodological steps involved in analyzing the function of genome wide association studies (GWAS)-identified variants, with emphasis on those affecting gene expression. We also discuss recent advancements in the methodologies and their advantages. We conclude by suggesting future study designs that will aid in the study of T1D risk variants.
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Affiliation(s)
- Ramesh Ram
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia.
- Centre of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia.
- Centre of Medical Research, University of Western Australia, Nedlands, WA 6009, Australia.
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191
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Perego J, Bourbon C, Chasson L, Laprie C, Spinelli L, Camosseto V, Gatti E, Pierre P. Guanabenz Prevents d-Galactosamine/Lipopolysaccharide-Induced Liver Damage and Mortality. Front Immunol 2017; 8:679. [PMID: 28659918 PMCID: PMC5468566 DOI: 10.3389/fimmu.2017.00679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/24/2017] [Indexed: 12/19/2022] Open
Abstract
Multi-organ failure in response to uncontrolled microbial infection is characterized by low blood pressure accompanied by a systemic over-inflammation state, caused by massive pro-inflammatory cytokines release and liver damage. Recently, the integrated stress response (ISR), characterized by eukaryotic translation initiation factor 2α (eIF2α) phosphorylation, was involved with controlling apoptosis in stressed hepatocytes and associated with poor survival to endotoxin challenge. Lipopolysaccharide (LPS) alone is able to induce the ISR in hepatocytes and can trigger massive liver damage along with tumor necrosis factor-alpha (TNF-α) expression. Consequently, drugs interfering with eIF2α phosphorylation may represent potential candidates for the treatment of such pathologies. We, therefore, used Guanabenz (GBZ), a small compound with enhancing eIF2α phosphorylation activity to evaluate its effect on bacterial LPS sensing and endotoxemia. GBZ is confirmed here to have an anti-inflammatory activity by increasing in vitro interleukin-10 (IL-10) production by LPS-stimulated dendritic cells. We further show that in the d-galactosamine (d-galN)/LPS-dependent lethality model, intraperitoneal injection of GBZ promoted mice survival, prevented liver damage, increased IL-10 levels, and inhibited TNF-α production. GBZ and its derivatives could therefore represent an interesting pharmacological solution to control systemic inflammation and associated acute liver failure.
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Affiliation(s)
- Jessica Perego
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France
| | | | - Lionel Chasson
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France
| | - Caroline Laprie
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France
| | - Lionel Spinelli
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France
| | | | - Evelina Gatti
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France.,Aveiro Health Sciences Program, Institute for Research in Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal.,International Associated Laboratory (LIA), CNRS "Mistra", Marseille, France
| | - Philippe Pierre
- CIML, Aix-Marseille University, CNRS, INSERM, Marseille, France.,Aveiro Health Sciences Program, Institute for Research in Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal.,International Associated Laboratory (LIA), CNRS "Mistra", Marseille, France
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192
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Allele-specific expression reveals interactions between genetic variation and environment. Nat Methods 2017; 14:699-702. [PMID: 28530654 PMCID: PMC5501199 DOI: 10.1038/nmeth.4298] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 04/20/2017] [Indexed: 12/13/2022]
Abstract
Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on association between environment and allele-specific expression (ASE). Combining RNA-sequencing of whole blood and extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared to only four using standard GxE testing. EAGLE provides new opportunities to identify GxE interactions using functional genomic data.
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193
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Ju JH, Shenoy SA, Crystal RG, Mezey JG. An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PLoS Comput Biol 2017; 13:e1005537. [PMID: 28505156 PMCID: PMC5448815 DOI: 10.1371/journal.pcbi.1005537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/30/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In light of these results, we discuss the broad impact eQTL that have been previously reported from the analysis of human data and suggest that considerable caution should be exercised when making biological inferences based on these reported eQTL.
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Affiliation(s)
- Jin Hyun Ju
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Sushila A. Shenoy
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, United States of America
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Weiss E, Rautou PE, Fasseu M, Giabicani M, de Chambrun M, Wan J, Minsart C, Gustot T, Couvineau A, Maiwall R, Hurtado-Nedelec M, Pilard N, Lebrec D, Valla D, Durand F, de la Grange P, Monteiro RC, Paugam-Burtz C, Lotersztajn S, Moreau R. Type I interferon signaling in systemic immune cells from patients with alcoholic cirrhosis and its association with outcome. J Hepatol 2017; 66:930-941. [PMID: 28040548 DOI: 10.1016/j.jhep.2016.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS In immune cells, constitutively and acutely produced type I interferons (IFNs) engage autocrine/paracrine signaling pathways to induce IFN-stimulated genes (ISGs). Enhanced activity of IFN signaling pathways can cause excessive inflammation and tissue damage. We aimed to investigate ISG expression in systemic immune cells from patients with decompensated alcoholic cirrhosis, and its association with outcome. METHODS Peripheral blood mononuclear cells (PBMCs) from patients and heathy subjects were stimulated or not with lipopolysaccharide (LPS, an IFN inducer) or increasing concentrations of IFN-β. The expression of 48 ISGs and ten "non-ISG" inflammatory cytokines were analyzed using RT-qPCR. RESULTS We developed an 8-ISG signature (IFN score) assessing ISG expression. LPS-stimulated ISG induction was significantly lower in PBMCs from patients with cirrhosis compared to healthy controls. Non-ISGs, however, showed higher induction. Lower induction of ISGs by LPS was not due to decreased IFN production by cirrhotic PBMCs or neutralization of secreted IFN, but a defective PBMC response to IFN. This defect was at least in part due to decreased constitutive ISG expression. Patients with the higher baseline IFN scores and ISG levels had the higher risk of death. At baseline, "non-ISG" cytokines did not correlate with outcome. CONCLUSIONS PBMCs from patients with decompensated alcoholic cirrhosis exhibit downregulated ISG expression, both constitutively and after an acute stimulus. Our finding that higher baseline PBMC ISG expression was associated with higher risk of death, suggests that constitutive ISG expression in systemic immune cells contributes to the prognosis of alcoholic cirrhosis. LAY SUMMARY Enhanced activity of IFN signaling pathways can cause excessive inflammation and tissue damage. Here we show that peripheral blood mononuclear cells (PBMCs) from patients with alcoholic cirrhosis exhibit a defect in interferon-stimulated genes (ISGs). We found that higher baseline ISG expression in PBMCs was associated with higher risk of death, revealing a probable contribution of ISG expression in immune cells to the outcome of alcoholic cirrhosis.
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Affiliation(s)
- Emmanuel Weiss
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Laboratoire d'Excellence Inflamex, ComUE Sorbonne Paris Cité, Paris, France; Département d'Anesthésie et Réanimation, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Pierre-Emmanuel Rautou
- Département Hospitalo-Universitaire (DHU) UNITY, Service d'Hépatologie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France; INSERM, U970, Paris Cardiovascular Research Center - PARCC, Paris, France; UMR S_970, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Magali Fasseu
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mikhael Giabicani
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Marc de Chambrun
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - JingHong Wan
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Charlotte Minsart
- Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Thierry Gustot
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium; Department of Gastroenterology, HepatoPancreatology and Digestive Oncology, C.U.B. Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Couvineau
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Rakhi Maiwall
- Department of Hepatology, Institute of Liver and Biliary Science, New Delhi, India
| | - Margarita Hurtado-Nedelec
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Service d'Immunologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
| | - Nathalie Pilard
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Didier Lebrec
- Département Hospitalo-Universitaire (DHU) UNITY, Service d'Hépatologie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Dominique Valla
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire (DHU) UNITY, Service d'Hépatologie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - François Durand
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire (DHU) UNITY, Service d'Hépatologie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | | | - Renato C Monteiro
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Laboratoire d'Excellence Inflamex, ComUE Sorbonne Paris Cité, Paris, France; Service d'Immunologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
| | - Catherine Paugam-Burtz
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Département d'Anesthésie et Réanimation, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Sophie Lotersztajn
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Laboratoire d'Excellence Inflamex, ComUE Sorbonne Paris Cité, Paris, France
| | - Richard Moreau
- INSERM, U1149, Centre de Recherche sur l'Inflammation (CRI), Clichy and Paris, France; UMR S_1149, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Laboratoire d'Excellence Inflamex, ComUE Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire (DHU) UNITY, Service d'Hépatologie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France.
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Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017; 356:eaah4573. [PMID: 28428369 PMCID: PMC5775029 DOI: 10.1126/science.aah4573] [Citation(s) in RCA: 1486] [Impact Index Per Article: 212.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/07/2017] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DCs) and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes. However, their identities and interrelationships are not fully understood. Using unbiased single-cell RNA sequencing (RNA-seq) of ~2400 cells, we identified six human DCs and four monocyte subtypes in human blood. Our study reveals a new DC subset that shares properties with plasmacytoid DCs (pDCs) but potently activates T cells, thus redefining pDCs; a new subdivision within the CD1C+ subset of DCs; the relationship between blastic plasmacytoid DC neoplasia cells and healthy DCs; and circulating progenitor of conventional DCs (cDCs). Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Gary Reynolds
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - James Fletcher
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Morgane Griesbeck
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | - Andrew Butler
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Shiwei Zheng
- New York Genome Center, New York University Center for Genomics and Systems Biology, New York, NY, USA
- New York University Center for Genomics and Systems Biology, New York, NY, USA
| | - Suzan Lazo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David Dixon
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - David McDonald
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Weibo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School
| | | | - Andrew A Lane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, UK
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Department of Medicine, Boston, MA, USA
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196
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Parnell GP, Booth DR. The Multiple Sclerosis (MS) Genetic Risk Factors Indicate both Acquired and Innate Immune Cell Subsets Contribute to MS Pathogenesis and Identify Novel Therapeutic Opportunities. Front Immunol 2017; 8:425. [PMID: 28458668 PMCID: PMC5394466 DOI: 10.3389/fimmu.2017.00425] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/27/2017] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is known to be a partially heritable autoimmune disease. The risk of developing MS increases from typically 1 in 1,000 in the normal population to 1 in 4 or so for identical twins where one twin is affected. Much of this heritability is now explained and is due almost entirely to genes affecting the immune response. The largest and first identified genetic risk factor is an allele from the MHC class II HLA-DRB1 gene, HLA-DRB1*15:01, which increases risk about threefold. The HLA-DRB1 gene is expressed in antigen-presenting cells, and its protein functions in presenting particular types of antigen to CD4 T cells. This discovery supported the development of the first successful immunomodulatory therapies: glatiramer acetate, which mimics the antigen presentation process, and interferon beta, which targets CD4 T cell activation. Over 200 genetic risk variants, all single nucleotide polymorphisms (SNPs), have now been described. The SNPs are located within, or close to, genes expressed predominantly in acquired and innate immune cell subsets, indicating that both contribute to MS pathogenesis. The risk alleles indicate variation in the regulation of gene expression, rather than protein variation, underpins genetic susceptibility. In this review, we discuss how the expression and function of the risk genes, as well as the effect on these of the risk SNPs, indicate specific acquired immune cell processes that are the target of current successful therapies, and also point to novel therapeutic approaches.
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Affiliation(s)
- Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - David R Booth
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
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197
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Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell 2017; 167:1125-1136.e8. [PMID: 27814509 DOI: 10.1016/j.cell.2016.10.020] [Citation(s) in RCA: 624] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 10/12/2016] [Indexed: 12/12/2022]
Abstract
Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Trees Jansen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Liesbeth Jacobs
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands; Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Centre Groningen, 9713 EX Groningen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands.
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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198
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Ter Horst R, Jaeger M, Smeekens SP, Oosting M, Swertz MA, Li Y, Kumar V, Diavatopoulos DA, Jansen AFM, Lemmers H, Toenhake-Dijkstra H, van Herwaarden AE, Janssen M, van der Molen RG, Joosten I, Sweep FCGJ, Smit JW, Netea-Maier RT, Koenders MMJF, Xavier RJ, van der Meer JWM, Dinarello CA, Pavelka N, Wijmenga C, Notebaart RA, Joosten LAB, Netea MG. Host and Environmental Factors Influencing Individual Human Cytokine Responses. Cell 2017; 167:1111-1124.e13. [PMID: 27814508 DOI: 10.1016/j.cell.2016.10.018] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/03/2016] [Accepted: 10/11/2016] [Indexed: 02/08/2023]
Abstract
Differences in susceptibility to immune-mediated diseases are determined by variability in immune responses. In three studies within the Human Functional Genomics Project, we assessed the effect of environmental and non-genetic host factors of the genetic make-up of the host and of the intestinal microbiome on the cytokine responses in humans. We analyzed the association of these factors with circulating mediators and with six cytokines after stimulation with 19 bacterial, fungal, viral, and non-microbial metabolic stimuli in 534 healthy subjects. In this first study, we show a strong impact of non-genetic host factors (e.g., age and gender) on cytokine production and circulating mediators. Additionally, annual seasonality is found to be an important environmental factor influencing cytokine production. Alpha-1-antitrypsin concentrations partially mediate the seasonality of cytokine responses, whereas the effect of vitamin D levels is limited. The complete dataset has been made publicly available as a comprehensive resource for future studies. PAPERCLIP.
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Affiliation(s)
- Rob Ter Horst
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Groningen 9700RB, the Netherlands
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Groningen 9700RB, the Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Groningen 9700RB, the Netherlands
| | - Dimitri A Diavatopoulos
- Laboratory of Pediatric Infectious Diseases and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Anne F M Jansen
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Helga Toenhake-Dijkstra
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Antonius E van Herwaarden
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Matthijs Janssen
- Department of Rheumatology, Rijnstate Hospital, Arnhem, Gelderland 6815AD, the Netherlands
| | - Renate G van der Molen
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Fred C G J Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Johannes W Smit
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands; Division of Endocrinology, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Romana T Netea-Maier
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands; Division of Endocrinology, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Mieke M J F Koenders
- Elkerliek Hospital, Clinical Chemistry, Helmond, Noord-Brabant 5700AB, the Netherlands
| | - Ramnik J Xavier
- Broad Institute of Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Jos W M van der Meer
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Charles A Dinarello
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands; Division of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Norman Pavelka
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Groningen 9700RB, the Netherlands; Centre for Immune Regulation and Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Oslo 0027, Norway
| | - Richard A Notebaart
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands.
| | - Mihai G Netea
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Gelderland 6500HB, the Netherlands.
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199
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Quach H, Quintana-Murci L. Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med 2017; 214:877-894. [PMID: 28351985 PMCID: PMC5379985 DOI: 10.1084/jem.20161942] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
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Affiliation(s)
- Hélène Quach
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France .,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
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200
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Yosef N, Regev A. Writ large: Genomic dissection of the effect of cellular environment on immune response. Science 2017; 354:64-68. [PMID: 27846493 DOI: 10.1126/science.aaf5453] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues.
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Affiliation(s)
- Nir Yosef
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA. .,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
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