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Xi X, Ruffieux H. A modeling framework for detecting and leveraging node-level information in Bayesian network inference. Biostatistics 2024:kxae021. [PMID: 38916966 DOI: 10.1093/biostatistics/kxae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/11/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
Bayesian graphical models are powerful tools to infer complex relationships in high dimension, yet are often fraught with computational and statistical challenges. If exploited in a principled way, the increasing information collected alongside the data of primary interest constitutes an opportunity to mitigate these difficulties by guiding the detection of dependence structures. For instance, gene network inference may be informed by the use of publicly available summary statistics on the regulation of genes by genetic variants. Here we present a novel Gaussian graphical modeling framework to identify and leverage information on the centrality of nodes in conditional independence graphs. Specifically, we consider a fully joint hierarchical model to simultaneously infer (i) sparse precision matrices and (ii) the relevance of node-level information for uncovering the sought-after network structure. We encode such information as candidate auxiliary variables using a spike-and-slab submodel on the propensity of nodes to be hubs, which allows hypothesis-free selection and interpretation of a sparse subset of relevant variables. As efficient exploration of large posterior spaces is needed for real-world applications, we develop a variational expectation conditional maximization algorithm that scales inference to hundreds of samples, nodes and auxiliary variables. We illustrate and exploit the advantages of our approach in simulations and in a gene network study which identifies hub genes involved in biological pathways relevant to immune-mediated diseases.
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Affiliation(s)
- Xiaoyue Xi
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SR, United Kingdom
| | - Hélène Ruffieux
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SR, United Kingdom
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2
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Fagundes RR, Bravo-Ruiseco G, Hu S, Kierans SJ, Weersma RK, Taylor CT, Dijkstra G, Harmsen HJM, Faber KN. Faecalibacterium prausnitzii promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway. Front Microbiol 2023; 14:1298304. [PMID: 38163085 PMCID: PMC10755969 DOI: 10.3389/fmicb.2023.1298304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Intestinal epithelial cells produce interleukin-18 (IL-18), a key factor in promoting epithelial barrier integrity. Here, we analyzed the potential role of gut bacteria and the hypoxia-inducible factor 1α (HIF1α) pathway in regulating mucosal IL18 expression in inflammatory bowel disease (IBD). Methods Mucosal samples from patients with IBD (n = 760) were analyzed for bacterial composition, IL18 levels and HIF1α pathway activation. Wild-type Caco-2 and CRISPR/Cas9-engineered Caco-2-HIF1A-null cells were cocultured with Faecalibacterium prausnitzii in a "Human oxygen-Bacteria anaerobic" in vitro system and analyzed by RNA sequencing. Results Mucosal IL18 mRNA levels correlated positively with the abundance of mucosal-associated butyrate-producing bacteria, in particular F. prausnitzii, and with HIF1α pathway activation in patients with IBD. HIF1α-mediated expression of IL18, either by a pharmacological agonist (dimethyloxallyl glycine) or F. prausnitzii, was abrogated in Caco-2-HIF1A-null cells. Conclusion Butyrate-producing gut bacteria like F. prausnitzii regulate mucosal IL18 expression in a HIF1α-dependent manner that may aid in mucosal healing in IBD.
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Affiliation(s)
- Raphael R. Fagundes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gabriela Bravo-Ruiseco
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Sarah J. Kierans
- School of Medicine and Medical Science and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Cormac T. Taylor
- School of Medicine and Medical Science and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Häder A, Schäuble S, Gehlen J, Thielemann N, Buerfent BC, Schüller V, Hess T, Wolf T, Schröder J, Weber M, Hünniger K, Löffler J, Vylkova S, Panagiotou G, Schumacher J, Kurzai O. Pathogen-specific innate immune response patterns are distinctly affected by genetic diversity. Nat Commun 2023; 14:3239. [PMID: 37277347 DOI: 10.1038/s41467-023-38994-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/25/2023] [Indexed: 06/07/2023] Open
Abstract
Innate immune responses vary by pathogen and host genetics. We analyze quantitative trait loci (eQTLs) and transcriptomes of monocytes from 215 individuals stimulated by fungal, Gram-negative or Gram-positive bacterial pathogens. We identify conserved monocyte responses to bacterial pathogens and a distinct antifungal response. These include 745 response eQTLs (reQTLs) and corresponding genes with pathogen-specific effects, which we find first in samples of male donors and subsequently confirm for selected reQTLs in females. reQTLs affect predominantly upregulated genes that regulate immune response via e.g., NOD-like, C-type lectin, Toll-like and complement receptor-signaling pathways. Hence, reQTLs provide a functional explanation for individual differences in innate response patterns. Our identified reQTLs are also associated with cancer, autoimmunity, inflammatory and infectious diseases as shown by external genome-wide association studies. Thus, reQTLs help to explain interindividual variation in immune response to infection and provide candidate genes for variants associated with a range of diseases.
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Affiliation(s)
- Antje Häder
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
| | - Sascha Schäuble
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
| | - Jan Gehlen
- Institute of Human Genetics, Philipps University of Marburg, 35033, Marburg, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, Julius Maximilians University of Wuerzburg, 97080, Wuerzburg, Germany
| | - Benedikt C Buerfent
- Institute of Human Genetics, Philipps University of Marburg, 35033, Marburg, Germany
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Vitalia Schüller
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Timo Hess
- Institute of Human Genetics, Philipps University of Marburg, 35033, Marburg, Germany
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Michael Weber
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute, 07743, Jena, Germany
| | - Kerstin Hünniger
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
- Institute for Hygiene and Microbiology, Julius Maximilians University of Wuerzburg, 97080, Wuerzburg, Germany
| | - Jürgen Löffler
- Department of Internal Medicine II, University Hospital Wuerzburg, Josef-Schneider-Strasse 2 /C11, 97080, Wuerzburg, Germany
| | - Slavena Vylkova
- Research Group Host Fungal Interfaces, Septomics Research Center and Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong SAR, China
| | - Johannes Schumacher
- Institute of Human Genetics, Philipps University of Marburg, 35033, Marburg, Germany.
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany.
| | - Oliver Kurzai
- Research Group Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, 07745, Jena, Germany.
- Institute for Hygiene and Microbiology, Julius Maximilians University of Wuerzburg, 97080, Wuerzburg, Germany.
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Sharma A, Rijavec M, Tomar S, Yamani A, Ganesan V, Krempski J, Schuler CF, Bunyavanich S, Korosec P, Hogan SP. Acute systemic myeloid inflammatory and stress response in severe food allergic reactions. Clin Exp Allergy 2023; 53:536-549. [PMID: 36756745 PMCID: PMC11157667 DOI: 10.1111/cea.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/20/2022] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Food allergic reactions can be severe and potentially life-threatening and the underlying immunological processes that contribute to the severity of reactions are poorly understood. The aim of this study is to integrate bulk RNA-sequencing of human and mouse peripheral blood mononuclear cells during food allergic reactions and in vivo mouse models of food allergy to identify dysregulated immunological processes associated with severe food allergic reactions. METHODS Bulk transcriptomics of whole blood from human and mouse following food allergic reactions combined with integrative differential expressed gene bivariate and module eigengene network analyses to identify the whole blood transcriptome associated with food allergy severity. In vivo validation immune cell and gene expression in mice following IgE-mediated reaction. RESULTS Bulk transcriptomics of whole blood from mice with different severity of food allergy identified gene ontology (GO) biological processes associated with innate and inflammatory immune responses, dysregulation of MAPK and NFkB signalling and identified 429 genes that correlated with reaction severity. Utilizing two independent human cohorts, we identified 335 genes that correlated with severity of peanut-induced food allergic reactions. Mapping mouse food allergy severity transcriptome onto the human transcriptome revealed 11 genes significantly dysregulated and correlated with severity. Analyses of whole blood from mice undergoing an IgE-mediated reaction revealed a rapid change in blood leukocytes particularly inflammatory monocytes (Ly6Chi Ly6G- ) and neutrophils that was associated with changes in CLEC4E, CD218A and GPR27 surface expression. CONCLUSIONS Collectively, IgE-mediated food allergy severity is associated with a rapid innate inflammatory response associated with acute cellular stress processes and dysregulation of peripheral blood inflammatory myeloid cell frequencies.
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Affiliation(s)
- Ankit Sharma
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sunil Tomar
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Amnah Yamani
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Varsha Ganesan
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - James Krempski
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Charles F Schuler
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Division of Allergy and Immunology, Michigan medicine University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY; Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Peter Korosec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon P. Hogan
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
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Murani E, Hadlich F. Exploration of genotype-by-environment interactions affecting gene expression responses in porcine immune cells. Front Genet 2023; 14:1157267. [PMID: 37007953 PMCID: PMC10061014 DOI: 10.3389/fgene.2023.1157267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
As one of the keys to healthy performance, robustness of farm animals is gaining importance, and with this comes increasing interest in genetic dissection of genotype-by-environment interactions (G×E). Changes in gene expression are among the most sensitive responses conveying adaptation to environmental stimuli. Environmentally responsive regulatory variation thus likely plays a central role in G×E. In the present study, we set out to detect action of environmentally responsive cis-regulatory variation by the analysis of condition-dependent allele specific expression (cd-ASE) in porcine immune cells. For this, we harnessed mRNA-sequencing data of peripheral blood mononuclear cells (PBMCs) stimulated in vitro with lipopolysaccharide, dexamethasone, or their combination. These treatments mimic common challenges such as bacterial infection or stress, and induce vast transcriptome changes. About two thirds of the examined loci showed significant ASE in at least one treatment, and out of those about ten percent exhibited cd-ASE. Most of the ASE variants were not yet reported in the PigGTEx Atlas. Genes showing cd-ASE were enriched in cytokine signaling in immune system and include several key candidates for animal health. In contrast, genes showing no ASE featured cell-cycle related functions. We confirmed LPS-dependent ASE for one of the top candidates, SOD2, which ranks among the major response genes in LPS-stimulated monocytes. The results of the present study demonstrate the potential of in vitro cell models coupled with cd-ASE analysis for the investigation of G×E in farm animals. The identified loci may benefit efforts to unravel the genetic basis of robustness and improvement of health and welfare in pigs.
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Wattacheril JJ, Raj S, Knowles DA, Greally JM. Using epigenomics to understand cellular responses to environmental influences in diseases. PLoS Genet 2023; 19:e1010567. [PMID: 36656803 PMCID: PMC9851565 DOI: 10.1371/journal.pgen.1010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
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Affiliation(s)
- Julia J. Wattacheril
- Department of Medicine, Center for Liver Disease and Transplantation, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, New York, United States of America
| | - Srilakshmi Raj
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - David A. Knowles
- New York Genome Center, New York, New York, United States of America
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - John M. Greally
- Division of Genomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
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7
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Taylor CA, Watson RA, Tong O, Ye W, Nassiri I, Gilchrist JJ, de Los Aires AV, Sharma PK, Koturan S, Cooper RA, Woodcock VK, Jungkurth E, Shine B, Coupe N, Payne MJ, Church DN, Naranbhai V, Groha S, Emery P, Mankia K, Freedman ML, Choueiri TK, Middleton MR, Gusev A, Fairfax BP. IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:2592-2600. [PMID: 36526722 PMCID: PMC9800275 DOI: 10.1038/s41591-022-02095-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.
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Affiliation(s)
- Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Weiyu Ye
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - James J Gilchrist
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alba Verge de Los Aires
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Surya Koturan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rosalin A Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Victoria K Woodcock
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Elsita Jungkurth
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas Coupe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Miranda J Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - David N Church
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Stefan Groha
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Oncology, University of Oxford, Oxford, UK.
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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Abstract
Research and practice in critical care medicine have long been defined by syndromes, which, despite being clinically recognizable entities, are, in fact, loose amalgams of heterogeneous states that may respond differently to therapy. Mounting translational evidence-supported by research on respiratory failure due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection-suggests that the current syndrome-based framework of critical illness should be reconsidered. Here we discuss recent findings from basic science and clinical research in critical care and explore how these might inform a new conceptual model of critical illness. De-emphasizing syndromes, we focus on the underlying biological changes that underpin critical illness states and that may be amenable to treatment. We hypothesize that such an approach will accelerate critical care research, leading to a richer understanding of the pathobiology of critical illness and of the key determinants of patient outcomes. This, in turn, will support the design of more effective clinical trials and inform a more precise and more effective practice at the bedside.
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9
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Flynn E, Lappalainen T. Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci 2022; 5:119-139. [PMID: 35483347 DOI: 10.1146/annurev-biodatasci-122120-010010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thousands of common genetic variants in the human population have been associated with disease risk and phenotypic variation by genome-wide association studies (GWAS). However, the majority of GWAS variants fall into noncoding regions of the genome, complicating our understanding of their regulatory functions, and few molecular mechanisms of GWAS variant effects have been clearly elucidated. Here, we set out to review genetic variant effects, focusing on expression quantitative trait loci (eQTLs), including their utility in interpreting GWAS variant mechanisms. We discuss the interrelated challenges and opportunities for eQTL analysis, covering determining causal variants, elucidating molecular mechanisms of action, and understanding context variability. Addressing these questions can enable better functional characterization of disease-associated loci and provide insights into fundamental biological questions of the noncoding genetic regulatory code and its control of gene expression. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Elise Flynn
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; , .,Department of Systems Biology, Columbia University, New York, NY, USA.,Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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10
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Lillehoj EP, Luzina IG, Atamas SP. Mammalian Neuraminidases in Immune-Mediated Diseases: Mucins and Beyond. Front Immunol 2022; 13:883079. [PMID: 35479093 PMCID: PMC9035539 DOI: 10.3389/fimmu.2022.883079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mammalian neuraminidases (NEUs), also known as sialidases, are enzymes that cleave off the terminal neuraminic, or sialic, acid resides from the carbohydrate moieties of glycolipids and glycoproteins. A rapidly growing body of literature indicates that in addition to their metabolic functions, NEUs also regulate the activity of their glycoprotein targets. The simple post-translational modification of NEU protein targets-removal of the highly electronegative sialic acid-affects protein folding, alters protein interactions with their ligands, and exposes or covers proteolytic sites. Through such effects, NEUs regulate the downstream processes in which their glycoprotein targets participate. A major target of desialylation by NEUs are mucins (MUCs), and such post-translational modification contributes to regulation of disease processes. In this review, we focus on the regulatory roles of NEU-modified MUCs as coordinators of disease pathogenesis in fibrotic, inflammatory, infectious, and autoimmune diseases. Special attention is placed on the most abundant and best studied NEU1, and its recently discovered important target, mucin-1 (MUC1). The role of the NEU1 - MUC1 axis in disease pathogenesis is discussed, along with regulatory contributions from other MUCs and other pathophysiologically important NEU targets.
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Affiliation(s)
- Erik P. Lillehoj
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Irina G. Luzina
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Research Service, Baltimore Veterans Affairs (VA) Medical Center, Baltimore, MD, United States
| | - Sergei P. Atamas
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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11
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Laubhahn K, Böck A, Zeber K, Unterschemmann S, Kunze S, Schedel M, Schaub B. 17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze. Pediatr Allergy Immunol 2022; 33:e13721. [PMID: 34919286 DOI: 10.1111/pai.13721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA expression at birth on the development of wheeze. METHODS Children were classified as multitrigger/viral/no wheeze until six years of age. The PAULINA/PAULCHEN birth cohorts were genotyped (n = 216; GSA-chip). mRNA expression of 17q21 and innate/adaptive genes was measured (qRT-PCR) in cord blood mononuclear cells. Expression quantitative trait loci (eQTL) and mediation analyses were performed. Genetic variation of 17q12-21 asthma-single nucleotide polymorphisms (SNPs) was summarized as the first principal component (PC1) and used to classify single SNP effects on gene expression as (locus)-dependent/independent eQTL SNPs. RESULTS Core region risk variants (IKZF3, ZPBP2, GSDMB, ORMDL3) were associated with multitrigger wheeze (OR: 3.05-5.43) and were locus-dependent eQTL SNPs with higher GSDMA, TLR2, TLR5, and lower TGFB1 expression. Increased risk of multitrigger wheeze with rs9303277 was in part mediated by TLR2 expression. Risk variants distal to the core region were mainly locus-independent eQTL SNPs with decreased CD209, CD86, TRAF6, RORA, and IL-9 expression. Distinct immune signatures in cord blood were associated either with multitrigger wheeze (increased innate genes, e.g., TLR2, IPS1, LY75) or viral wheeze (decreased NF-κB genes, e.g., TNFAIP3 and TNIP2). CONCLUSION Locus-dependent eQTL SNPs (core region) associated with increased inflammatory genes (primarily TLR2) at birth and subsequent multitrigger wheeze indicate that early priming and imbalance may be crucial for asthma pathophysiology. Locus-independent eQTL SNPs (mainly distal region, rs1007654) may be involved in the initiation of dendritic cell activation/maturation (TRAF6) and interaction with T cells (CD209, CD86). Identifying potential mechanistic pathways at birth may point to critical key points during early immune development predisposing to asthma.
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Affiliation(s)
- Kristina Laubhahn
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research - DZL, LMU Munich, Munich, Germany
| | - Andreas Böck
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
| | - Kathrin Zeber
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
| | - Sandra Unterschemmann
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michaela Schedel
- Department of Pulmonary Medicine, University Medical Center Essen-Ruhrlandklinik, Essen, Germany.,Department of Pulmonary Medicine, University Medicine Essen-University Hospital, Essen, Germany
| | - Bianca Schaub
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research - DZL, LMU Munich, Munich, Germany.,Member of the CHildhood Allergy and tolerance consortium (CHAMP), LMU Munich, Munich, Germany
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12
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Brandt M, Kim-Hellmuth S, Ziosi M, Gokden A, Wolman A, Lam N, Recinos Y, Daniloski Z, Morris JA, Hornung V, Schumacher J, Lappalainen T. An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation? PLoS Genet 2021; 17:e1009684. [PMID: 34314424 PMCID: PMC8345867 DOI: 10.1371/journal.pgen.1009684] [Citation(s) in RCA: 12] [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: 04/01/2020] [Revised: 08/06/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk variant for autoimmune disease, rs17622517 in an intron of C5ORF56, affects the expression of the transcription factor IRF1 20 kb away. The cis-regulatory effect specific to IRF1 is active under early immune stimulus, with a large number of trans-eQTL effects across the genome under late LPS response. Using CRISPRi silencing, we showed that perturbation of the SNP locus downregulates IRF1 and causes widespread transcriptional effects. Genome editing by CRISPR had suggestive recapitulation of the LPS-specific trans-eQTL signal and lent support for the rs17622517 site being functional. Our results suggest that this common genetic variant affects inter-individual response to immune stimuli via regulation of IRF1. For this autoimmune GWAS locus, our work provides evidence of the functional variant, demonstrates a condition-specific enhancer effect, identifies IRF1 as the likely causal gene in cis, and indicates that overactivation of the downstream immune-related pathway may be the cellular mechanism increasing disease risk. This work not only provides rare experimental validation of a master-regulatory trans-eQTL, but also demonstrates the power of eQTL mapping to build mechanistic hypotheses amenable for experimental follow-up using the CRISPR toolkit. Although many genetic loci have been associated to disease, understanding how these variants impact molecular and cellular functions to impact disease risk have been challenging. Here, we first used blood cells from a large number of individuals and stimulated them in the laboratory with a proxy for bacterial infection. We identified that a genetic variant associated to autoimmune diseases also affects the expression of the nearby transcription factor IRF1 gene in early immune response, followed by expression change of other genes in late immune response. We then studied this effect in cell lines, using the CRISPR approach to silence the activity of the genomic element of this variant and cause mutations at that position. We found evidence that this autoimmune disease -associated variant is located in a genomic regulatory element that responds to immune stimulus and affects expression of IRF1 and a complex gene regulatory network. Thus, our characterization of genetic regulatory variation in the human population combined with experimental follow-up suggests a plausible, previously uncharacterized molecular mechanism that may underlie this genetic variant’s effect on immune disease risk.
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Affiliation(s)
- Margot Brandt
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Sarah Kim-Hellmuth
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Marcello Ziosi
- New York Genome Center, New York, New York, United States of America
| | - Alper Gokden
- New York Genome Center, New York, New York, United States of America
| | - Aaron Wolman
- New York Genome Center, New York, New York, United States of America
| | - Nora Lam
- New York Genome Center, New York, New York, United States of America
- Program of Pathobiology and Mechanisms of Disease, Columbia University, New York, New York, United States of America
| | - Yocelyn Recinos
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Zharko Daniloski
- New York Genome Center, New York, New York, United States of America
- New York University, Department of Biology, New York, New York, United States of America
| | - John A. Morris
- New York Genome Center, New York, New York, United States of America
- New York University, Department of Biology, New York, New York, United States of America
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail:
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13
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Leite Dantas R, Freff J, Ambrée O, Beins EC, Forstner AJ, Dannlowski U, Baune BT, Scheu S, Alferink J. Dendritic Cells: Neglected Modulators of Peripheral Immune Responses and Neuroinflammation in Mood Disorders? Cells 2021; 10:941. [PMID: 33921690 PMCID: PMC8072712 DOI: 10.3390/cells10040941] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/25/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Affective disorders (AD) including major depressive disorder (MDD) and bipolar disorder (BD) are common mood disorders associated with increased disability and poor health outcomes. Altered immune responses characterized by increased serum levels of pro-inflammatory cytokines and neuroinflammation are common findings in patients with AD and in corresponding animal models. Dendritic cells (DCs) represent a heterogeneous population of myeloid cells that orchestrate innate and adaptive immune responses and self-tolerance. Upon sensing exogenous and endogenous danger signals, mature DCs secrete proinflammatory factors, acquire migratory and antigen presenting capacities and thus contribute to neuroinflammation in trauma, autoimmunity, and neurodegenerative diseases. However, little is known about the involvement of DCs in the pathogenesis of AD. In this review, we summarize the current knowledge on DCs in peripheral immune responses and neuroinflammation in MDD and BD. In addition, we consider the impact of DCs on neuroinflammation and behavior in animal models of AD. Finally, we will discuss therapeutic perspectives targeting DCs and their effector molecules in mood disorders.
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Affiliation(s)
- Rafael Leite Dantas
- Department of Mental Health, University of Münster, 48149 Münster, Germany; (R.L.D.); (J.F.); (U.D.); (B.T.B.)
- Cells in Motion Interfaculty Centre, University of Münster, 48149 Münster, Germany
| | - Jana Freff
- Department of Mental Health, University of Münster, 48149 Münster, Germany; (R.L.D.); (J.F.); (U.D.); (B.T.B.)
- Cells in Motion Interfaculty Centre, University of Münster, 48149 Münster, Germany
| | - Oliver Ambrée
- Department of Behavioural Biology, University of Osnabrück, 49076 Osnabrück, Germany;
- Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Eva C. Beins
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127 Bonn, Germany; (E.C.B.); (A.J.F.)
| | - Andreas J. Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127 Bonn, Germany; (E.C.B.); (A.J.F.)
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, 52428 Jülich, Germany
| | - Udo Dannlowski
- Department of Mental Health, University of Münster, 48149 Münster, Germany; (R.L.D.); (J.F.); (U.D.); (B.T.B.)
| | - Bernhard T. Baune
- Department of Mental Health, University of Münster, 48149 Münster, Germany; (R.L.D.); (J.F.); (U.D.); (B.T.B.)
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Stefanie Scheu
- Institute of Medical Microbiology and Hospital Hygiene, University of Düsseldorf, 40225 Düsseldorf, Germany;
| | - Judith Alferink
- Department of Mental Health, University of Münster, 48149 Münster, Germany; (R.L.D.); (J.F.); (U.D.); (B.T.B.)
- Cells in Motion Interfaculty Centre, University of Münster, 48149 Münster, Germany
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14
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Bertrams W, Jung AL, Maxheim M, Schmeck B. [Role of genetic factors in pneumonia and COVID-19]. PNEUMOLOGE 2021; 18:212-217. [PMID: 33716601 PMCID: PMC7934978 DOI: 10.1007/s10405-021-00385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/25/2022]
Abstract
Die Pneumonie ist die Infektionskrankheit mit der weltweit höchsten Mortalität. Die häufigsten Erreger sind Bakterien, es gibt jedoch auch epidemisch oder pandemisch auftretende virale Lungenentzündungen durch Influenza- oder Coronaviren, wie die aktuelle Pandemie durch das SARS Coronavirus 3766 Fälle (SARS-CoV-2). Wichtige Herausforderungen liegen neben dem Auftreten von Antibiotikaresistenzen und Immunpathologien etwa in der Sepsis in der Betrachtung der Suszeptibilität individueller Patienten: Hier werden vor allen Dingen das Lebensalter, Medikamente und Komorbiditäten betrachtet. Es gibt jedoch auch klare Hinweise für genetische Einflüsse auf das individuelle Risiko, an einer Pneumonie zu erkranken oder einen schweren Verlauf der Erkrankung zu entwickeln. In diesem Beitrag wollen wir die genetischen Einflüsse auf die Pneumonie und ihre klinische Bedeutung darstellen.
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Affiliation(s)
- Wilhelm Bertrams
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Anna Lena Jung
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Michael Maxheim
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
| | - Bernd Schmeck
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
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15
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Ford BD, Moncada Giraldo D, Margaroli C, Giacalone VD, Brown MR, Peng L, Tirouvanziam R. Functional and Transcriptional Adaptations of Blood Monocytes Recruited to the Cystic Fibrosis Airway Microenvironment In Vitro. Int J Mol Sci 2021; 22:2530. [PMID: 33802410 PMCID: PMC7959310 DOI: 10.3390/ijms22052530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) lung disease is dominated by the recruitment of myeloid cells (neutrophils and monocytes) from the blood which fail to clear the lung of colonizing microbes. In prior in vitro studies, we showed that blood neutrophils migrated through the well-differentiated lung epithelium into the CF airway fluid supernatant (ASN) mimic the dysfunction of CF airway neutrophils in vivo, including decreased bactericidal activity despite an increased metabolism. Here, we hypothesized that, in a similar manner to neutrophils, blood monocytes undergo significant adaptations upon recruitment to CFASN. To test this hypothesis, primary human blood monocytes were transmigrated in our in vitro model into the ASN from healthy control (HC) or CF subjects to mimic in vivo recruitment to normal or CF airways, respectively. Surface phenotype, metabolic and bacterial killing activities, and transcriptomic profile by RNA sequencing were quantified post-transmigration. Unlike neutrophils, monocytes were not metabolically activated, nor did they show broad differences in activation and scavenger receptor expression upon recruitment to the CFASN compared to HCASN. However, monocytes recruited to CFASN showed decreased bactericidal activity. RNASeq analysis showed strong effects of transmigration on monocyte RNA profile, with differences between CFASN and HCASN conditions, notably in immune signaling, including lower expression in the former of the antimicrobial factor ISG15, defensin-like chemokine CXCL11, and nitric oxide-producing enzyme NOS3. While monocytes undergo qualitatively different adaptations from those seen in neutrophils upon recruitment to the CF airway microenvironment, their bactericidal activity is also dysregulated, which could explain why they also fail to protect CF airways from infection.
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Affiliation(s)
- Bijean D. Ford
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (B.D.F.); (D.M.G.); (V.D.G.); (M.R.B.)
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Diego Moncada Giraldo
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (B.D.F.); (D.M.G.); (V.D.G.); (M.R.B.)
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Camilla Margaroli
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Vincent D. Giacalone
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (B.D.F.); (D.M.G.); (V.D.G.); (M.R.B.)
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Milton R. Brown
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (B.D.F.); (D.M.G.); (V.D.G.); (M.R.B.)
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Limin Peng
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA;
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (B.D.F.); (D.M.G.); (V.D.G.); (M.R.B.)
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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16
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Yang Y, Zhang C, Jing D, He H, Li X, Wang Y, Qin Y, Xiao X, Xiong H, Zhou G. IRF5 Acts as a Potential Therapeutic Marker in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2021; 27:407-417. [PMID: 32737976 DOI: 10.1093/ibd/izaa200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic inflammatory disorders. As is well known, interferon regulatory factor (IRF) 5 is closely associated with the pathogenesis of various inflammatory diseases. But the exact role of IRF5 in IBD remains unclear. METHODS In this study, we detected IRF5 expression in peripheral blood mononuclear cells (PBMCs) and inflamed mucosa from IBD patients by immunohistochemistry, western blot, and quantitative real-time polymerase chain reaction. Peripheral blood CD4+ T cells were stimulated with inflammatory cytokines and transfected by lentivirus. RESULTS In active IBD patients, the expression of IRF5 in PBMCs and inflamed colonic tissues was obviously increased and significantly associated with disease activity. Ectopic overexpression of IRF5 could promote the differentiation of IBD CD4+ T cells into Th1 and Th17 cells by regulating T-bet and RAR related orphan receptor C, whereas knockdown of IRF5 had the opposite effects. Tumor necrosis factor (TNF)-α upregulated expression of IRF5 in CD4+ T cells, but anti-TNF treatment with infliximab could markedly reduce IRF5 expression in CD4+ T cells and intestinal mucosa of CD patients. CONCLUSION Our study reveals a novel mechanism that IRF5 levels are correlated with disease activity in IBD and might function as a possible marker for the management of IBD via regulating Th1 and Th17 immune responses and cytokine production.
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Affiliation(s)
- Yonghong Yang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China.,Department of Central Laboratory, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Cui Zhang
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University, Shanghai, P.R. China
| | - Dehuai Jing
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Heng He
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Xiaoyu Li
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, P.R. China
| | - Yibo Wang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Yufen Qin
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Xiao Xiao
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong, P.R. China
| | - Guangxi Zhou
- Department of Gastroenterology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, P.R. China.,Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong, P.R. China
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17
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Kashani B, Zandi Z, Pourbagheri-Sigaroodi A, Bashash D, Ghaffari SH. The role of toll-like receptor 4 (TLR4) in cancer progression: A possible therapeutic target? J Cell Physiol 2020; 236:4121-4137. [PMID: 33230811 DOI: 10.1002/jcp.30166] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/13/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
The toll-like receptor (TLR) family consists of vital receptors responsible for pattern recognition in innate immunity, making them the core proteins involved in pathogen detection and eliciting immune responses. The most studied member of this family, TLR4, has been the center of attention regarding its contributory role in many inflammatory diseases including sepsis shock and asthma. Notably, mounting pieces of evidence have proved that this receptor is aberrantly expressed on the tumor cells and the tumor microenvironment in a wide range of cancer types and it is highly associated with the initiation of tumorigenesis as well as tumor progression and drug resistance. Cancer therapy using TLR4 inhibitors has recently drawn scientists' attention, and the promising results of such studies may pave the way for more investigation in the foreseeable future. This review will introduce the key proteins of the TLR4 pathway and how they interact with major growth factors in the tumor microenvironment. Moreover, we will discuss the many aspects of tumor progression affected by the activation of this receptor and provide an overview of the recent therapeutic approaches using various TLR4 antagonists.
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Affiliation(s)
- Bahareh Kashani
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Zandi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed H Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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18
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Abstract
Human genetic studies of diseases that are multifactorial and prevalent have generated a wealth of knowledge about the genetic architecture of chronic diseases. Generalizable attributes are shaping the development of models to explain how the human genome influences our health and can be leveraged to improve it. Importantly, both rare and common genetic variants contribute to disease risk and provide complementary information. Although initial genetic studies of alopecia areata have yielded insight with high clinical impact, there remains a number of important unanswered questions pertaining to disease biology and patient care that could be addressed by further genetic investigations.
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Affiliation(s)
- Lynn Petukhova
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA.
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19
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Gresle MM, Jordan MA, Stankovich J, Spelman T, Johnson LJ, Laverick L, Hamlett A, Smith LD, Jokubaitis VG, Baker J, Haartsen J, Taylor B, Charlesworth J, Bahlo M, Speed TP, Brown MA, Field J, Baxter AG, Butzkueven H. Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells. Life Sci Alliance 2020; 3:3/7/e202000650. [PMID: 32518073 PMCID: PMC7283543 DOI: 10.26508/lsa.202000650] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
At least 200 single-nucleotide polymorphisms (SNPs) are associated with multiple sclerosis (MS) risk. A key function that could mediate SNP-encoded MS risk is their regulatory effects on gene expression. We performed microarrays using RNA extracted from purified immune cell types from 73 untreated MS cases and 97 healthy controls and then performed Cis expression quantitative trait loci mapping studies using additive linear models. We describe MS risk expression quantitative trait loci associations for 129 distinct genes. By extending these models to include an interaction term between genotype and phenotype, we identify MS risk SNPs with opposing effects on gene expression in cases compared with controls, namely, rs2256814 MYT1 in CD4 cells (q = 0.05) and rs12087340 RF00136 in monocyte cells (q = 0.04). The rs703842 SNP was also associated with a differential effect size on the expression of the METTL21B gene in CD8 cells of MS cases relative to controls (q = 0.03). Our study provides a detailed map of MS risk loci that function by regulating gene expression in cell types relevant to MS.
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Affiliation(s)
- Melissa M Gresle
- Department of Medicine, University of Melbourne, Parkville, Australia.,Melbourne Brain Centre, Royal Melbourne Hospital, University of Melbourne, Parkville, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Margaret A Jordan
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Jim Stankovich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Tim Spelman
- Department of Medicine, University of Melbourne, Parkville, Australia.,Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Laura J Johnson
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Louise Laverick
- Department of Medicine, University of Melbourne, Parkville, Australia
| | - Alison Hamlett
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Letitia D Smith
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Vilija G Jokubaitis
- Department of Medicine, University of Melbourne, Parkville, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Josephine Baker
- Multiple Sclerosis Clinical & Research Unit, Melbourne Health, Royal Melbourne Hospital, Parkville, Australia
| | - Jodi Haartsen
- Eastern Clinical Research Unit, Eastern Health, Box Hill, Australia
| | - Bruce Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Jac Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Terence P Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia.,Guy's and St Thomas' NHS Foundation Trust and King's College London NIHR Biomedical Research Centre, London, England
| | - Judith Field
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Alan G Baxter
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
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20
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Ruffieux H, Davison AC, Hager J, Inshaw J, Fairfax BP, Richardson S, Bottolo L. A Global-Local Approach for Detecting Hotspots in Multiple-Response Regression. Ann Appl Stat 2020; 14:905-928. [PMID: 34992707 PMCID: PMC7612176 DOI: 10.1214/20-aoas1332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We tackle modelling and inference for variable selection in regression problems with many predictors and many responses. We focus on detecting hotspots, that is, predictors associated with several responses. Such a task is critical in statistical genetics, as hotspot genetic variants shape the architecture of the genome by controlling the expression of many genes and may initiate decisive functional mechanisms underlying disease endpoints. Existing hierarchical regression approaches designed to model hotspots suffer from two limitations: their discrimination of hotspots is sensitive to the choice of top-level scale parameters for the propensity of predictors to be hotspots, and they do not scale to large predictor and response vectors, for example, of dimensions 103-105 in genetic applications. We address these shortcomings by introducing a flexible hierarchical regression framework that is tailored to the detection of hotspots and scalable to the above dimensions. Our proposal implements a fully Bayesian model for hotspots based on the horseshoe shrinkage prior. Its global-local formulation shrinks noise globally and, hence, accommodates the highly sparse nature of genetic analyses while being robust to individual signals, thus leaving the effects of hotspots unshrunk. Inference is carried out using a fast variational algorithm coupled with a novel simulated annealing procedure that allows efficient exploration of multimodal distributions.
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Affiliation(s)
| | | | | | - Jamie Inshaw
- Wellcome Centre for Human Genetics, Oxford, University of Oxford
| | - Benjamin P. Fairfax
- Department of Oncology, MRC Weatherall Institute for Molecular Medicine, University of Oxford
| | - Sylvia Richardson
- MRC Biostatistics Unit, University of Cambridge
- Alan Turing Institute
| | - Leonardo Bottolo
- MRC Biostatistics Unit, University of Cambridge
- Alan Turing Institute
- Department of Medical Genetics, University of Cambridge
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21
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CD16 + monocytes give rise to CD103 +RALDH2 +TCF4 + dendritic cells with unique transcriptional and immunological features. Blood Adv 2019; 2:2862-2878. [PMID: 30381402 DOI: 10.1182/bloodadvances.2018020123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/03/2018] [Indexed: 12/23/2022] Open
Abstract
Classical CD16- vs intermediate/nonclassical CD16+ monocytes differ in their homing potential and biological functions, but whether they differentiate into dendritic cells (DCs) with distinct contributions to immunity against bacterial/viral pathogens remains poorly investigated. Here, we employed a systems biology approach to identify clinically relevant differences between CD16+ and CD16- monocyte-derived DCs (MDDCs). Although both CD16+ and CD16- MDDCs acquire classical immature/mature DC markers in vitro, genome-wide transcriptional profiling revealed unique molecular signatures for CD16+ MDDCs, including adhesion molecules (ITGAE/CD103), transcription factors (TCF7L2/TCF4), and enzymes (ALDH1A2/RALDH2), whereas CD16- MDDCs exhibit a CDH1/E-cadherin+ phenotype. Of note, lipopolysaccharides (LPS) upregulated distinct transcripts in CD16+ (eg, CCL8, SIGLEC1, MIR4439, SCIN, interleukin [IL]-7R, PLTP, tumor necrosis factor [TNF]) and CD16- MDDCs (eg, MMP10, MMP1, TGM2, IL-1A, TNFRSF11A, lysosomal-associated membrane protein 1, MMP8). Also, unique sets of HIV-modulated genes were identified in the 2 subsets. Further gene set enrichment analysis identified canonical pathways that pointed to "inflammation" as the major feature of CD16+ MDDCs at immature stage and on LPS/HIV exposure. Finally, functional validations and meta-analysis comparing the transcriptome of monocyte and MDDC subsets revealed that CD16+ vs CD16- monocytes preserved their superior ability to produce TNF-α and CCL22, as well as other sets of transcripts (eg, TCF4), during differentiation into DC. These results provide evidence that monocyte subsets are transcriptionally imprinted/programmed with specific differentiation fates, with intermediate/nonclassical CD16+ monocytes being precursors for pro-inflammatory CD103+RALDH2+TCF4+ DCs that may play key roles in mucosal immunity homeostasis/pathogenesis. Thus, alterations in the CD16+ /CD16- monocyte ratios during pathological conditions may dramatically influence the quality of MDDC-mediated immunity.
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22
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Intestinal and Limb Ischemic Preconditioning Provides a Combined Protective Effect in the Late Phase, But not in the Early Phase, Against Intestinal Injury Induced by Intestinal Ischemia-Reperfusion in Rats. Shock 2019; 49:596-603. [PMID: 28786831 DOI: 10.1097/shk.0000000000000956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Intestinal ischemia/reperfusion (I/R) injury is associated with high morbidity and mortality. This study aimed to compare the protective efficacy of intestinal ischemic preconditioning (IIPC) and limb ischemic preconditioning (LIPC) against intestinal I/R injury and investigate their combined protective effect and the underlying mechanism. Male Sprague-Dawley rats were pretreated with IIPC, LIPC, or IIPC plus LIPC (combined), and intestinal I/R or sham operation was performed. The animals were sacrificed at 2 and 24 h after reperfusion and then blood and tissue samples were harvested for further analyses. In additional groups of animals, a 7-day survival study was conducted. The results showed that ischemic preconditioning (IPC) improved the survival rate and attenuated intestinal edema, injury, and apoptosis. IPC decreased the levels of tumor necrosis factor-α, interleukin -6, malondialdehyde and myeloperoxidase, and increased the activity of superoxide dismutase in serum and intestine after the I/R event. IPC downregulated the expression of Toll-like receptor-4 (TLR4) and nuclear factor-kappa B (NF-κB). The effect of combined pretreatment was better than that of single pretreatment in the late phase (24 h), but not in the early phase (2 h). The study demonstrated that IPC could significantly attenuate intestinal injury induced by intestinal I/R via inhibiting inflammation, oxidative stress, and apoptosis. IIPC and LIPC conferred no synergy in protecting I/R-induced intestinal injury in the early phase, but combined preconditioning had clearly stronger protection in the late phase, which was associated with the inhibition of the activated TLR4/NF-κB signaling pathway. It suggested that LIPC or combined preconditioning could potentially be applied in the clinical settings of surgical patient care.
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23
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Khan MM, Ernst O, Manes NP, Oyler BL, Fraser IDC, Goodlett DR, Nita-Lazar A. Multi-Omics Strategies Uncover Host-Pathogen Interactions. ACS Infect Dis 2019; 5:493-505. [PMID: 30857388 DOI: 10.1021/acsinfecdis.9b00080] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the success of the Human Genome Project, large-scale systemic projects became a reality that enabled rapid development of the systems biology field. Systems biology approaches to host-pathogen interactions have been instrumental in the discovery of some specifics of Gram-negative bacterial recognition, host signal transduction, and immune tolerance. However, further research, particularly using multi-omics approaches, is essential to untangle the genetic, immunologic, (post)transcriptional, (post)translational, and metabolic mechanisms underlying progression from infection to clearance of microbes. The key to understanding host-pathogen interactions lies in acquiring, analyzing, and modeling multimodal data obtained through integrative multi-omics experiments. In this article, we will discuss how multi-omics analyses are adding to our understanding of the molecular basis of host-pathogen interactions and systemic maladaptive immune response of the host to microbes and microbial products.
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Affiliation(s)
- Mohd M. Khan
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), 9000 Rockville Pike, Bethesda, Maryland 20814, United States
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, Maryland 21201, United States
| | - Orna Ernst
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), 9000 Rockville Pike, Bethesda, Maryland 20814, United States
| | - Nathan P. Manes
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), 9000 Rockville Pike, Bethesda, Maryland 20814, United States
| | - Benjamin L. Oyler
- University of Maryland School of Medicine, 655 W. Baltimore Street, Baltimore, Maryland 21201, United States
| | - Iain D. C. Fraser
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), 9000 Rockville Pike, Bethesda, Maryland 20814, United States
| | - David R. Goodlett
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), 9000 Rockville Pike, Bethesda, Maryland 20814, United States
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24
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Shan N, Wang Z, Hou L. Identification of trans-eQTLs using mediation analysis with multiple mediators. BMC Bioinformatics 2019; 20:126. [PMID: 30925861 PMCID: PMC6440281 DOI: 10.1186/s12859-019-2651-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Mapping expression quantitative trait loci (eQTLs) has provided insight into gene regulation. Compared to cis-eQTLs, the regulatory mechanisms of trans-eQTLs are less known. Previous studies suggest that trans-eQTLs may regulate expression of remote genes by altering the expression of nearby genes. Trans-association has been studied in the mediation analysis with a single mediator. However, prior applications with one mediator are prone to model misspecification due to correlations between genes. Motivated from the observation that trans-eQTLs are more likely to associate with more than one cis-gene than randomly selected SNPs in the GTEx dataset, we developed a computational method to identify trans-eQTLs that are mediated by multiple mediators. Results We proposed two hypothesis tests for testing the total mediation effect (TME) and the component-wise mediation effects (CME), respectively. We demonstrated in simulation studies that the type I error rates were controlled in both tests despite model misspecification. The TME test was more powerful than the CME test when the two mediation effects are in the same direction, while the CME test was more powerful than the TME test when the two mediation effects are in opposite direction. Multiple mediator analysis had increased power to detect mediated trans-eQTLs, especially in large samples. In the HapMap3 data, we identified 11 mediated trans-eQTLs that were not detected by the single mediator analysis in the combined samples of African populations. Moreover, the mediated trans-eQTLs in the HapMap3 samples are more likely to be trait-associated SNPs. In terms of computation, although there is no limit in the number of mediators in our model, analysis takes more time when adding additional mediators. In the analysis of the HapMap3 samples, we included at most 5 cis-gene mediators. Majority of the trios we considered have one or two mediators. Conclusions Trans-eQTLs are more likely to associate with multiple cis-genes than randomly selected SNPs. Mediation analysis with multiple mediators improves power of identification of mediated trans-eQTLs, especially in large samples. Electronic supplementary material The online version of this article (10.1186/s12859-019-2651-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nayang Shan
- Center for Statistical Science, Tsinghua University, Beijing, 100084, China.,Department of Industrial Engineering, Tsinghua University, Beijing, 100084, China
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Lin Hou
- Center for Statistical Science, Tsinghua University, Beijing, 100084, China. .,Department of Industrial Engineering, Tsinghua University, Beijing, 100084, China. .,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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25
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Buerfent BC, Gölz L, Hofmann A, Rühl H, Stamminger W, Fricker N, Hess T, Oldenburg J, Nöthen MM, Schumacher J, Hübner MP, Hoerauf A. Transcriptome-wide analysis of filarial extract-primed human monocytes reveal changes in LPS-induced PTX3 expression levels. Sci Rep 2019; 9:2562. [PMID: 30796272 PMCID: PMC6385373 DOI: 10.1038/s41598-019-38985-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 01/15/2019] [Indexed: 12/24/2022] Open
Abstract
Filarial nematodes modulate immune responses in their host to enable their survival and mediate protective effects against autoimmunity and allergies. In this study, we examined the immunomodulatory capacity of extracts from the human pathogenic filaria Brugia malayi (BmA) on human monocyte responses in a transcriptome-wide manner to identify associated pathways and diseases. As previous transcriptome studies often observed quiescent responses of innate cells to filariae, the potential of BmA to alter LPS driven responses was investigated by analyzing >47.000 transcripts of monocytes from healthy male volunteers stimulated with BmA, Escherichia coli LPS or a sequential stimulation of both. In comparison to ~2200 differentially expressed genes in LPS-only stimulated monocytes, only a limited number of differentially expressed genes were identified upon BmA priming before LPS re-stimulation with only PTX3↓ reaching statistical significance after correcting for multiple testing. Nominal significant differences were reached for metallothioneins↑, MMP9↑, CXCL5/ENA-78↑, CXCL6/GCP-2↑, TNFRSF21↓, and CCL20/MIP3α↓ and were confirmed by qPCR or ELISA. Flow cytometric analysis of activation markers revealed a reduced LPS-induced expression of HLA-DR and CD86 on BmA-primed monocytes as well as a reduced apoptosis of BmA-stimulated monocytes. While our experimental design does not allow a stringent extrapolation of our results to the development of filarial pathology, several genes that were identified in BmA-primed monocytes had previously been associated with filarial pathology, supporting the need for further research.
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Affiliation(s)
- B C Buerfent
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - L Gölz
- Department of Orthodontics, Center of Dento-Maxillo-Facial Medicine, University of Bonn, Bonn, Germany
- Department of Orthodontics and Orofacial Orthopedics, University Hospital of Erlangen, Erlangen, Germany
| | - A Hofmann
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - H Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, Germany
| | - W Stamminger
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
| | - N Fricker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - T Hess
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - J Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, Germany
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - J Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - M P Hübner
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany.
| | - A Hoerauf
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
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26
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Husquin LT, Rotival M, Fagny M, Quach H, Zidane N, McEwen LM, MacIsaac JL, Kobor MS, Aschard H, Patin E, Quintana-Murci L. Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation. Genome Biol 2018; 19:222. [PMID: 30563547 PMCID: PMC6299574 DOI: 10.1186/s13059-018-1601-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, their genetic determinants, and their respective causal impact on immune gene regulation remain elusive. RESULTS We report extensive population differences in DNA methylation between 156 individuals of African and European descent, detected in primary monocytes that are used as a model of a major innate immunity cell type. Most of these differences (~ 70%) are driven by DNA sequence variants nearby CpG sites, which account for ~ 60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans, including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variation in DNA methylation is associated with varying gene expression levels following mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~ 20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation. CONCLUSION Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.
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Affiliation(s)
- Lucas T. Husquin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Maud Fagny
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine (CNRGH), CEA-Institut de Biologie François Jacob, 91000 Evry, France
| | - Hélène Quach
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Nora Zidane
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Lisa M. McEwen
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Hugues Aschard
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
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27
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Rodrigues PM, Perugorria MJ, Santos-Laso A, Bujanda L, Beuers U, Banales JM. Primary biliary cholangitis: A tale of epigenetically-induced secretory failure? J Hepatol 2018; 69:1371-1383. [PMID: 30193962 DOI: 10.1016/j.jhep.2018.08.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/14/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
Abstract
Primary biliary cholangitis (PBC) is a chronic cholestatic liver disease associated with autoimmune-related destruction of small to medium size intrahepatic bile ducts. The aetiology of PBC is unknown and its pathogenesis remains obscure. Both genetic variants and environmental factors have been linked to increased PBC susceptibility, with other alterations known to cooperate in disease pathobiology. Increasing evidence indicates the presence of epigenetic abnormalities in PBC, particularly alterations of cholangiocellular microRNAs (miRNAs or miRs). This review highlights and discusses the most relevant epigenetic alterations found in patients with PBC, focusing on the role of miR-506 in the promotion of cholestasis and immune activation.
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Affiliation(s)
- Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Alvaro Santos-Laso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain
| | - Ulrich Beuers
- Tytgat Institute for Liver and Intestinal Research and Department of Gastroenterology & Hepatology, Amsterdam Gastroenterology and Metabolism, AMC, Amsterdam, The Netherlands
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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28
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Barruet E, Morales BM, Cain CJ, Ton AN, Wentworth KL, Chan TV, Moody TA, Haks MC, Ottenhoff TH, Hellman J, Nakamura MC, Hsiao EC. NF-κB/MAPK activation underlies ACVR1-mediated inflammation in human heterotopic ossification. JCI Insight 2018; 3:122958. [PMID: 30429363 DOI: 10.1172/jci.insight.122958] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Inflammation helps regulate normal growth and tissue repair. Although bone morphogenetic proteins (BMPs) and inflammation are known contributors to abnormal bone formation, how these pathways interact in ossification remains unclear. METHODS We examined this potential link in patients with fibrodysplasia ossificans progressiva (FOP), a genetic condition of progressive heterotopic ossification caused by activating mutations in the Activin A type I receptor (ACVR1/ALK2). FOP patients show exquisite sensitivity to trauma, suggesting that BMP pathway activation may alter immune responses. We studied primary blood, monocyte, and macrophage samples from control and FOP subjects using multiplex cytokine, gene expression, and protein analyses; examined CD14+ primary monocyte and macrophage responses to TLR ligands; and assayed BMP, TGF-β activated kinase 1 (TAK1), and NF-κB pathways. RESULTS FOP subjects at baseline without clinically evident heterotopic ossification showed increased serum IL-3, IL-7, IL-8, and IL-10. CD14+ primary monocytes treated with the TLR4 activator LPS showed increased CCL5, CCR7, and CXCL10; abnormal cytokine/chemokine secretion; and prolonged activation of the NF-κB pathway. FOP macrophages derived from primary monocytes also showed abnormal cytokine/chemokine secretion, increased TGF-β production, and p38MAPK activation. Surprisingly, SMAD phosphorylation was not significantly changed in the FOP monocytes/macrophages. CONCLUSIONS Abnormal ACVR1 activity causes a proinflammatory state via increased NF-κB and p38MAPK activity. Similar changes may contribute to other types of heterotopic ossification, such as in scleroderma and dermatomyositis; after trauma; or with recombinant BMP-induced bone fusion. Our findings suggest that chronic antiinflammatory treatment may be useful for heterotopic ossification.
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Affiliation(s)
- Emilie Barruet
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Blanca M Morales
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Corey J Cain
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Amy N Ton
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Kelly L Wentworth
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Tea V Chan
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Tania A Moody
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
| | - Mariëlle C Haks
- Leiden University Medical Center, Department of Infectious Diseases, Leiden, Netherlands
| | - Tom Hm Ottenhoff
- Leiden University Medical Center, Department of Infectious Diseases, Leiden, Netherlands
| | - Judith Hellman
- Department of Anesthesia and Perioperative Care, UCSF, San Francisco, California, USA
| | - Mary C Nakamura
- Division of Rheumatology, Department of Medicine, San Francisco VA Health Care System, UCSF, San Francisco, California, USA
| | - Edward C Hsiao
- Division of Endocrinology and Metabolism, Department of Medicine, and the Institute for Human Genetics, UCSF, San Francisco, California, USA
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Nelson CP, Erridge C. Are toll-like receptors potential drug targets for atherosclerosis? Evidence from genetic studies to date. Immunogenetics 2018; 71:1-11. [PMID: 30327825 DOI: 10.1007/s00251-018-1092-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/09/2018] [Indexed: 01/08/2023]
Abstract
Low-density lipoprotein cholesterol lowering, most notably via statin therapy, has successfully reduced the burden of coronary artery disease (CAD) in recent decades. However, the residual risk remaining even after aggressive lipid lowering has renewed interest in alternative targets. Anti-inflammatory drugs are thought to have much potential in this context, but side effects associated with long-term use of conventional anti-inflammatories, such as NSAIDs and glucocorticoids, preclude their use as preventive agents for CAD. Evidence from epidemiological studies and murine models of atherosclerosis suggests that toll-like receptors (TLRs) may have utility as targets for more focused anti-inflammatories, but it remains unclear if this pathway is causally related to CAD in man. Here, we review recent insight into this question gained from genetic studies of cardiovascular risk and innate immune function, focussing on the potential of Mendelian randomisation approaches based on intracellular-signalling pathways to identify and prioritise targets for drug development.
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Affiliation(s)
- Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
| | - Clett Erridge
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK. .,Department of Biomedical and Forensic Sciences, Anglia Ruskin University, East Rd, Cambridge, CB1 1PT, UK.
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30
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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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31
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Fu S, Liu H, Chen X, Qiu Y, Ye C, Liu Y, Wu Z, Guo L, Hou Y, Hu CAA. Baicalin Inhibits Haemophilus Parasuis-Induced High-Mobility Group Box 1 Release during Inflammation. Int J Mol Sci 2018; 19:ijms19051307. [PMID: 29702580 PMCID: PMC5983759 DOI: 10.3390/ijms19051307] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/04/2018] [Accepted: 04/24/2018] [Indexed: 02/07/2023] Open
Abstract
Haemophilus parasuis (H. parasuis) can cause Glässer’s disease in pigs. However, the molecular mechanism of the inflammation response induced by H. parasuis remains unclear. The high-mobility group box 1 (HMGB1) protein is related to the pathogenesis of various infectious pathogens, but little is known about whether H. parasuis can induce the release of HMGB1 in piglet peripheral blood monocytes. Baicalin displays important anti-inflammatory and anti-microbial activities. In the present study, we investigated whether H. parasuis can trigger the secretion of HMGB1 in piglet peripheral blood monocytes and the anti-inflammatory effect of baicalin on the production of HMGB1 in peripheral blood monocytes induced by H. parasuis during the inflammation response. In addition, host cell responses stimulated by H. parasuis were determined with RNA-Seq. The RNA-Seq results showed that H. parasuis infection provokes the expression of cytokines and the activation of numerous pathways. In addition, baicalin significantly reduced the release of HMGB1 in peripheral blood monocytes induced by H. parasuis. Taken together, our study showed that H. parasuis can induce the release of HMGB1 and baicalin can inhibit HMGB1 secretion in an H. parasuis-induced peripheral blood monocytes model, which may provide a new strategy for preventing the inflammatory disorders induced by H. parasuis.
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Affiliation(s)
- Shulin Fu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Huashan Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Xiao Chen
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yinsheng Qiu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Chun Ye
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yu Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Zhongyuan Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Ling Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Yongqing Hou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan 430023, China.
| | - Chien-An Andy Hu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, China.
- Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
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32
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Gajbhiye R, McKinnon B, Mortlock S, Mueller M, Montgomery G. Genetic Variation at Chromosome 2q13 and Its Potential Influence on Endometriosis Susceptibility Through Effects on the IL-1 Family. Reprod Sci 2018; 25:1307-1317. [PMID: 29669463 DOI: 10.1177/1933719118768688] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Endometriosis is characterized by the growth of epithelial and stromal cells outside the uterine cavity. It has a complex etiology and affects ∼10% of reproductive age women. It is accompanied by a chronic inflammatory response with substantial evidence to indicate genetic susceptibility. The causal genes and their pathways leading to endometriosis, however, are still unknown. Recently, genomewide association studies on endometriosis identified 14 genomic risk loci in women of European and Japanese ancestry. It is becoming increasingly clear that these risk regions are intergenic and thus contribute to disease susceptibility through regulatory mechanisms, most likely mediated through regulation of genes within a restricted distance from the risk variants. One endometriosis risk locus has been detected at chromosome 2q13 within an inflammatory-rich region of gene transcripts and thus may play a role in the inflammation component of the disease. We carried out detailed analysis of the genomic region 250 kb on either side of sentinel SNP rs10167914 and identified 21 transcripts which contained 6 interleukin (IL)-1 family genes, 3 previously reported coding genes that have a relationship to inflammation, 4 novel coding, or pseudogenes, and 8 noncoding RNA transcripts. Through an extensive literature search, we examined the roles these genes and their resultant proteins play in endometriosis pathogenesis. The results suggest alteration in the expression the IL-1 family transcripts either alone or as a complex milieu could have a significant influence on endometriosis and should be prioritized for future study on the implications of inflammation on endometriotic lesions.
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Affiliation(s)
- Rahul Gajbhiye
- 1 Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia.,3 Department of Clinical Research, ICMR-National Institute for Research in Reproductive Health, Parel, Mumbai, Maharashtra, India
| | - Brett McKinnon
- 2 Department of Obstetrics and Gynaecology, Inselspital, Berne University Hospital, Bern, Switzerland
| | - Sally Mortlock
- 1 Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
| | - Michael Mueller
- 2 Department of Obstetrics and Gynaecology, Inselspital, Berne University Hospital, Bern, Switzerland
| | - Grant Montgomery
- 1 Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
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33
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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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34
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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: 171] [Impact Index Per Article: 28.5] [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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35
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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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36
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A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nat Genet 2017; 49:1437-1449. [PMID: 28892060 PMCID: PMC5660607 DOI: 10.1038/ng.3947] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 08/11/2017] [Indexed: 02/07/2023]
Abstract
A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) using functional and regulatory annotations that relate to the cells, tissues, and pathophysiology of IBD. Our model consists of individual networks constructed using molecular data generated from intestinal samples isolated from three populations of patients with IBD at different stages of disease. We performed key driver analysis to identify genes predicted to modulate network regulatory states associated with IBD, prioritizing and prospectively validating 12 of the top key drivers experimentally. This validated key driver set not only introduces new regulators of processes central to IBD but also provides the integrated circuits of genetic, molecular, and clinical traits that can be directly queried to interrogate and refine the regulatory framework defining IBD.
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37
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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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38
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Spanou E, Kalisperati P, Pateras IS, Papalampros A, Barbouti A, Tzioufas AG, Kotsinas A, Sougioultzis S. Genetic Variability as a Regulator of TLR4 and NOD Signaling in Response to Bacterial Driven DNA Damage Response (DDR) and Inflammation: Focus on the Gastrointestinal (GI) Tract. Front Genet 2017; 8:65. [PMID: 28611823 PMCID: PMC5447025 DOI: 10.3389/fgene.2017.00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
The fundamental role of human Toll-like receptors (TLRs) and NOD-like receptors (NLRs), the two most studied pathogen recognition receptors (PRRs), is the protection against pathogens and excessive tissue injury. Recent evidence supports the association between TLR/NLR gene mutations and susceptibility to inflammatory, autoimmune, and malignant diseases. PRRs also interfere with several cellular processes, such as cell growth, apoptosis, cell proliferation, differentiation, autophagy, angiogenesis, cell motility and migration, and DNA repair mechanisms. We briefly review the impact of TLR4 and NOD1/NOD2 and their genetic variability in the process of inflammation, tumorigenesis and DNA repair, focusing in the gastrointestinal tract. We also review the available data on new therapeutic strategies utilizing TLR/NLR agonists and antagonists for cancer, allergic diseases, viral infections and vaccine development against both infectious diseases and cancer.
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Affiliation(s)
- Evagelia Spanou
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Polyxeni Kalisperati
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Ioannis S. Pateras
- Department of Histology and Embryology, University of AthensAthens, Greece
| | - Alexandros Papalampros
- 1st Department of Surgery, “Laikon” General Hospital, University of AthensAthens, Greece
| | - Alexandra Barbouti
- Department of Anatomy-Histology-Embryology, University of IoanninaIoannina, Greece
| | - Athanasios G. Tzioufas
- Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
| | | | - Stavros Sougioultzis
- Gastroenterology Division, Department of Pathophysiology, “Laikon” General Hospital, University of AthensAthens, Greece
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39
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Woodward NC, Levine MC, Haghani A, Shirmohammadi F, Saffari A, Sioutas C, Morgan TE, Finch CE. Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo. J Neuroinflammation 2017; 14:84. [PMID: 28410596 PMCID: PMC5391610 DOI: 10.1186/s12974-017-0858-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/29/2017] [Indexed: 12/05/2022] Open
Abstract
Background Exposure to traffic-related air pollution (TRAP) is associated with accelerated cognitive aging and higher dementia risk in human populations. Rodent brains respond to TRAP with activation of astrocytes and microglia, increased inflammatory cytokines, and neurite atrophy. A role for Toll-like receptor 4 (TLR4) was suggested in mouse TLR4-knockouts, which had attenuated lung macrophage responses to air pollution. Methods To further analyze these mechanisms, we examined mixed glial cultures (astrocytes and microglia) for RNA responses to nanoscale particulate matter (nPM; diameter <0.2 μm), a well-characterized nanoscale particulate matter subfraction of TRAP collected from a local freeway (Morgan et al. Environ Health Perspect 2011; 119,1003–1009, 2011). The nPM was compared with responses to the endotoxin lipopolysaccharide (LPS), a classic TLR4 ligand, using Affymetrix whole genome microarray in rats. Expression patterns were analyzed by significance analysis of microarrays (SAM) for fold change and by weighted gene co-expression network analysis (WGCNA) to identify modules of shared responses between nPM and LPS. Finally, we examined TLR4 activation in hippocampal tissue from mice chronically exposed to nPM. Results SAM and WGCNA analyses showed strong activation of TLR4 and NF-κB by both nPM and LPS. TLR4 siRNA attenuated TNFα and other inflammatory responses to nPM in vitro, via the MyD88-dependent pathway. In vivo, mice chronically exposed to nPM showed increased TLR4, MyD88, TNFα, and TNFR2 RNA, and decreased NF-κB and TRAF6 RNA TLR4 and NF-κB responses in the hippocampus. Conclusions These results show TLR4 activation is integral in brain inflammatory responses to air pollution, and warrant further study of TLR4 in accelerated cognitive aging by air pollution. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0858-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas C Woodward
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Morgan C Levine
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Amin Haghani
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Farimah Shirmohammadi
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Arian Saffari
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Constantinos Sioutas
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Todd E Morgan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA. .,Dornsife College, University of Southern California, Los Angeles, CA, USA.
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Mishra C, Kumar S, Yathish H. Predicting the effect of non synonymous SNPs in bovine TLR4 gene. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Abstract
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i.e., testing for association of all transcript-marker pairs. However these "one at-a-time" strategies are (1) unable to control the number of false-positives when an intricate Linkage Disequilibrium structure is present and (2) are often underpowered to detect the full spectrum of trans-acting regulatory effects. Here we present our viewpoint on the most recent advances on eQTL mapping approaches, with a focus on Bayesian methodology. We review the advantages of the Bayesian approach over frequentist methods and provide an empirical example of polygenic eQTL mapping to illustrate the different properties of frequentist and Bayesian methods. Finally, we discuss how multivariate eQTL mapping approaches have distinctive features with respect to detection of polygenic effects, accuracy, and interpretability of the results.
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Affiliation(s)
- Martha Imprialou
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Box 238, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Department of Mathematics, Imperial College London, 180 Queen's Gate, London, SW7 2AZ, UK.
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Abstract
The hematopoietic system plays a major role in human health. Two studies by Astle et al. and Chen et al. published in this issue of Cell use genome-wide association and functional genomics approaches to provide deep insights into the role of genetic variants in hematological traits. We discuss these discoveries and future strategies toward completing our understanding of the genetic basis for variation in human traits.
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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 10027, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10027, USA.
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Gölz L, Buerfent BC, Hofmann A, Rühl H, Fricker N, Stamminger W, Oldenburg J, Deschner J, Hoerauf A, Nöthen MM, Schumacher J, Hübner MP, Jäger A. Genome-wide transcriptome induced by nickel in human monocytes. Acta Biomater 2016; 43:369-382. [PMID: 27477848 DOI: 10.1016/j.actbio.2016.07.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/20/2016] [Accepted: 07/27/2016] [Indexed: 12/22/2022]
Abstract
UNLABELLED Nickel-containing alloys are frequently used in the biomedical field, although, owing to corrosive processes metal ion leaching is inevitable. Due to nickel ion (Ni(2+)) leaching several adverse effects are described in the literature. However, only a few studies evaluated the genetic profile of Ni(2+) in human cells which is of great importance since nickel-induced effects differ between humans and mice as a result of species-specific receptor variability. Thus, we investigated gene expression induced by Ni(2+)in human monocytes using a transcriptome-wide approach determining new target genes implicated in nickel-induced pathologies. Monocytes were isolated from healthy volunteers of Central European origin using stringent inclusion criteria. Cells were challenged with different Ni(2+) concentrations. Array-based gene expression analysis was performed comprising more than 47,000 transcripts followed by pathway analyses. Transcriptional data were validated by protein and cell surface markers. Ni(2+) significantly influenced the expression of 1385 transcripts in a dose-dependent manner. Apart from known targets (CCL20↑, PTGS2↑, MTs↑, SLCs↑), we identified new candidates implicated in Ni(2+)-elicited processes (various microRNAs↑, INSIG1↑, NAMPT↑, MS4A6A↓, DHRS9↓). Several of these transcripts correspond to immunity, inflammation and were shown to be involved in cellular reactions related to hypersensitivity, cancer, colitis, and encephalitis. Moreover, 459 canonical pathways/signaling, 500 pathologies and 2687 upstream regulators were detected. Protein results validated our findings. To our knowledge, the present systematic transcriptome-wide expression study is the first which explored Ni(2+)-elicited cell responses in human primary monocytes identifying new target genes, pathways and upstream regulators of relevance to diagnostic and therapeutic strategies. STATEMENT OF SIGNIFICANCE Nickel is widely applied in the biomedical field, although several adverse effects are documented in the literature due to nickel ion (Ni(2+)) leaching. In humans, allergic reactions like contact dermatitis are the most common adverse effect to Ni(2+), whereas serious concerns relate to possible systemic and carcinogenic activities. Using a systematic genome-wide transcriptional approach in human primary monocytes unveil new target genes, pathways and upstream regulators implicated in nickel-elicited immune response which are of significance to diagnostic and therapeutic strategies. This approach provides new information of how host-derived immune response contributes to the interaction with antigens and supports the interplay between metal ions and systemic diseases.
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Ferreira MAR, Jansen R, Willemsen G, Penninx B, Bain LM, Vicente CT, Revez JA, Matheson MC, Hui J, Tung JY, Baltic S, Le Souëf P, Montgomery GW, Martin NG, Robertson CF, James A, Thompson PJ, Boomsma DI, Hopper JL, Hinds DA, Werder RB, Phipps S. Gene-based analysis of regulatory variants identifies 4 putative novel asthma risk genes related to nucleotide synthesis and signaling. J Allergy Clin Immunol 2016; 139:1148-1157. [PMID: 27554816 DOI: 10.1016/j.jaci.2016.07.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Hundreds of genetic variants are thought to contribute to variation in asthma risk by modulating gene expression. Methods that increase the power of genome-wide association studies (GWASs) to identify risk-associated variants are needed. OBJECTIVE We sought to develop a method that aggregates the evidence for association with disease risk across expression quantitative trait loci (eQTLs) of a gene and use this approach to identify asthma risk genes. METHODS We developed a gene-based test and software package called EUGENE that (1) is applicable to GWAS summary statistics; (2) considers both cis- and trans-eQTLs; (3) incorporates eQTLs identified in different tissues; and (4) uses simulations to account for multiple testing. We applied this approach to 2 published asthma GWASs (combined n = 46,044) and used mouse studies to provide initial functional insights into 2 genes with novel genetic associations. RESULTS We tested the association between asthma and 17,190 genes that were found to have cis- and/or trans-eQTLs across 16 published eQTL studies. At an empirical FDR of 5%, 48 genes were associated with asthma risk. Of these, for 37, the association was driven by eQTLs located in established risk loci for allergic disease, including 6 genes not previously implicated in disease cause (eg, LIMS1, TINF2, and SAFB). The remaining 11 significant genes represent potential novel genetic associations with asthma. The association with 4 of these replicated in an independent GWAS: B4GALT3, USMG5, P2RY13, and P2RY14, which are genes involved in nucleotide synthesis or nucleotide-dependent cell activation. In mouse studies, P2ry13 and P2ry14-purinergic receptors activated by adenosine 5-diphosphate and UDP-sugars, respectively-were upregulated after allergen challenge, notably in airway epithelial cells, eosinophils, and neutrophils. Intranasal exposure with receptor agonists induced the release of IL-33 and subsequent eosinophil infiltration into the lungs. CONCLUSION We identified novel associations between asthma and eQTLs for 4 genes related to nucleotide synthesis/signaling and demonstrated the power of gene-based analyses of GWASs.
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Affiliation(s)
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Brenda Penninx
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Lisa M Bain
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Joana A Revez
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Melanie C Matheson
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Jennie Hui
- PathWest Laboratory Medicine of Western Australia, Nedlands, Australia; School of Population Health, University of Western Australia, Nedlands, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Australia; Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Nedlands, Australia
| | | | - Svetlana Baltic
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, Nedlands, Australia
| | - Peter Le Souëf
- School of Paediatrics and Child Health, Princess Margaret Hospital for Children, Subiaco, Australia
| | | | | | - Colin F Robertson
- Respiratory Medicine, Murdoch Children's Research Institute, Melbourne, Australia
| | - Alan James
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Nedlands, Australia; School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia; Department of Pulmonary Physiology and Sleep Medicine, West Australian Sleep Disorders Research Institute, Nedlands, Australia
| | - Philip J Thompson
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, Nedlands, Australia; School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - John L Hopper
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | | | - Rhiannon B Werder
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Simon Phipps
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
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Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KGC. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. Genome Med 2016; 8:76. [PMID: 27435189 PMCID: PMC4952362 DOI: 10.1186/s13073-016-0329-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. METHODS We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. RESULTS Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant hits. CONCLUSIONS This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.
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Affiliation(s)
- Arianne C. Richard
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - James E. Peters
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - James C. Lee
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Golnaz Vahedi
- />Department of Genetics, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Alejandro A. Schäffer
- />Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894 USA
| | - Richard M. Siegel
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paul A. Lyons
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Kenneth G. C. Smith
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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Abstract
Interferon regulatory factor 5 (IRF5) has been demonstrated as a key transcription factor of the immune system, playing important roles in modulating inflammatory immune responses in numerous cell types including dendritic cells, macrophages, and B cells. As well as driving the expression of type I interferon in antiviral responses, IRF5 is also crucial for driving macrophages toward a proinflammatory phenotype by regulating cytokine and chemokine expression and modulating B-cell maturity and antibody production. This review highlights the functional importance of IRF5 in a disease setting, by discussing polymorphic mutations at the human Irf5 locus that lead to susceptibility to systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease. In concordance with this, we also discuss lessons in IRF5 functionality learned from murine in vivo models of autoimmune disease and inflammation and hypothesize that modulation of IRF5 activity and expression could provide potential therapeutic benefits in the clinic.
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Affiliation(s)
- Hayley L Eames
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.
| | - Alastair L Corbin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.
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47
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Gölz L, Buerfent BC, Hofmann A, Hübner MP, Rühl H, Fricker N, Schmidt D, Johannes O, Jepsen S, Deschner J, Hoerauf A, Nöthen MM, Schumacher J, Jäger A. Genome-wide transcriptome induced by Porphyromonas gingivalis LPS supports the notion of host-derived periodontal destruction and its association with systemic diseases. Innate Immun 2015; 22:72-84. [PMID: 26608307 DOI: 10.1177/1753425915616685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Chronic periodontitis (CP) is a prevalent pathogen-associated inflammatory disorder characterized by the destruction of tooth-supporting tissues, and linked to several systemic diseases. Both the periodontopathogen Porphyromonas gingivalis (Pg), and the genetically determined host immune response, are hypothesized to play a crucial role in this association. To identify new target genes for CP and its associated systemic diseases, we investigated the transcriptome induced by Pg in human monocytes using a genome-wide approach. Monocytes were isolated from healthy male volunteers of European origin and challenged with the Pg virulence factor LPS. Array-based gene expression analysis comprising >47,000 transcripts was performed followed by pathway analyses. Transcriptional data were validated by protein and cell surface markers. LPS Pg challenge led to the significant induction of 902 transcripts. Besides known periodontitis-associated targets, several new candidates were identified (CCL23↑, INDO↑, GBP 1/4↑, CFB↑, ISG20↑, MIR155HG↑, DHRS9↓). Moreover, various transcripts correspond to the host immune response, and have been linked to cancer, atherosclerosis and arthritis, thus highlighting the systemic impact of CP. Protein data of immunological markers validated our results. The present findings expand understanding of Pg elicited immune responses, and indicate new target genes and pathways of relevance to diagnostic and therapeutic strategies.
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Affiliation(s)
- Lina Gölz
- Center of Dento-Maxillo-Facial Medicine, University Hospital of Bonn, Bonn, Germany
| | - Benedikt C Buerfent
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | - Marc P Hübner
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | - David Schmidt
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany
| | - Oldenburg Johannes
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital of Bonn, Bonn, Germany
| | - Søren Jepsen
- Center of Dento-Maxillo-Facial Medicine, University Hospital of Bonn, Bonn, Germany
| | - James Deschner
- Center of Dento-Maxillo-Facial Medicine, University Hospital of Bonn, Bonn, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Bonn, Germany German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn, Germany
| | | | - Andreas Jäger
- Center of Dento-Maxillo-Facial Medicine, University Hospital of Bonn, Bonn, Germany
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48
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Messemaker TC, Huizinga TW, Kurreeman F. Immunogenetics of rheumatoid arthritis: Understanding functional implications. J Autoimmun 2015. [DOI: 10.1016/j.jaut.2015.07.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P, Saeij JPJ. Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection. PLoS Genet 2015; 11:e1005619. [PMID: 26510153 PMCID: PMC4625001 DOI: 10.1371/journal.pgen.1005619] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/29/2015] [Indexed: 12/18/2022] Open
Abstract
Macrophages display flexible activation states that range between pro-inflammatory (classical activation) and anti-inflammatory (alternative activation). These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and inflammatory diseases. Several macrophage- or immune-related genes have been shown to modulate infectious and inflammatory disease pathogenesis. However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging. We integrated transcriptional profiling and linkage analyses to determine the genetic basis for the differential murine macrophage response to inflammatory stimuli and to infection with the obligate intracellular parasite Toxoplasma gondii. We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes. In addition, we show that the difference between AJ and C57BL/6J macrophages in controlling Toxoplasma growth after stimulation with interferon gamma and tumor necrosis factor alpha mapped to chromosome 3, proximal to the Guanylate binding protein (Gbp) locus that is known to modulate the murine macrophage response to Toxoplasma. Using an shRNA-knockdown strategy, we show that the transcript levels of an RNA helicase, Ddx1, regulates strain differences in the amount of nitric oxide produced by macrophage after stimulation with interferon gamma and tumor necrosis factor. Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits. Macrophages provide a first line of defense against invading pathogens and play an important role in the initiation and resolution of immune responses. When in contact with pathogens or immune factors, such as cytokines, macrophages assume activation states that range between pro-inflammatory (classical activation) and anti-inflammatory (alternative activation). Even though it is known that macrophages from different individuals are biased towards one of the various activation states, the genetic factors that define individual differences in macrophage activation are not fully understood. Additionally, although macrophages are important in infectious disease pathogenesis, how individual differences in macrophage activation contribute to individual differences in susceptibility to infectious disease is just emerging. We used macrophages from genetically segregating mice to show that discrete transcriptional programs, which are modulated by specific genomic regions, modulate differences in macrophage activation. Murine macrophages differences in controlling Toxoplasma growth mapped to chromosome 3, proximal to the Guanylate binding protein (Gbp) locus that is known to modulate the murine macrophage response to Toxoplasma. Using a shRNA-mediated knockdown approach, we show that the DEAD box polypeptide 1 (Ddx1) modulates nitric oxide production in macrophages stimulated with interferon gamma and tumor necrosis factor. These findings are a step towards the identification of genes that regulate macrophage phenotypes and disease outcome.
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Affiliation(s)
- Musa A. Hassan
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (MAH); (JPJS)
| | - Kirk D. Jensen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vincent Butty
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kenneth Hu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Erwan Boedec
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- School of Biotechnology, University of Strasbourg, Strasbourg, France
| | - Pjotr Prins
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Jeroen P. J. Saeij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Pathology, Microbiology & Immunology, University of California, Davis, Davis, California, United States of America
- * E-mail: (MAH); (JPJS)
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50
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Andiappan AK, Melchiotti R, Poh TY, Nah M, Puan KJ, Vigano E, Haase D, Yusof N, San Luis B, Lum J, Kumar D, Foo S, Zhuang L, Vasudev A, Irwanto A, Lee B, Nardin A, Liu H, Zhang F, Connolly J, Liu J, Mortellaro A, Wang DY, Poidinger M, Larbi A, Zolezzi F, Rotzschke O. Genome-wide analysis of the genetic regulation of gene expression in human neutrophils. Nat Commun 2015; 6:7971. [PMID: 26259071 PMCID: PMC4918343 DOI: 10.1038/ncomms8971] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/01/2015] [Indexed: 02/01/2023] Open
Abstract
Neutrophils are an abundant immune cell type involved in both antimicrobial defence and autoimmunity. The regulation of their gene expression, however, is still largely unknown. Here we report an eQTL study on isolated neutrophils from 114 healthy individuals of Chinese ethnicity, identifying 21,210 eQTLs on 832 unique genes. Unsupervised clustering analysis of these eQTLs confirms their role in inflammatory responses and immunological diseases but also indicates strong involvement in dermatological pathologies. One of the strongest eQTL identified (rs2058660) is also the tagSNP of a linkage block reported to affect leprosy and Crohn's disease in opposite directions. In a functional study, we can link the C allele with low expression of the β-chain of IL18-receptor (IL18RAP). In neutrophils, this results in a reduced responsiveness to IL-18, detected both on the RNA and protein level. Thus, the polymorphic regulation of human neutrophils can impact beneficial as well as pathological inflammatory responses. Neutrophils are abundant immune cells important for antimicrobial defence and in autoimmunity. Here, by mapping expression quantitative trait loci (eQTL) in neutrophils of Chinese ethnicity from Singapore, Andiappan et al. provide a resource for understanding immune-related trait associated genetic variants.
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Affiliation(s)
- Anand Kumar Andiappan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Rossella Melchiotti
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Tuang Yeow Poh
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Michelle Nah
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Kia Joo Puan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Elena Vigano
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Doreen Haase
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Nurhashikin Yusof
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Boris San Luis
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Dilip Kumar
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Shihui Foo
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Li Zhuang
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Anusha Vasudev
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Astrid Irwanto
- Department of Human Genetics, Genome institute of Singapore (GIS), Singapore, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Alessandra Nardin
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China.,Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China.,School of Medicine, Shandong University, Shandong Provincial Medical Center for Dermatovenereology, Jinan, Shandong, China.,Shandong Provincial Institute of Dermatology and Venereology, Provincial Academy of Medical Science, Jinan, Shandong, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China.,Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China.,School of Medicine, Shandong University, Shandong Provincial Medical Center for Dermatovenereology, Jinan, Shandong, China.,Shandong Provincial Institute of Dermatology and Venereology, Provincial Academy of Medical Science, Jinan, Shandong, China
| | - John Connolly
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Jianjun Liu
- Department of Human Genetics, Genome institute of Singapore (GIS), Singapore, Singapore.,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Alessandra Mortellaro
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - De Yun Wang
- Department of Otolaryngology, National University of Singapore, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
| | - Olaf Rotzschke
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), #04-06, 8A Biomedical Grove, Singapore, Singapore
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