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Huang QQ, Tang HHF, Teo SM, Mok D, Ritchie SC, Nath AP, Brozynska M, Salim A, Bakshi A, Holt BJ, Khor CC, Sly PD, Holt PG, Holt KE, Inouye M. Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. Nat Commun 2020; 11:3761. [PMID: 32724101 PMCID: PMC7387553 DOI: 10.1038/s41467-020-17477-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic immune-mediated diseases of adulthood often originate in early childhood. To investigate genetic associations between neonatal immunity and disease, we map expression quantitative trait loci (eQTLs) in resting myeloid cells and CD4+ T cells from cord blood samples, as well as in response to lipopolysaccharide (LPS) or phytohemagglutinin (PHA) stimulation, respectively. Cis-eQTLs are largely specific to cell type or stimulation, and 31% and 52% of genes with cis-eQTLs have response eQTLs (reQTLs) in myeloid cells and T cells, respectively. We identified cis regulatory factors acting as mediators of trans effects. There is extensive colocalisation between condition-specific neonatal cis-eQTLs and variants associated with immune-mediated diseases, in particular CTSH had widespread colocalisation across diseases. Mendelian randomisation shows causal neonatal gene expression effects on disease risk for BTN3A2, HLA-C and others. Our study elucidates the genetics of gene expression in neonatal immune cells, and aetiological origins of autoimmune and allergic diseases. Some immune-mediated diseases may originate in early childhood. The authors mapped eQTLs and response eQTLs to various stimuli in neonatal myeloid cells and T cells, and revealed their potential role in immune-mediated diseases using colocalisation and Mendelian randomisation.
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Affiliation(s)
- Qin Qin Huang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shu Mei Teo
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Danny Mok
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marta Brozynska
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Agus Salim
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne School of Population and Global Health, Carlton, VIC, 3053, Australia
| | - Andrew Bakshi
- Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Barbara J Holt
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Chiea Chuen Khor
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Peter D Sly
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, 4101, Australia
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, 4101, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,The London School of Hygiene and Tropical Medicine, London, WC1E 7TH, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK. .,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. .,National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK. .,The Alan Turing Institute, London, UK. .,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. .,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
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Varricchi G, Marone G, Spadaro G, Russo M, Granata F, Genovese A, Marone G. Novel Biological Therapies in Severe Asthma: Targeting the Right Trait. Curr Med Chem 2019; 26:2801-2822. [PMID: 29318959 DOI: 10.2174/0929867325666180110094542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 12/23/2022]
Abstract
Asthma is a heterogeneous disease characterized by chronic airway inflammation that results in a wide spectrum of clinical manifestations. Patients with severe asthma represent a substantial share of consumption of healthcare resources and hospitalization. Moreover, these patients are at risk of increased morbidity and mortality. Recently, several phenotypes and endotypes of asthma have been identified. The identification of specific subtypes of asthma is fundamental for optimizing the clinical benefit of novel treatments. Although in most patients the disease can be controlled by some combination of pharmacologic agents, in some 5-10% of patients the disease remains uncontrolled. Several monoclonal antibodies (mAbs) targeting pathogenetic molecules (e.g., IgE, IL-5, IL- 5Rα, IL-4, IL-13, TSLP) are currently available or under development for the treatment of different forms of severe type 2 asthma. The identification of diagnostic and predictive biomarkers (e.g., IgE, blood eosinophil count, FeNO, periostin, etc.) has revolutioned the field of targeted therapy in severe asthma. Monoclonal antibodies targeting Th2-driven inflammation are generally safe in adult patients with moderate-to-severe asthma. The long-term safety of these biologics is a relevant issue that should be addressed. Unfortunately, little is known about non-type 2 asthma. Further studies are needed to identify biomarkers to guide targeted therapies of different forms of non-type 2 asthma.
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Affiliation(s)
- Gilda Varricchi
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,WAO Center of Excellence, Naples, Italy
| | - Giancarlo Marone
- Department of Public Health, University of Naples Federico II, Naples, Italy.,Monaldi Hospital, Naples, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,WAO Center of Excellence, Naples, Italy
| | - Michele Russo
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy
| | - Francescopaolo Granata
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,WAO Center of Excellence, Naples, Italy
| | - Arturo Genovese
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,WAO Center of Excellence, Naples, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences (DISMET), University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,WAO Center of Excellence, Naples, Italy.,Institute of Experimental Endocrinology and Oncology "Gaetano Salvatore", National Research Council (CNR), Naples, Italy
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