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Riesmeijer SA, Nolte IM, Olde Loohuis LM, Reus LM, Boltz T, Ng M, Furniss D, Werker PMN, Ophoff RA. Polygenic Risk Associations with Clinical Characteristics and Recurrence of Dupuytren Disease. Plast Reconstr Surg 2024; 153:573e-583e. [PMID: 37257093 PMCID: PMC10876167 DOI: 10.1097/prs.0000000000010775] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/22/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Dupuytren disease (DD) is a common complex trait, with varying severity and incompletely understood cause. Genome-wide association studies (GWAS) have identified risk loci. In this article, we examine whether genetic risk profiles of DD in patients are associated with clinical variation and disease severity and with patient genetic risk profiles of genetically correlated traits, including body mass index (BMI), triglycerides, high-density lipoproteins, type 2 diabetes mellitus, and endophenotypes fasting glucose and glycated hemoglobin. METHODS The authors used a well-characterized cohort of 1461 DD patients with available phenotypic and genetic data. Phenotype data include age at onset, recurrence, and family history of disease. Polygenic risk scores (PRSs) of DD, BMI, triglycerides, high-density lipoprotein, type 2 diabetes, fasting glucose, and hemoglobin A1c using various significance thresholds were calculated with PRSice using the most recent GWAS summary statistics. Control data from LifeLines were used to determine P value cutoffs for PRS generation explaining most variance. RESULTS The PRS for DD was significantly associated with a positive family history for DD, age at onset, disease onset before the age of 50, and recurrence. We also found a significant negative correlation between the PRSs for DD and BMI. CONCLUSIONS Although GWAS studies of DD are designed to identify genetic risk factors distinguishing case/control status, we show that the genetic risk profile for DD also explains part of its clinical variation and disease severity. The PRS may therefore aid in accurate prognostication, choosing initial treatment and in personalized medicine in the future. CLINICAL QUESTION/LEVEL OF EVIDENCE Risk, III.
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Affiliation(s)
- Sophie A. Riesmeijer
- From the Departments of Plastic Surgery
- Epidemiology, University of Groningen, University Medical Center Groningen
| | - Ilja M. Nolte
- Epidemiology, University of Groningen, University Medical Center Groningen
| | - Loes M. Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Lianne M. Reus
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam University Medical Center
| | - Toni Boltz
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford
| | | | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
- Department of Psychiatry, Erasmus University Rotterdam, Erasmus Medical Center
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2
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Kullaya VI, Temba GS, Vadaq N, Njau J, Boahen CK, Nkambule BB, Thibord F, Chen MH, Pecht T, Lyamuya F, Kumar V, Netea MG, Mmbaga BT, van der Ven A, Johnson AD, de Mast Q. Genetic and nongenetic drivers of platelet reactivity in healthy Tanzanian individuals. J Thromb Haemost 2024; 22:805-817. [PMID: 38029856 DOI: 10.1016/j.jtha.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Platelets play a key role in hemostasis, inflammation, and cardiovascular diseases. Platelet reactivity is highly variable between individuals. The drivers of this variability in populations from Sub-Saharan Africa remain largely unknown. OBJECTIVES We aimed to investigate the nongenetic and genetic determinants of platelet reactivity in healthy adults living in a rapidly urbanizing area in Northern Tanzania. METHODS Platelet activation and reactivity were measured by platelet P-selectin expression and the binding of fibrinogen in unstimulated blood and after ex vivo stimulation with adenosine diphosphate and PAR-1 and PAR-4 ligands. We then analyzed the associations of platelet parameters with host genetic and nongenetic factors, environmental factors, plasma inflammatory markers, and plasma metabolites. RESULTS Only a few associations were found between platelet reactivity parameters and plasma inflammatory markers and nongenetic host and environmental factors. In contrast, untargeted plasma metabolomics revealed a large number of associations with food-derived metabolites, including phytochemicals that were previously reported to inhibit platelet reactivity. Genome-wide single-nucleotide polymorphism genotyping identified 2 novel single-nucleotide polymorphisms (rs903650 and rs4789332) that were associated with platelet reactivity at the genome-wide level (P < 5 × 10-8) as well as a number of variants in the PAR4 gene (F2RL3) that were associated with PAR4-induced reactivity. CONCLUSION Our study uncovered factors that determine variation in platelet reactivity in a population in East Africa that is rapidly transitioning to an urban lifestyle, including the importance of genetic ancestry and the gradual abandoning of the traditional East African diet.
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Affiliation(s)
- Vesla I Kullaya
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania; Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Godfrey S Temba
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Tanzania; Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Judith Njau
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Collins K Boahen
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bongani B Nkambule
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Florian Thibord
- National Heart, Lung, and Blood Institute, Population Sciences Branch, Framingham, Massachusetts, USA
| | - Ming-Huei Chen
- National Heart, Lung, and Blood Institute, Population Sciences Branch, Framingham, Massachusetts, USA
| | - Tal Pecht
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Furaha Lyamuya
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Vinod Kumar
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department for Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania; Department of Pediatrics, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Andre van der Ven
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute, Population Sciences Branch, Framingham, Massachusetts, USA
| | - Quirijn de Mast
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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3
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Boahen CK, Abee H, Ponce IR, Joosten LAB, Netea MG, Kumar V. Sex-biased genetic regulation of inflammatory proteins in the Dutch population. BMC Genomics 2024; 25:154. [PMID: 38326779 PMCID: PMC10851559 DOI: 10.1186/s12864-024-10065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Significant differences in immune responses, prevalence or susceptibility of diseases and treatment responses have been described between males and females. Despite this, sex-differentiation analysis of the genetic architecture of inflammatory proteins is largely unexplored. We performed sex-stratified meta-analysis after protein quantitative trait loci (pQTL) mapping using inflammatory biomarkers profiled using targeted proteomics (Olink inflammatory panel) of two population-based cohorts of Europeans. RESULTS Even though, around 67% of the pQTLs demonstrated shared effect between sexes, colocalization analysis identified two loci in the males (LINC01135 and ITGAV) and three loci (CNOT10, SRD5A2, and LILRB5) in the females with evidence of sex-dependent modulation by pQTL variants. Furthermore, we identified pathways with relevant functions in the sex-biased pQTL variants. We also showed through cross-validation that the sex-specific pQTLs are linked with sex-specific phenotypic traits. CONCLUSION Our study demonstrates the relevance of genetic sex-stratified analysis in the context of genetic dissection of protein abundances among individuals and reveals that, sex-specific pQTLs might mediate sex-linked phenotypes. Identification of sex-specific pQTLs associated with sex-biased diseases can help realize the promise of individualized treatment.
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Affiliation(s)
- Collins K Boahen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Hannah Abee
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Isis Ricaño Ponce
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacia, Cluj-Napoca-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, the Netherlands.
- Nitte (Deemed to Be University), Medical Sciences Complex, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangalore, 575018, India.
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4
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Flores Gomez D, Bekkering S, Ter Horst R, Cossins B, van den Munckhof ICL, Rutten JHW, Joosten LAB, Netea MG, Riksen NP. The effect of leptin on trained innate immunity and on systemic inflammation in subjects with obesity. J Leukoc Biol 2024; 115:374-384. [PMID: 37776323 DOI: 10.1093/jleuko/qiad118] [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: 03/15/2023] [Revised: 07/26/2023] [Accepted: 09/10/2023] [Indexed: 10/02/2023] Open
Abstract
Leptin is associated with cardiometabolic complications of obesity, such as metabolic syndrome and atherosclerosis. In obese men, the presence of metabolic syndrome is associated with higher circulating leptin and interleukin (IL)-6 concentrations and increased monocyte cytokine production capacity. Here, we investigated the effects of leptin on monocyte function and systemic inflammatory markers in obese individuals. We specifically explored whether leptin can induce long-term changes in innate immune function by inducing innate immune memory (also called trained immunity). We exposed human primary monocytes for 24 h to relevant leptin concentrations in vitro and measured cytokine production. In addition, after removing leptin, we incubated monocytes for 5 d in culture medium, and we restimulated them on day 6 to assess cytokine production capacity, phagocytosis, and foam cell formation. Direct stimulation with leptin did not induce cytokine production, but exposure to 50 ng/mL leptin augmented lipopolysaccharide- and R848-induced tumor necrosis factor α (TNF-α) production after 1 wk. In a separate in vivo study in a cohort of 302 obese subjects (body mass index [BMI] >27 kg/m2, 55 to 81 yr), we measured circulating leptin, inflammatory markers, and cytokine production upon ex vivo stimulation of isolated peripheral blood mononuclear cells. Circulating leptin concentrations positively correlated with circulating IL-1β and IL-6, which was more pronounced in men than in women. Four single nucleotide polymorphisms in the leptin gene influenced circulating IL-6 concentrations in men, suggesting a direct effect of leptin on IL-6. In conclusion, in vitro, leptin does not directly stimulate monocytes to produce cytokines, yet induces long-term monocyte hyperresponsiveness, i.e. trained immunity. In obese subjects, leptin is associated with circulating IL-6 in a sex-dependent manner. The underlying mechanisms of the sex-specific effect of leptin on innate immune cells remain to be further investigated.
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Affiliation(s)
- Daniela Flores Gomez
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Siroon Bekkering
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Rob Ter Horst
- Center for Molecular Medicine, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria
| | - Benjamin Cossins
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Strada Victor Babeș 8, Cluj-Napoca 400347, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
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5
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Moorlag SJCFM, Folkman L, Ter Horst R, Krausgruber T, Barreca D, Schuster LC, Fife V, Matzaraki V, Li W, Reichl S, Mourits VP, Koeken VACM, de Bree LCJ, Dijkstra H, Lemmers H, van Cranenbroek B, van Rijssen E, Koenen HJPM, Joosten I, Xu CJ, Li Y, Joosten LAB, van Crevel R, Netea MG, Bock C. Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity. Immunity 2024; 57:171-187.e14. [PMID: 38198850 DOI: 10.1016/j.immuni.2023.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/16/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024]
Abstract
Immune responses are tightly regulated yet highly variable between individuals. To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live-attenuated vaccine induces not only an adaptive immune response against tuberculosis but also triggers innate immune activation and memory that are indicative of trained immunity. We established personal immune profiles and chromatin accessibility maps over a 90-day time course of BCG vaccination in 323 individuals. Our analysis uncovered genetic and epigenetic predictors of baseline immunity and immune response. BCG vaccination enhanced the innate immune response specifically in individuals with a dormant immune state at baseline, rather than providing a general boost of innate immunity. This study advances our understanding of BCG's heterologous immune-stimulatory effects and trained immunity in humans. Furthermore, it highlights the value of epigenetic cell states for connecting immune function with genotype and the environment.
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Affiliation(s)
- Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lukas Folkman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Rob Ter Horst
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Linda C Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Fife
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wenchao Li
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Stephan Reichl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Bandim Health Project, OPEN, Institute of Clinical Research, University of Southern Denmark, Odense University Hospital, Odense, Denmark; Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Helga Dijkstra
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bram van Cranenbroek
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther van Rijssen
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria.
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6
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Al-Ali AK, Al-Rubaish AM, Alali RA, Almansori MS, Al-Jumaan MA, Alshehri AM, Al-Madan MS, Vatte C, Cherlin T, Young S, Verma SS, Morahan G, Koeleman BPC, Keating BJ. Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts. Sci Rep 2023; 13:21866. [PMID: 38072966 PMCID: PMC10711020 DOI: 10.1038/s41598-023-49105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover novel genetic variants impacting disease risk due to a high rate of consanguinity. Genome-wide genotyping (GWG), imputation and GWAS followed by meta-analysis were performed based on two independent Saudi Arabian studies comprising 3950 MI patients and 2324 non-MI controls. Meta-analyses were then performed with these two Saudi MI studies and the CardioGRAMplusC4D and UK BioBank GWAS as controls. Meta-analyses of the two Saudi MI studies resulted in 17 SNPs with genome-wide significance. Meta-analyses of all 4 studies revealed 66 loci with genome-wide significance levels of p < 5 × 10-8. All of these variants, except rs2764203, have previously been reported as MI-associated loci or to have high linkage disequilibrium with known loci. One SNP association in Shisa family member 5 (SHISA5) (rs11707229) was evident at a much higher frequency in the Saudi MI populations (> 12% MAF). In conclusion, our results replicated many MI associations, whereas in Saudi-only GWAS (meta-analyses), several new loci were implicated that require future validation and functional analyses.
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Affiliation(s)
- Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia.
| | - Abdullah M Al-Rubaish
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Rudaynah A Alali
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Almansori
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed A Al-Jumaan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Emergency Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - Abdullah M Alshehri
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Al-Madan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Pediatrics, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - ChittiBabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia
| | - Tess Cherlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia Young
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, 85500/3508 GA, The Netherlands
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Li W, Moorlag SJCFM, Koeken VACM, Röring RJ, de Bree LCJ, Mourits VP, Gupta MK, Zhang B, Fu J, Zhang Z, Grondman I, van Meijgaarden KE, Zhou L, Alaswad A, Joosten LAB, van Crevel R, Xu CJ, Netea MG, Li Y. A single-cell view on host immune transcriptional response to in vivo BCG-induced trained immunity. Cell Rep 2023; 42:112487. [PMID: 37155329 DOI: 10.1016/j.celrep.2023.112487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/22/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
Bacillus Calmette-Guérin (BCG) vaccination is a prototype model for the study of trained immunity (TI) in humans, and results in a more effective response of innate immune cells upon stimulation with heterologous stimuli. Here, we investigate the heterogeneity of TI induction by single-cell RNA sequencing of immune cells collected from 156 samples. We observe that both monocytes and CD8+ T cells show heterologous transcriptional responses to lipopolysaccharide, with an active crosstalk between these two cell types. Furthermore, the interferon-γ pathway is crucial in BCG-induced TI, and it is upregulated in functional high responders. Data-driven analyses and functional experiments reveal STAT1 to be one of the important transcription factors for TI shared in all identified monocyte subpopulations. Finally, we report the role of type I interferon-related and neutrophil-related TI transcriptional programs in patients with sepsis. These findings provide comprehensive insights into the importance of monocyte heterogeneity during TI in humans.
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Affiliation(s)
- Wenchao Li
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Rutger J Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Manoj K Gupta
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Bowen Zhang
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Jianbo Fu
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Zhenhua Zhang
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Inge Grondman
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Liang Zhou
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Ahmed Alaswad
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Yang Li
- Department of Computational Biology of Individualised Medicine, Centre for Individualised Infection Medicine (CiiM), a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Lower Saxony, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
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8
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de Figueiredo AMB, dos Santos JC, Kischkel B, Ardiansyah E, Oosting M, Guimarães Matos G, Barreto Neves Oliveira I, van de Veerdonk F, Netea MG, Soares CMDA, Ribeiro-Dias F, Joosten LAB. Genome-Wide Association Study Reveals CLEC7A and PROM1 as Potential Regulators of Paracoccidioides brasiliensis-Induction of Cytokine Production in Peripheral Blood Mononuclear Cells. J Fungi (Basel) 2023; 9:jof9040428. [PMID: 37108883 PMCID: PMC10144159 DOI: 10.3390/jof9040428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis caused by fungi of the genus Paracoccidioides and the different clinical forms of the disease are associated with the host immune responses. Quantitative trait loci mapping analysis was performed to assess genetic variants associated with mononuclear-cells-derived cytokines induced by P. brasiliensis on 158 individuals. We identified the rs11053595 SNP, which is present in the CLEC7A gene (encodes the Dectin-1 receptor) and the rs62290169 SNP located in the PROM1 gene (encodes CD133) associated with the production of IL-1β and IL-22, respectively. Functionally, the blockade of the dectin-1 receptor abolished the IL-1β production in P. brasiliensis-stimulated PBMCs. Moreover, the rs62290169-GG genotype was associated with higher frequency of CD38+ Th1 cells in PBMCs cultured with P. brasiliensis yeasts. Therefore, our research indicates that the CLEC7A and PROM1 genes are important for the cytokine response induced by P. brasiliensis and may influence the Paracoccidioidomycosis disease outcome.
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9
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Genetic regulators of cytokine responses upon BCG vaccination in children from West Africa. J Genet Genomics 2023:S1673-8527(23)00008-5. [PMID: 36681271 DOI: 10.1016/j.jgg.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Genetic variation is a key factor influencing cytokine production capacity, but which genetic loci regulate cytokine production before and after vaccination, particularly in African population is unknown. Here, we aimed to identify single-nucleotide polymorphisms (SNPs) controlling cytokine responses (cQTLs) after microbial stimulation in infants of West-African ancestry, comprising of low-birth-weight neonates randomized to bacillus Calmette-Guérin (BCG) vaccine-at-birth (intervention) or to the usual delayed BCG (control). Genome-wide cytokine QTL mapping revealed 12 independent cQTLs loci, of which the LINC01082-LINC00917 locus influenced more than half of the cytokine-stimulation pairs assessed. Furthermore, nine distinct cQTLs were found among infants randomized to BCG. Functional validation confirmed that several complement genes affect cytokine response after BCG vaccination. We observed a limited overlap of common cQTLs between the West-African infants and cohorts of Western European individuals. These data reveal strong population-specific genetic effects on cytokine production and may indicate new opportunities for therapeutic intervention and vaccine development in African populations.
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10
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Fernandes Santos CA, Rodrigues da Costa S, Silva Boiteux L, Grattapaglia D, Silva-Junior OB. Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae. PLoS One 2022; 17:e0273959. [PMID: 36322533 PMCID: PMC9629644 DOI: 10.1371/journal.pone.0273959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Tropical fruit tree species constitute a yet untapped supply of outstanding diversity of taste and nutritional value, barely developed from the genetics standpoint, with scarce or no genomic resources to tackle the challenges arising in modern breeding practice. We generated a de novo genome assembly of the Psidium guajava, the super fruit “apple of the tropics”, and successfully transferred 14,268 SNP probesets from Eucalyptus to Psidium at the nucleotide level, to detect genomic loci linked to resistance to the root knot nematode (RKN) Meloidogyne enterolobii derived from the wild relative P. guineense. Significantly associated loci with resistance across alternative analytical frameworks, were detected at two SNPs on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome to determine the order and orientation of the contigs. The P. guineense-derived resistance response to RKN and disease onset is conceivably triggered by mineral nutrients and phytohormone homeostasis or signaling with the involvement of the miRNA pathway. Hotspots of mapped resistance quantitative trait loci and functional annotation in the same genomic region of Eucalyptus provide further indirect support to our results, highlighting the evolutionary conservation of genomes across genera of Myrtaceae in the adaptation to pathogens. Marker assisted introgression of the resistance loci mapped should accelerate the development of improved guava cultivars and hybrid rootstocks.
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Affiliation(s)
| | - Soniane Rodrigues da Costa
- Graduate program in Genetic Resources, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology (CENARGEN), Brasília, Distrito Federal, Brazil
- * E-mail:
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11
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Matzaraki V, Beno A, Jaeger M, Gresnigt MS, Keur N, Boahen C, Cunha C, Gonçalves SM, Leite L, Lacerda JF, Campos A, van de Veerdonk FL, Joosten L, Netea MG, Carvalho A, Kumar V. Genetic determinants of fungi-induced ROS production are associated with the risk of invasive pulmonary aspergillosis. Redox Biol 2022; 55:102391. [PMID: 35834984 PMCID: PMC9283926 DOI: 10.1016/j.redox.2022.102391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species (ROS) are an essential component of the host defense against fungal infections. However, little is known about how common genetic variation affects ROS-mediated antifungal host defense. In the present study, we investigated the genetic factors that regulate ROS production capacity in response to the two human fungal pathogens: Candida albicans and Aspergillus fumigatus. We investigated fungal-stimulated ROS production by immune cells isolated from a population-based cohort of approximately 200 healthy individuals (200FG cohort), and mapped ROS-quantitative trait loci (QTLs). We identified several genetic loci that regulate ROS levels (P < 9.99 × 10-6), with some of these loci being pathogen-specific, and others shared between the two fungi. These ROS-QTLs were investigated for their influence on the risk of invasive pulmonary aspergillosis (IPA) in a disease relevant context. We stratified hematopoietic stem-cell transplant (HSCT) recipients based on the donor's SNP genotype and tested their impact on the risk of IPA. We identified rs4685368 as a ROS-QTL locus that was significantly associated with an increased risk of IPA after controlling for patient age and sex, hematological malignancy, type of transplantation, conditioning regimen, acute graft-versus-host-disease grades III-IV, and antifungal prophylaxis. Collectively, this data provides evidence that common genetic variation can influence ROS production capacity, and, importantly, the risk of developing IPA among HSCT recipients. This evidence warrants further research for patient stratification based on the genetic profiling that would allow the identifications of patients at high-risk for an invasive fungal infection, and who would benefit the most from a preventive strategy.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
| | - Alexandra Beno
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Mark S Gresnigt
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena, Germany
| | - Nick Keur
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Collins Boahen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Luis Leite
- Serviço de Transplantação de Medula Óssea (STMO), Instituto Português de Oncologia do Porto, Porto, Portugal
| | - João F Lacerda
- Serviço de Hematologia e Transplantação de Medula, Hospital de Santa Maria, Lisboa, Portugal; Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - António Campos
- Serviço de Transplantação de Medula Óssea (STMO), Instituto Português de Oncologia do Porto, Porto, Portugal
| | - Frank L van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Leo Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700RB, the Netherlands; Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
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12
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Ricaño-Ponce I, Peeters T, Matzaraki V, Houben B, Achten R, Cools P, Netea MG, Gyssens IC, Kumar V. Impact of Human Genetic Variation on C-Reactive Protein Concentrations and Acute Appendicitis. Front Immunol 2022; 13:862742. [PMID: 35693796 PMCID: PMC9174512 DOI: 10.3389/fimmu.2022.862742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background Acute appendicitis is one of the most common abdominal emergencies worldwide. Both environmental and genetic factors contribute to the disease. C-reactive protein (CRP) is an important biomarker in the diagnosis of acute appendicitis. CRP concentrations are significantly affected by genetic variation. However, whether such genetic variation is causally related to appendicitis risk remains unclear. In this study, the causal relationship between single-nucleotide polymorphisms (SNPs) associated with circulating CRP concentrations and the risk and severity of acute appendicitis was investigated. Methods CRP concentrations in serum of appendicitis patients (n = 325) were measured. Appendicitis was categorized as complicated/uncomplicated and gangrenous/non-gangrenous. Imputed SNP data (n = 287) were generated. A genome-wide association study (GWAS) on CRP concentrations and appendicitis severity was performed. Intersection and colocalization of the GWAS results were performed with appendicitis and CRP-associated loci from the Pan-UKBB cohort. A functional-genomics approach to prioritize genes was employed. Results Thirteen percent of significant CRP quantitative trait loci (QTLs) that were previously identified in a large cohort of healthy individuals were replicated in our small patient cohort. Significant enrichment of CRP-QTLs in association with appendicitis was observed. Among these shared loci, the two top loci at chromosomes 1q41 and 8p23.1 were characterized. The top SNP at chromosome 1q41 is located within the promoter of H2.0 Like Homeobox (HLX) gene, which is involved in blood cell differentiation, and liver and gut organogeneses. The expression of HLX is increased in the appendix of appendicitis patients compared to controls. The locus at 8p23.1 contains multiple genes, including cathepsin B (CTSB), which is overexpressed in appendix tissue from appendicitis patients. The risk allele of the top SNP in this locus also increases CTSB expression in the sigmoid colon of healthy individuals. CTSB is involved in collagen degradation, MHC class II antigen presentation, and neutrophil degranulation. Conclusions The results of this study prioritize HLX and CTSB as potential causal genes for appendicitis and suggest a shared genetic mechanism between appendicitis and CRP concentrations.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Toon Peeters
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Infectious Diseases & Immunity, Jessa Hospital, Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bert Houben
- Department of General and Abdominal Surgery, Jessa Hospital, Hasselt, Belgium
| | - Ruth Achten
- Department of General and Abdominal Surgery, Jessa Hospital, Hasselt, Belgium
| | - Peter Cools
- Department of Abdominal Surgery, GZA Hospital, Antwerpen, Belgium
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Inge C Gyssens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Infectious Diseases & Immunity, Jessa Hospital, Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangalore, India
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13
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Chu X, Janssen AWM, Koenen H, Chang L, He X, Joosten I, Stienstra R, Kuijpers Y, Wijmenga C, Xu CJ, Netea MG, Tack CJ, Li Y. A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes. eLife 2022; 11:73709. [PMID: 35638288 PMCID: PMC9205632 DOI: 10.7554/elife.73709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The large inter-individual variability in immune-cell composition and function determines immune responses in general and susceptibility o immune-mediated diseases in particular. While much has been learned about the genetic variants relevant for type 1 diabetes (T1D), the pathophysiological mechanisms through which these variations exert their effects remain unknown. Methods: Blood samples were collected from 243 patients with T1D of Dutch descent. We applied genetic association analysis on >200 immune-cell traits and >100 cytokine production profiles in response to stimuli measured to identify genetic determinants of immune function, and compared the results obtained in T1D to healthy controls. Results: Genetic variants that determine susceptibility to T1D significantly affect T cell composition. Specifically, the CCR5+ regulatory T cells associate with T1D through the CCR region, suggesting a shared genetic regulation. Genome-wide quantitative trait loci (QTLs) mapping analysis of immune traits revealed 15 genetic loci that influence immune responses in T1D, including 12 that have never been reported in healthy population studies, implying a disease-specific genetic regulation. Conclusions: This study provides new insights into the genetic factors that affect immunological responses in T1D. Funding: This work was supported by an ERC starting grant (no. 948207) and a Radboud University Medical Centre Hypatia grant (2018) to YL and an ERC advanced grant (no. 833247) and a Spinoza grant of the Netherlands Association for Scientific Research to MGN CT received funding from the Perspectief Biomarker Development Center Research Programme, which is (partly) financed by the Netherlands Organisation for Scientific Research (NWO). AJ was funded by a grant from the European Foundation for the Study of Diabetes (EFSD/AZ Macrovascular Programme 2015). XC was supported by the China Scholarship Council (201706040081). Every year around the world, over 100,000 people are diagnosed with type 1 diabetes. This disease develops when the immune system mistakenly destroys the cells that produce a hormone called insulin, leaving affected individuals unable to regulate their blood sugar levels. Type 1 diabetes patients must rely on regular injections of manufactured insulin to survive. The composition and activity of the human immune system is under genetic control, and people with certain changes in their genes are more susceptible than others to develop type 1 diabetes. Previous studies have identified around 60 locations in the human DNA (known as loci) associated with the condition, but it remains unclear how these loci influence the immune system and whether diabetes will emerge. Chu, Janssen, Koenen et al. explored how variations in genetic information can influence the composition of the immune system, and the type of molecules it releases to perform its role. To do so, blood samples from 243 individuals of Dutch descent with type 1 diabetes were collected, and genetic associations were investigated. The results revealed that a major type of immune actors known as T cells are under the control of genetic factors associated with type 1 diabetes susceptibility. For instance, a specific type of T cells showed shared genetic control with type 1 diabetes. In addition, 15 loci were identified that influenced immune responses in the patients. Among those, 12 have never been reported to be involved in immune responses in healthy people, implying that these regions might only regulate the immune system of individuals with type 1 diabetes and other similar disorders. Finally, Chu, Janssen, Koenen et al. propose 11 genes within the identified loci as potential targets for new diabetes medication. These results represent an important resource for researchers exploring the genetic and immune basis of type 1 diabetes, and they could open new avenues for drug development.
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Affiliation(s)
- Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | - Anna W M Janssen
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Hans Koenen
- Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Linzhung Chang
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
| | - Xuehui He
- Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Rinke Stienstra
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Yunus Kuijpers
- Department of Computational Biology for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover, Germany
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover, Germany
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Cees J Tack
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Yang Li
- Department of Computational Biology for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover, Germany
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14
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Temba GS, Vadaq N, Wan J, Kullaya V, Huskens D, Pecht T, Jaeger M, Boahen CK, Matzaraki V, Broeders W, Joosten LAB, Faradz SMH, Kibiki G, Middeldorp S, Cavalieri D, Lionetti P, de Groot PG, Schultze JL, Netea MG, Kumar V, de Laat B, Mmbaga BT, van der Ven AJ, Roest M, de Mast Q. Differences in thrombin and plasmin generation potential between East African and Western European adults: The role of genetic and non-genetic factors. J Thromb Haemost 2022; 20:1089-1105. [PMID: 35102686 PMCID: PMC9305795 DOI: 10.1111/jth.15657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Geographic variability in coagulation across populations and their determinants are poorly understood. OBJECTIVE To compare thrombin (TG) and plasmin (PG) generation parameters between healthy Tanzanian and Dutch individuals, and to study associations with inflammation and different genetic, host and environmental factors. METHODS TG and PG parameters were measured in 313 Tanzanians of African descent living in Tanzania and 392 Dutch of European descent living in the Netherlands and related to results of a dietary questionnaire, circulating inflammatory markers, genotyping, and plasma metabolomics. RESULTS Tanzanians exhibited an enhanced TG and PG capacity, compared to Dutch participants. A higher proportion of Tanzanians had a TG value in the upper quartile with a PG value in the lower/middle quartile, suggesting a relative pro-coagulant state. Tanzanians also displayed an increased normalized thrombomodulin sensitivity ratio, suggesting reduced sensitivity to protein C. In Tanzanians, PG parameters (lag time and TTP) were associated with seasonality and food-derived plasma metabolites. The Tanzanians had higher concentrations of pro-inflammatory cytokines, which correlated strongly with TG and PG parameters. There was limited overlap in genetic variation associated with TG and PG parameters between the two cohorts. Pathway analysis of genetic variants in the Tanzanian cohort revealed multiple immune pathways that were enriched with TG and PG traits, confirming the importance of co-regulation between coagulation and inflammation. CONCLUSIONS Tanzanians have an enhanced TG and PG potential compared to Dutch individuals, which may relate to differences in inflammation, genetics and diet. These observations highlight the importance of better understanding of the geographic variability in coagulation across populations.
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Affiliation(s)
- Godfrey S. Temba
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
- Department of Medical Biochemistry and Molecular BiologyKilimanjaro Christian Medical University College (KCMUCo)MoshiTanzania
| | - Nadira Vadaq
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
- Center for Tropical and Infectious Diseases (CENTRID)Faculty of MedicineDr. Kariadi HospitalDiponegoro UniversitySemarangIndonesia
| | - Jun Wan
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Vesla Kullaya
- Department of Medical Biochemistry and Molecular BiologyKilimanjaro Christian Medical University College (KCMUCo)MoshiTanzania
- Kilimanjaro Clinical Research InstituteKilimanjaro Christian Medical CenterMoshiTanzania
| | - Dana Huskens
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Tal Pecht
- Department for Genomics and ImmunoregulationLife & Medical Sciences (LIMES) InstituteUniversity of BonnBonnGermany
- Systems MedicineGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Martin Jaeger
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Collins K. Boahen
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Vasiliki Matzaraki
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Wieteke Broeders
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Leo A. B. Joosten
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Sultana M. H. Faradz
- Division of Human GeneticsCenter for Biomedical Research (CEBIOR)Faculty of MedicineDiponegoro University/Diponegoro National HospitalSemarangIndonesia
| | - Gibson Kibiki
- Kilimanjaro Clinical Research InstituteKilimanjaro Christian Medical CenterMoshiTanzania
| | - Saskia Middeldorp
- Department of Internal MedicineRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | | | - Paolo Lionetti
- Departement NEUROFARBAMeyer Children's HospitalUniversity of Florence – Gastroenterology and Nutrition UnitFlorenceItaly
| | - Philip G. de Groot
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Joachim L. Schultze
- Department for Genomics and ImmunoregulationLife & Medical Sciences (LIMES) InstituteUniversity of BonnBonnGermany
- Systems MedicineGerman Center for Neurodegenerative Diseases (DZNE)BonnGermany
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and University of BonnBonnGermany
| | - Mihai G. Netea
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
- Department for Immunology and MetabolismLife & Medical Sciences (LIMES) InstituteUniversity of BonnBonnGermany
| | - Vinod Kumar
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
- Department of GeneticsUniversity Medical Centre GroningenUniversity of GroningenGroningenthe Netherlands
| | - Bas de Laat
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research InstituteKilimanjaro Christian Medical CenterMoshiTanzania
- Department of PaediatricsKilimanjaro Christian Medical University College (KCMUCo)MoshiTanzania
| | - Andre J. van der Ven
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
| | - Mark Roest
- Synapse Research InstituteCardiovascular Research Institute MaastrichtMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Quirijn de Mast
- Department of Internal MedicineRadboudumc Center for Infectious DiseasesRadboud Institute of Health Science (RIHS)Radboud university medical centerNijmegenthe Netherlands
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15
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Ramírez-Sánchez AD, Chu X, Modderman R, Kooy-Winkelaar Y, Koletzko S, Korponay-Szabó IR, Troncone R, Wijmenga C, Mearin L, Withoff S, Jonkers IH, Li Y. Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells From Pediatric Coeliac Disease Patients Suggests Potential Pre-Seroconversion Markers. Front Immunol 2022; 13:843086. [PMID: 35371081 PMCID: PMC8964997 DOI: 10.3389/fimmu.2022.843086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/22/2022] [Indexed: 11/30/2022] Open
Abstract
Celiac Disease (CeD) is a complex immune disorder involving villous atrophy in the small intestine that is triggered by gluten intake. Current CeD diagnosis is based on late-stage pathophysiological parameters such as detection of specific antibodies in blood and histochemical detection of villus atrophy and lymphocyte infiltration in intestinal biopsies. To date, no early onset biomarkers are available that would help prevent widespread villous atrophy and severe symptoms and co-morbidities. To search for novel CeD biomarkers, we used single-cell RNA sequencing (scRNAseq) to investigate PBMC samples from 11 children before and after seroconversion for CeD and 10 control individuals matched for age, sex and HLA-genotype. We generated scRNAseq profiles of 9559 cells and identified the expected major cellular lineages. Cell proportions remained stable across the different timepoints and health conditions, but we observed differences in gene expression profiles in specific cell types when comparing patient samples before and after disease development and comparing patients with controls. Based on the time when transcripts were differentially expressed, we could classify the deregulated genes as biomarkers for active CeD or as potential pre-diagnostic markers. Pathway analysis showed that active CeD biomarkers display a transcriptional profile associated with antigen activation in CD4+ T cells, whereas NK cells express a subset of biomarker genes even before CeD diagnosis. Intersection of biomarker genes with CeD-associated genetic risk loci pinpointed genetic factors that might play a role in CeD onset. Investigation of potential cellular interaction pathways of PBMC cell subpopulations highlighted the importance of TNF pathways in CeD. Altogether, our results pinpoint genes and pathways that are altered prior to and during CeD onset, thereby identifying novel potential biomarkers for CeD diagnosis in blood.
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Affiliation(s)
- Aarón D Ramírez-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Xiaojing Chu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Rutger Modderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yvonne Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München (LMU) Klinikum Munich, Munich, Germany.,Department of Pediatric Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Ilma R Korponay-Szabó
- Coeliac Disease Center, Heim Pál National Paediatric Institute, Budapest, Hungary.,Department of Paediatrics, Faculty of Medicine and Clinical Center, University of Debrecen, Debrecen, Hungary
| | - Riccardo Troncone
- Department of Medical Translational Sciences and European Laboratory for the Investigation of Food Induced Diseases, University Federico II, Naples, Italy
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Luisa Mearin
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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16
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Boahen CK, Temba GS, Kullaya VI, Matzaraki V, Joosten LAB, Kibiki G, Mmbaga BT, van der Ven A, de Mast Q, Netea MG, Kumar V. A functional genomics approach in Tanzanian population identifies distinct genetic regulators of cytokine production compared to European population. Am J Hum Genet 2022; 109:471-485. [PMID: 35167808 DOI: 10.1016/j.ajhg.2022.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/24/2022] [Indexed: 12/23/2022] Open
Abstract
Humans exhibit remarkable interindividual and interpopulation immune response variability upon microbial challenges. Cytokines play a vital role in regulating inflammation and immune responses, but dysregulation of cytokine responses has been implicated in different disease states. Host genetic factors were previously shown to significantly impact cytokine response heterogeneity mainly in European-based studies, but it is unclear whether these findings are transferable to non-European individuals. Here, we aimed to identify genetic variants modulating cytokine responses in healthy adults of East African ancestry from Tanzania. We leveraged both cytokine and genetic data and performed genome-wide cytokine quantitative trait loci (cQTLs) mapping. The results were compared with another cohort of healthy adults of Western European ancestry via direct overlap and functional enrichment analyses. We also performed meta-analyses to identify cQTLs with congruent effect direction in both populations. In the Tanzanians, cQTL mapping identified 80 independent suggestive loci and one genome-wide significant locus (TBC1D22A) at chromosome 22; SNP rs12169244 was associated with IL-1b release after Salmonella enteritidis stimulation. Remarkably, the identified cQTLs varied significantly when compared to the European cohort, and there was a very limited percentage of overlap (1.6% to 1.9%). We further observed ancestry-specific pathways regulating induced cytokine responses, and there was significant enrichment of the interferon pathway specifically in the Tanzanians. Furthermore, contrary to the Europeans, genetic variants in the TLR10-TLR1-TLR6 locus showed no effect on cytokine response. Our data reveal both ancestry-specific effects of genetic variants and pathways on cytokine response heterogeneity, hence arguing for the importance of initiatives to include diverse populations into genomics research.
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Affiliation(s)
- Collins K Boahen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands
| | - Godfrey S Temba
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi 251, Tanzania
| | - Vesla I Kullaya
- Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi 251, Tanzania; Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi 251, Tanzania
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi 251, Tanzania; Department of Paediatrics, Kilimanjaro Christian Medical University College, Moshi 251, Tanzania
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi 251, Tanzania
| | - Andre van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Medical Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi 251, Tanzania
| | - Quirijn de Mast
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53115, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen 9700, the Netherlands; Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Medical Sciences Complex, Deralakatte, Mangalore 575018, India.
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17
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Lo Faro V, Nolte IM, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Mitochondrial Genome Study Identifies Association Between Primary Open-Angle Glaucoma and Variants in MT-CYB, MT-ND4 Genes and Haplogroups. Front Genet 2021; 12:781189. [PMID: 34976016 PMCID: PMC8719162 DOI: 10.3389/fgene.2021.781189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Background and purpose: Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by death of retinal ganglion cells and atrophy of the optic nerve head. The susceptibility of the optic nerve to damage has been shown to be mediated by mitochondrial dysfunction. In this study, we aimed to determine a possible association between mitochondrial SNPs or haplogroups and POAG. Methods: Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) were genotyped using the Illumina Infinium Global Screening Array-24 (GSA) 700K array set. Genetic analyses were performed in a POAG case-control study involving the cohorts, Groningen Longitudinal Glaucoma Study-Lifelines Cohort Study and Amsterdam Glaucoma Study, including 721 patients and 1951 controls in total. We excluded samples not passing quality control for nuclear genotypes and samples with low call rate for mitochondrial variation. The mitochondrial variants were analyzed both as SNPs and haplogroups. These were determined with the bioinformatics software HaploGrep, and logistic regression analysis was used for the association, as well as for SNPs. Results: Meta-analysis of the results from both cohorts revealed a significant association between POAG and the allele A of rs2853496 [odds ratio (OR) = 0.64; p = 0.006] within the MT-ND4 gene, and for the T allele of rs35788393 (OR = 0.75; p = 0.041) located in the MT-CYB gene. In the mitochondrial haplogroup analysis, the most significant p-value was reached by haplogroup K (p = 1.2 × 10−05), which increases the risk of POAG with an OR of 5.8 (95% CI 2.7–13.1). Conclusion: We identified an association between POAG and polymorphisms in the mitochondrial genes MT-ND4 (rs2853496) and MT-CYB (rs35788393), and with haplogroup K. The present study provides further evidence that mitochondrial genome variations are implicated in POAG. Further genetic and functional studies are required to substantiate the association between mitochondrial gene polymorphisms and POAG and to define the pathophysiological mechanisms of mitochondrial dysfunction in glaucoma.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jacoline B. Ten Brink
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, Netherlands
- *Correspondence: Arthur A. Bergen,
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18
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Moorlag SJCFM, Matzaraki V, van Puffelen JH, van der Heijden C, Keating S, Groh L, Röring RJ, Bakker OB, Koeken VACM, de Bree LCJ, Smeekens SP, Oosting M, Gamboa RA, Riksen NP, Xavier RJ, Wijmenga C, Kumar V, van Crevel R, Novakovic B, Joosten LAB, Li Y, Netea MG. An integrative genomics approach identifies KDM4 as a modulator of trained immunity. Eur J Immunol 2021; 52:431-446. [PMID: 34821391 PMCID: PMC9299854 DOI: 10.1002/eji.202149577] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 09/29/2021] [Accepted: 11/19/2021] [Indexed: 01/21/2023]
Abstract
Innate immune cells are able to build memory characteristics via a process termed “trained immunity.” Host factors that influence the magnitude of the individual trained immunity response remain largely unknown. Using an integrative genomics approach, our study aimed to prioritize and understand the role of specific genes in trained immunity responses. In vitro‐induced trained immunity responses were assessed in two independent population‐based cohorts of healthy individuals, the 300 Bacillus Calmette‐Guérin (300BCG; n = 267) and 200 Functional Genomics (200FG; n = 110) cohorts from the Human Functional Genomics Project. Genetic loci that influence cytokine responses upon trained immunity were identified by conducting a meta‐analysis of QTLs identified in the 300BCG and 200FG cohorts. From the identified QTL loci, we functionally validated the role of PI3K‐Akt signaling pathway and two genes that belong to the family of Siglec receptors (Siglec‐5 and Siglec‐14). Furthermore, we identified the H3K9 histone demethylases of the KDM4 family as major regulators of trained immunity responses. These data pinpoint an important role of metabolic and epigenetic processes in the regulation of trained immunity responses, and these findings may open new avenues for vaccine design and therapeutic interventions.
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Affiliation(s)
- Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jelmer H van Puffelen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sam Keating
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laszlo Groh
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rutger Jan Röring
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L Charlotte J de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark.,Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raúl Aguirre Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands.,K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Norway
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningenor, Groningen, The Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Boris Novakovic
- Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, and Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hannover, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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19
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Kong L, Moorlag SJCFM, Lefkovith A, Li B, Matzaraki V, van Emst L, Kang HA, Latorre I, Jaeger M, Joosten LAB, Netea MG, Xavier RJ. Single-cell transcriptomic profiles reveal changes associated with BCG-induced trained immunity and protective effects in circulating monocytes. Cell Rep 2021; 37:110028. [PMID: 34788625 DOI: 10.1016/j.celrep.2021.110028] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/31/2021] [Accepted: 10/29/2021] [Indexed: 11/19/2022] Open
Abstract
Bacillus Calmette-Guérin (BCG) vaccine is one of the most widely used vaccines worldwide. In addition to protection against tuberculosis, BCG confers a degree of non-specific protection against other infections by enhancing secondary immune responses to heterologous pathogens, termed "trained immunity." To better understand BCG-induced immune reprogramming, we perform single-cell transcriptomic measurements before and after BCG vaccination using secondary immune stimulation with bacterial lipopolysaccharide (LPS). We find that BCG reduces systemic inflammation and identify 75 genes with altered LPS responses, including inflammatory mediators such as CCL3 and CCL4 that have a heightened response. Co-expression analysis reveals that gene modules containing these cytokines lose coordination after BCG. Other modules exhibit increased coordination, including several humanin nuclear isoforms that we confirm induce trained immunity in vitro. Our results link in vivo BCG administration to single-cell transcriptomic changes, validated in human genetics experiments, and highlight genes that are putatively responsible for non-specific protective effects of BCG.
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Affiliation(s)
- Lingjia Kong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Simone J C F M Moorlag
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Ariel Lefkovith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bihua Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Liesbeth van Emst
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Heather A Kang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Isabel Latorre
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Martin Jaeger
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400000, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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20
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Chu X, Jaeger M, Beumer J, Bakker OB, Aguirre-Gamboa R, Oosting M, Smeekens SP, Moorlag S, Mourits VP, Koeken VACM, de Bree C, Jansen T, Mathews IT, Dao K, Najhawan M, Watrous JD, Joosten I, Sharma S, Koenen HJPM, Withoff S, Jonkers IH, Netea-Maier RT, Xavier RJ, Franke L, Xu CJ, Joosten LAB, Sanna S, Jain M, Kumar V, Clevers H, Wijmenga C, Netea MG, Li Y. Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease. Genome Biol 2021; 22:198. [PMID: 34229738 PMCID: PMC8259168 DOI: 10.1186/s13059-021-02413-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors. RESULT We systematically investigate circulating metabolites in a cohort of 500 healthy subjects (500FG) in whom immune function and activity are deeply measured and whose genetics are profiled. Our data reveal that several major metabolic pathways, including the alanine/glutamate pathway and the arachidonic acid pathway, have a strong impact on cytokine production in response to ex vivo stimulation. We also examine the genetic regulation of metabolites associated with immune phenotypes through genome-wide association analysis and identify 29 significant loci, including eight novel independent loci. Of these, one locus (rs174584-FADS2) associated with arachidonic acid metabolism is causally associated with Crohn's disease, suggesting it is a potential therapeutic target. CONCLUSION This study provides a comprehensive map of the integration between the blood metabolome and immune phenotypes, reveals novel genetic factors that regulate blood metabolite concentrations, and proposes an integrative approach for identifying new disease treatment targets.
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Affiliation(s)
- Xiaojing Chu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584, CT, Utrecht, the Netherlands
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Raul Aguirre-Gamboa
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Simone Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Charlotte de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Trees Jansen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Ian T Mathews
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
- La Jolla Institute, La Jolla, CA, USA
| | - Khoi Dao
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Mahan Najhawan
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, 6525, GA, Nijmegen, the Netherlands
| | | | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, 6525, GA, Nijmegen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Romana T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, MA, 02114, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584, CT, Utrecht, the Netherlands
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands.
- Department of Immunology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372, Oslo, Norway.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany.
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands.
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.
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21
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oxLDL-Induced Trained Immunity Is Dependent on Mitochondrial Metabolic Reprogramming. IMMUNOMETABOLISM 2021; 3:e210025. [PMID: 34267957 PMCID: PMC7611242 DOI: 10.20900/immunometab20210025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Following brief exposure to endogenous atherogenic particles, such as oxidized low-density lipoprotein (oxLDL), monocytes/macrophages can adopt a long-term pro-inflammatory phenotype, which is called trained immunity. This mechanism might contribute to the chronic low-grade inflammation that characterizes atherosclerosis. In this study, we aim to elucidate immunometabolic pathways that drive oxLDL-induced trained immunity. Primary isolated human monocytes were exposed to oxLDL for 24 h, and after five days stimulated with LPS to measure the cytokine production capacity. RNA-sequencing revealed broad increases in genes enriched in mitochondrial pathways after 24 h of oxLDL exposure. Further omics profiling of oxLDL-trained macrophages via intracellular metabolomics showed an enrichment for tricarboxylic acid (TCA) cycle metabolites. Single cell analysis revealed that oxLDL-trained macrophages contain larger mitochondria, potentially likely linked to increased oxidative phosphorylation (OXPHOS) activity. Co-incubation with pharmacological blockers of OXPHOS inhibited oxLDL-induced trained immunity. The relevance of OXPHOS was confirmed in a cohort of 243 healthy subjects showing that genetic variation in genes coding for enzymes relevant to OXPHOS correlated with the capacity of monocytes to be trained with oxLDL. Interestingly, OXPHOS appears to play an important role in the increased cytokine hyperresponsiveness by oxLDL-trained macrophages. The TCA-cycle can also be fuelled by glutamine and free fatty acids, and pharmacological blockade of these pathways could prevent oxLDL-induced trained immunity. This study demonstrates that the mitochondria of oxLDL-trained macrophages undergo changes to their function and form with OXPHOS being an important mechanism for trained immunity, which could unveil novel pharmacological targets to prevent atherogenesis.
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22
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Mourits VP, Helder LS, Matzaraki V, Koeken VACM, Groh L, de Bree LCJ, Moorlag SJCFM, van der Heijden CDCC, Keating ST, van Puffelen JH, Jaeger M, Joosten LAB, Netea MG. The role of sirtuin 1 on the induction of trained immunity. Cell Immunol 2021; 366:104393. [PMID: 34147841 DOI: 10.1016/j.cellimm.2021.104393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/31/2021] [Accepted: 06/05/2021] [Indexed: 11/26/2022]
Abstract
Sirtuin 1 (SIRT1) has been described to modify immune responses by modulation of gene transcription. As transcriptional reprogramming is the molecular substrate of trained immunity, a de facto innate immune memory, we investigated the role of SIRT1 in the induction of trained immunity. We identified various SIRT1 genetic single nucleotide polymorphisms affecting innate and adaptive cytokine production of human peripheral blood mononuclear cells (PBMCs) in response to various stimuli on the one hand, and in vitro induction of trained immunity on the other hand. Furthermore, inhibition of SIRT1 upregulated pro-inflammatory innate cytokine production upon stimulation of PBMCs. However, inhibition of SIRT1 in vitro had no effect on cytokine responses upon induction of trained immunity, while activation of SIRT1 mildly modified trained immunity responses. In conclusion, SIRT1 modifies innate cytokine production by PBMCs in response to various microbes, but has only a secondary role for BCG and β-glucan-induced trained immunity responses.
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Affiliation(s)
- Vera P Mourits
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonie S Helder
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Laszlo Groh
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - L Charlotte J de Bree
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark; Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Simone J C F M Moorlag
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte D C C van der Heijden
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Samuel T Keating
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jelmer H van Puffelen
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
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23
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Ferreira AV, Koeken VACM, Matzaraki V, Kostidis S, Alarcon-Barrera JC, de Bree LCJ, Moorlag SJCFM, Mourits VP, Novakovic B, Giera MA, Netea MG, Domínguez-Andrés J. Glutathione Metabolism Contributes to the Induction of Trained Immunity. Cells 2021; 10:cells10050971. [PMID: 33919212 PMCID: PMC8143087 DOI: 10.3390/cells10050971] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
The innate immune system displays heterologous memory characteristics, which are characterized by stronger responses to a secondary challenge. This phenomenon termed trained immunity relies on epigenetic and metabolic rewiring of innate immune cells. As reactive oxygen species (ROS) production has been associated with the trained immunity phenotype, we hypothesized that the increased ROS levels and the main intracellular redox molecule glutathione play a role in the induction of trained immunity. Here we show that pharmacological inhibition of ROS in an in vitro model of trained immunity did not influence cell responsiveness; the modulation of glutathione levels reduced pro-inflammatory cytokine production in human monocytes. Single nucleotide polymorphisms (SNPs) in genes involved in glutathione metabolism were found to be associated with changes in pro-inflammatory cytokine production capacity upon trained immunity. Also, plasma glutathione concentrations were positively associated with ex vivo IL-1β production, a biomarker of trained immunity, produced by monocytes of BCG-vaccinated individuals. In conclusion, glutathione metabolism is involved in the induction of trained immunity, and future studies are warranted to explore its functional consequences in human diseases.
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Affiliation(s)
- Anaisa V. Ferreira
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Correspondence: (A.V.F.); (J.D.-A.); Tel.: +31-2436-16636 (J.D.-A.)
| | - Valerie A. C. M. Koeken
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
- TWINCORE, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 30625 Hannover, Germany
- Centre for Individualised Infection Medicine (CiiM), Department of Computational Biology for Individualised Infection Medicine, a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands; (S.K.); (J.C.A.-B.); (M.A.G.)
| | - Juan Carlos Alarcon-Barrera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands; (S.K.); (J.C.A.-B.); (M.A.G.)
| | - L. Charlotte J. de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
| | - Simone J. C. F. M. Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
| | - Vera P. Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
| | - Boris Novakovic
- Epigenetics Research, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Martin A. Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands; (S.K.); (J.C.A.-B.); (M.A.G.)
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands; (V.A.C.M.K.); (V.M.); (L.C.J.d.B.); (S.J.C.F.M.M.); (V.P.M.); (M.G.N.)
- Correspondence: (A.V.F.); (J.D.-A.); Tel.: +31-2436-16636 (J.D.-A.)
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24
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Urban living in healthy Tanzanians is associated with an inflammatory status driven by dietary and metabolic changes. Nat Immunol 2021; 22:287-300. [PMID: 33574617 DOI: 10.1038/s41590-021-00867-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/29/2020] [Indexed: 01/28/2023]
Abstract
Sub-Saharan Africa currently experiences an unprecedented wave of urbanization, which has important consequences for health and disease patterns. This study aimed to investigate and integrate the immune and metabolic consequences of rural or urban lifestyles and the role of nutritional changes associated with urban living. In a cohort of 323 healthy Tanzanians, urban as compared to rural living was associated with a pro-inflammatory immune phenotype, both at the transcript and protein levels. We identified different food-derived and endogenous circulating metabolites accounting for these differences. Serum from urban dwellers induced reprogramming of innate immune cells with higher tumor necrosis factor production upon microbial re-stimulation in an in vitro model of trained immunity. These data demonstrate important shifts toward an inflammatory phenotype associated with an urban lifestyle and provide new insights into the underlying dietary and metabolic factors, which may affect disease epidemiology in sub-Sahara African countries.
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25
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Degenhardt F, Mayr G, Wendorff M, Boucher G, Ellinghaus E, Ellinghaus D, ElAbd H, Rosati E, Hübenthal M, Juzenas S, Abedian S, Vahedi H, Thelma BK, Yang SK, Ye BD, Cheon JH, Datta LW, Daryani NE, Ellul P, Esaki M, Fuyuno Y, McGovern DPB, Haritunians T, Hong M, Juyal G, Jung ES, Kubo M, Kugathasan S, Lenz TL, Leslie S, Malekzadeh R, Midha V, Motyer A, Ng SC, Okou DT, Raychaudhuri S, Schembri J, Schreiber S, Song K, Sood A, Takahashi A, Torres EA, Umeno J, Alizadeh BZ, Weersma RK, Wong SH, Yamazaki K, Karlsen TH, Rioux JD, Brant SR, Franke A. Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations. Hum Mol Genet 2021; 30:356-369. [PMID: 33555323 PMCID: PMC8098114 DOI: 10.1093/hmg/ddab017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabrielle Boucher
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Dermatology, Venerology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Homayon Vahedi
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi 110021, India
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naser Ebrahim Daryani
- Department of Gastroenterology, Emam Hospital, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Myhunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 351-0198, Japan
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Pediatric Institute, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Stephen Leslie
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Vandana Midha
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Allan Motyer
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - David T Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Centre for Genetics and Genomics Versus Arthritis, Division of Musculosceletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - John Schembri
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Ajit Sood
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, Riken, Yokohama, 230-0045, Japan
| | - Esther A Torres
- Department of Medicine, University of Puerto Rico Center for IBD, University of Puerto Rico School of Medicine, Rio Piedras, San Juan, PR 00936-5067, USA
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700 AB Groningen, The Netherlands
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway.,Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, 0372 Oslo, Norway
| | - John D Rioux
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Medicine, Rutgers Robert Wood Johnson School of Medicine and Department of Genetics, Rutgers University Brunswick and Piscataway, NJ 08903-0019, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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Kuijpers Y, Chu X, Jaeger M, Moorlag SJ, Koeken VA, Zhang B, de Nooijer A, Grondman I, Janssen N, Mourits VP, J. de Bree LC, de Mast Q, van de Veerdonk FL, Joosten LA, Li Y, Netea MG, Xu C. The genetic risk for COVID-19 severity is associated with defective innate immune responses.. [DOI: 10.1101/2020.11.10.20229203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
AbstractRecent genome-wide association studies (GWASs) of COVID-19 patients of European ancestry have identified genetic loci significantly associated with disease severity (1). Here, we employed the detailed clinical, immunological and multi-omics dataset of the Human Functional Genomics Projects (HFGP) to explore the physiological significance of the host genetic variants that influence susceptibility to severe COVID-19. A genomics investigation intersected with functional characterization of individuals with high genetic risk for severe COVID-19 susceptibility identified several major patterns: i. a large impact of genetically determined innate immune responses in COVID-19, with increased susceptibility for severe disease in individuals with defective monocyte-derived cytokine production; ii. genetic susceptibility related to ABO blood groups is probably mediated through the von Willebrand factor (VWF) and endothelial dysfunction. We further validated these identified associations at transcript and protein levels by using independent disease cohorts. These insights allow a physiological understanding of genetic susceptibility to severe COVID-19, and indicate pathways that could be targeted for prevention and therapy.One Sentence summaryIn this study, we explore the physiological significance of the genetic variants associated with COVID-19 severity using detailed clinical, immunological and multi-omics data from large cohorts. Our findings allow a physiological understanding of genetic susceptibility to severe COVID-19, and indicate pathways that could be targeted for prevention and therapy.
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27
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de Alwis R, My Phuc T, Yu Hang Bai B, Le Thi Quynh N, Thi Thanh Tam P, Thi Ngoc Dung T, Thi Thanh Nhan N, Vinh C, Van Hien H, Thanh Hoang Nhat L, Thi Thu Hong N, Thi Mong Tuyen N, Thi Thuy Trang H, Phuong Thao L, Thi Ngoc Diep V, Thi Hai Chau P, Quan Thinh L, Thi Ngoc Thu H, Nguyet Hang N, Cong Danh M, Doan Hao T, Anh Dao T, Dai L, Thi Huyen Diu V, Thi En N, Thi Tuyet Hanh N, Thi Hanh L, Pham Thu Hien H, Thi Thuy Linh N, Darton TC, Thwaites GE, Kestelyn E, Lan Vi L, Thi Thuy Tien B, Thi Diem Tuyet H, Anderson C, Baker S. The influence of human genetic variation on early transcriptional responses and protective immunity following immunization with Rotarix vaccine in infants in Ho Chi Minh City in Vietnam: A study protocol for an open single-arm interventional trial. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16090.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Rotavirus (RoV) remains the leading cause of acute gastroenteritis in infants and children aged under five years in both high- and low-middle-income countries (LMICs). In LMICs, RoV infections are associated with substantial mortality. Two RoV vaccines (Rotarix and Rotateq) are widely available for use in infants, both of which have been shown to be highly efficacious in Europe and North America. However, for unknown reasons, these RoV vaccines have markedly lower efficacy in LMICs. We hypothesize that poor RoV vaccine efficacy across in certain regions may be associated with genetic heritability or gene expression in the human host. Methods/design: We designed an open-label single-arm interventional trial with the Rotarix RoV vaccine to identify genetic and transcriptomic markers associated with generating a protective immune response against RoV. Overall, 1,000 infants will be recruited prior to Expanded Program on Immunization (EPI) vaccinations at two months of age and vaccinated with oral Rotarix vaccine at two and three months, after which the infants will be followed-up for diarrheal disease until 18 months of age. Blood sampling for genetics, transcriptomics, and immunological analysis will be conducted before each Rotarix vaccination, 2-3 days post-vaccination, and at each follow-up visit (i.e. 6, 12 and 18 months of age). Stool samples will be collected during each diarrheal episode to identify RoV infection. The primary outcome will be Rotarix vaccine failure events (i.e. symptomatic RoV infection despite vaccination), secondary outcomes will be antibody responses and genotypic characterization of the infection virus in Rotarix failure events. Discussion: This study will be the largest and best powered study of its kind to be conducted to date in infants, and will be critical for our understanding of RoV immunity, human genetics in the Vietnam population, and mechanisms determining RoV vaccine-mediated protection. Registration: ClinicalTrials.gov, ID: NCT03587389. Registered on 16 July 2018.
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Tam V, Patel N, Turcotte M, Bossé Y, Paré G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet 2019; 20:467-484. [PMID: 31068683 DOI: 10.1038/s41576-019-0127-1] [Citation(s) in RCA: 871] [Impact Index Per Article: 174.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWAS) involve testing genetic variants across the genomes of many individuals to identify genotype-phenotype associations. GWAS have revolutionized the field of complex disease genetics over the past decade, providing numerous compelling associations for human complex traits and diseases. Despite clear successes in identifying novel disease susceptibility genes and biological pathways and in translating these findings into clinical care, GWAS have not been without controversy. Prominent criticisms include concerns that GWAS will eventually implicate the entire genome in disease predisposition and that most association signals reflect variants and genes with no direct biological relevance to disease. In this Review, we comprehensively assess the benefits and limitations of GWAS in human populations and discuss the relevance of performing more GWAS.
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Affiliation(s)
- Vivian Tam
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Nikunj Patel
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Michelle Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec City, Québec, Canada.,Department of Molecular Medicine, Laval University, Québec City, Quebec, Canada
| | - Guillaume Paré
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada. .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada. .,Inserm UMRS 954 N-GERE (Nutrition-Genetics-Environmental Risks), University of Lorraine, Faculty of Medicine, Nancy, France.
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29
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Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019; 10:2176. [PMID: 31092817 PMCID: PMC6520353 DOI: 10.1038/s41467-019-09976-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.
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Affiliation(s)
- John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Bart Ferwerda
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Philip H C Kremer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicole E Wheeler
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- The Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Mercedes Valls Serón
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | | | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Alienke J Wijmega-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Anne L Wyllie
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Aeilko H Zwinderman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Zitta B Harboe
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, DK-2300, Denmark
| | - Lene F Lundbo
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Lisette C P G M de Groot
- Department of Human Nutrition, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Natasja M van Schoor
- Amsterdam UMC, VU University, Department of Epidemiology and Biostatistics, Amsterdam Public Health, Van der Boechorststraat 7, Amsterdam, 1007 MB, The Netherlands
| | - Nathalie van der Velde
- Amsterdam UMC, University of Amsterdam, Department of Internal Medicine, Geriatrics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Centre Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Lars H Ängquist
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, DK-2000, Denmark
| | - Thorkild I A Sørensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Copenhagen, DK-2200, Denmark
- The Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-1014, Denmark
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mignon du Plessis
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Susan Nzenze
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Julian Parkhill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Shabir Madhi
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Anne von Gottberg
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Arie van der Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC/RIVM, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Matthijs C Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Jeffrey C Barrett
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Genomics Plc, East Road, Cambridge, CB1 1BH, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
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30
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James JA, Chen H, Young KA, Bemis EA, Seifert J, Bourn RL, Deane KD, Demoruelle MK, Feser M, O'Dell JR, Weisman MH, Keating RM, Gaffney PM, Kelly JA, Langefeld CD, Harley JB, Robinson W, Hafler DA, O'Connor KC, Buckner J, Guthridge JM, Norris JM, Holers VM. Latent autoimmunity across disease-specific boundaries in at-risk first-degree relatives of SLE and RA patients. EBioMedicine 2019; 42:76-85. [PMID: 30952617 PMCID: PMC6491794 DOI: 10.1016/j.ebiom.2019.03.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Autoimmune disease prevention requires tools to assess an individual's risk of developing a specific disease. One tool is disease-associated autoantibodies, which accumulate in an asymptomatic preclinical period. However, patients sometimes exhibit autoantibodies associated with a different disease classification. When and how these alternative autoantibodies first appear remain unknown. This cross-sectional study characterizes alternative autoimmunity, and associated genetic and environmental factors, in unaffected first-degree relatives (FDRs) of patients, who exhibit increased future risk for the same disease. METHODS Samples (n = 1321) from disease-specific autoantibody-positive (aAb+) systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 1 diabetes (T1D) patients; and unaffected aAb+ and autoantibody-negative (aAb-) SLE and RA FDRs were tested for SLE, RA, and T1D aAbs, as well as anti-tissue transglutaminase, anti-cardiolipin and anti-thyroperoxidase. FDR SLE and RA genetic risk scores (GRS) were calculated. FINDINGS Alternative autoimmunity occurred in SLE patients (56%) and FDRs (57·4%), RA patients (32·6%) and FDRs (34·8%), and T1D patients (43%). Expanded autoimmunity, defined as autoantibodies spanning at least two other diseases, occurred in 18·5% of SLE patients, 16·4% of SLE FDRs, 7·8% of RA patients, 5·3% of RA FDRs, and 10·8% of T1D patients. SLE FDRs were more likely to have alternative (odds ratio [OR] 2·44) and expanded (OR 3·27) autoimmunity than RA FDRs. Alternative and expanded autoimmunity were associated with several environmental exposures. Alternative autoimmunity was associated with a higher RA GRS in RA FDRs (OR 1·41), and a higher SLE GRS in aAb+ RA FDRs (OR 1·87), but not in SLE FDRs. INTERPRETATION Autoimmunity commonly crosses disease-specific boundaries in systemic (RA, SLE) and organ-specific (T1D) autoimmune diseases. Alternative autoimmunity is more common in SLE FDRs than RA FDRs, and is influenced by genetic and environmental factors. These findings have substantial implications for preclinical disease pathogenesis and autoimmune disease prevention studies. FUND: NIH U01AI101981, R01AR051394, U19AI082714, P30AR053483, P30GM103510, U54GM104938, U01AI101934, R01AI024717, U01AI130830, I01BX001834, & U01HG008666.
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Affiliation(s)
- Judith A James
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Hua Chen
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | | | - Rebecka L Bourn
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | | | | | | | | | | | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, The University of Cincinnati College of Medicine, and Cincinnati US Department of Veterans Affairs VA Medical Center, Cincinnati, OH, USA
| | | | | | | | - Jane Buckner
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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31
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Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, der Sloot KWJ V, Peters V, Van Dullemen HM, Visschedijk MC, EAM F, Swertz MA, Dijkstra G, Weersma RK. The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol 2019; 19:5. [PMID: 30621600 PMCID: PMC6325838 DOI: 10.1186/s12876-018-0917-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients. CONSTRUCTION AND CONTENT We initiated the 1000IBD project ( https://1000ibd.org ) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing. UTILITY AND DISCUSSION All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive ( https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models. CONCLUSIONS We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.
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Affiliation(s)
- Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K. J. Van der Velde
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. D. Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - A. Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - V. Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - L. M. Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Van der Sloot KWJ
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - V. Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - H. M. Van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - M. C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - Festen EAM
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. A. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - G. Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - R. K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
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Fazia T, Pastorino R, Foco L, Han L, Abney M, Beecham A, Hadjixenofontos A, Guo H, Gentilini D, Papachristou C, Bitti PP, Ticca A, Berzuini C, McCauley JL, Bernardinelli L. Investigating multiple sclerosis genetic susceptibility on the founder population of east-central Sardinia via association and linkage analysis of immune-related loci. Mult Scler 2018; 24:1815-1824. [PMID: 28933650 DOI: 10.1177/1352458517732841] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND A wealth of single-nucleotide polymorphisms (SNPs) responsible for multiple sclerosis (MS) susceptibility have been identified; however, they explain only a fraction of MS heritability. OBJECTIVES We contributed to discovery of new MS susceptibility SNPs by studying a founder population with high MS prevalence. METHODS We analyzed ImmunoChip data from 15 multiplex families and 94 unrelated controls from the Nuoro Province, Sardinia, Italy. We tested each SNP for both association and linkage with MS, the linkage being explored in terms of identity-by-descent (IBD) sharing excess and using gene dropping to compute a corresponding empirical p-value. By targeting regions that are both associated and in linkage with MS, we increase chances of identifying interesting genomic regions. RESULTS We identified 486 MS-associated (p < 1 × 10-4) and 18,426 MS-linked (p < 0.05) SNPs. A total of 111 loci were both linked and associated with MS, 18 of them pointing to 14 non-major histocompatibility complex (MHC) genes, and 93 of them located in the MHC region. CONCLUSION We discovered new suggestive signals and confirmed some previously identified ones. We believe this to represent a significant step toward an understanding of the genetic basis of MS.
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Affiliation(s)
- Teresa Fazia
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
| | - Roberta Pastorino
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
| | - Luisa Foco
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy; Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Lide Han
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ashley Beecham
- John P. Hussmann Institute for Human Genomics and Dr John Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Athena Hadjixenofontos
- John P. Hussmann Institute for Human Genomics and Dr John Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Hui Guo
- Center for Biostatistics, Institute of Population Health, The University of Manchester, Manchester, UK
| | - Davide Gentilini
- Unità di Bioinformatica e Statistica Genomica, Istituto Auxologico Italiano-IRCCS, Milano, Italy
| | | | - Pier Paolo Bitti
- Immunoematologia e Medicina Trasfusionale, Ospedale "San Francesco" Nuoro, ASSL Nuoro, Azienda Tutela Salute Sardegna, Nuoro, Italy
| | - Anna Ticca
- Neurologia e Stroke Unit, Ospedale "San Francesco" Nuoro, ASSL Nuoro, Azienda Tutela Salute Sardegna, Nuoro, Italy
| | - Carlo Berzuini
- Center for Biostatistics, Institute of Population Health, The University of Manchester, Manchester, UK
| | - Jacob L McCauley
- John P. Hussmann Institute for Human Genomics and Dr John Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Science, University of Pavia, Pavia, Italy
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Jeong C, Witonsky DB, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. PLoS Genet 2018; 14:e1007650. [PMID: 30188897 PMCID: PMC6143271 DOI: 10.1371/journal.pgen.1007650] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/18/2018] [Accepted: 08/21/2018] [Indexed: 12/21/2022] Open
Abstract
Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. The results of genome-wide association analyses and tests for polygenic adaptations showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.
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Affiliation(s)
- Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - David B. Witonsky
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal
| | | | - Cynthia M. Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Geoff Childs
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Sienna R. Craig
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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34
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Huckins LM, Hatzikotoulas K, Southam L, Thornton LM, Steinberg J, Aguilera-McKay F, Treasure J, Schmidt U, Gunasinghe C, Romero A, Curtis C, Rhodes D, Moens J, Kalsi G, Dempster D, Leung R, Keohane A, Burghardt R, Ehrlich S, Hebebrand J, Hinney A, Ludolph A, Walton E, Deloukas P, Hofman A, Palotie A, Palta P, van Rooij FJA, Stirrups K, Adan R, Boni C, Cone R, Dedoussis G, van Furth E, Gonidakis F, Gorwood P, Hudson J, Kaprio J, Kas M, Keski-Rahonen A, Kiezebrink K, Knudsen GP, Slof-Op 't Landt MCT, Maj M, Monteleone AM, Monteleone P, Raevuori AH, Reichborn-Kjennerud T, Tozzi F, Tsitsika A, van Elburg A, Collier DA, Sullivan PF, Breen G, Bulik CM, Zeggini E. Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. Mol Psychiatry 2018; 23:1169-1180. [PMID: 29155802 PMCID: PMC5828108 DOI: 10.1038/mp.2017.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 12/12/2022]
Abstract
Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. To date, only one genome-wide significant locus associated with AN has been identified. We performed an exome-chip based genome-wide association studies (GWAS) in 2158 cases from nine populations of European origin and 15 485 ancestrally matched controls. Unlike previous studies, this GWAS also probed association in low-frequency and rare variants. Sixteen independent variants were taken forward for in silico and de novo replication (11 common and 5 rare). No findings reached genome-wide significance. Two notable common variants were identified: rs10791286, an intronic variant in OPCML (P=9.89 × 10-6), and rs7700147, an intergenic variant (P=2.93 × 10-5). No low-frequency variant associations were identified at genome-wide significance, although the study was well-powered to detect low-frequency variants with large effect sizes, suggesting that there may be no AN loci in this genomic search space with large effect sizes.
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Affiliation(s)
- L M Huckins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K Hatzikotoulas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L Southam
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L M Thornton
- Department of Psychiatry and Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Steinberg
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - F Aguilera-McKay
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - J Treasure
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - U Schmidt
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - C Gunasinghe
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - A Romero
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - C Curtis
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D Rhodes
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J Moens
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - G Kalsi
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D Dempster
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R Leung
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - A Keohane
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R Burghardt
- Klinik für Kinder- und Jugendpsychiatrie, Psychotherapie und Psychosomatik Klinikum Frankfurt, Frankfurt, Germany
| | - S Ehrlich
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Dresden, Germany
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - J Hebebrand
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - A Hinney
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - A Ludolph
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - E Walton
- Division of Psychological & Social Medicine and Developmental Neurosciences, Technische Universität Dresden, Faculty of Medicine, University Hospital C.G. Carus, Dresden, Germany
- Department of Psychology, Georgia State University, Atlanta, GA, USA
| | - P Deloukas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - A Hofman
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Palotie
- Center for Human Genome Research at the Massachusetts General Hospital, Boston, MA, USA
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - P Palta
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - F J A van Rooij
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - K Stirrups
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - R Adan
- Brain Center Rudolf Magnus, Department of Neuroscience and Pharmacology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Boni
- INSERM U984, Centre of Psychiatry and Neuroscience, Paris, France
| | - R Cone
- Mary Sue Coleman Director, Life Sciences Institute, Professor of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - G Dedoussis
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - E van Furth
- Rivierduinen Eating Disorders Ursula, Leiden, Zuid-Holland, The Netherlands
| | - F Gonidakis
- Eating Disorders Unit, 1st Department of Psychiatry, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - P Gorwood
- INSERM U984, Centre of Psychiatry and Neuroscience, Paris, France
| | - J Hudson
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, USA
| | - J Kaprio
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - M Kas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - A Keski-Rahonen
- Department of Public Health, Clinicum, University of Helsinki, Helsinki, Finland
| | - K Kiezebrink
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - G-P Knudsen
- Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | | | - M Maj
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - A M Monteleone
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - P Monteleone
- Department of Medicine and Surgery, Section of Neurosciences, University of Salerno, Salerno, Italy
| | - A H Raevuori
- Department of Public Health, Clinicum, University of Helsinki, Helsinki, Finland
| | - T Reichborn-Kjennerud
- Department of Genetics, Environment and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - F Tozzi
- eHealth Lab-Computer Science Department, University of Cyprus, Nicosia, Cyprus
| | - A Tsitsika
- Adolescent Health Unit (A.H.U.), 2nd Department of Pediatrics – Medical School, University of Athens "P. & A. Kyriakou" Children's Hospital, Athens, Greece
| | - A van Elburg
- Center for Eating Disorders Rintveld, University of Utrecht, Utrecht, The Netherlands
| | - D A Collier
- Eli Lilly and Company, Erl Wood Manor, Windlesham, UK
| | - P F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden
| | - G Breen
- Social Genetic and Developmental Psychiatry, King's College London, London, UK
| | - C M Bulik
- Department of Psychiatry and Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden
| | - E Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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35
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Imhann F, Vila AV, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 2018; 67:108-119. [PMID: 27802154 PMCID: PMC5699972 DOI: 10.1136/gutjnl-2016-312135] [Citation(s) in RCA: 467] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/15/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Patients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset and the heterogeneous presentation of IBD. Therefore, we performed a case-control analysis of the gut microbiota, the host genome and the clinical phenotypes of IBD. DESIGN Stool samples, peripheral blood and extensive phenotype data were collected from 313 patients with IBD and 582 truly healthy controls, selected from a population cohort. The gut microbiota composition was assessed by tag-sequencing the 16S rRNA gene. All participants were genotyped. We composed genetic risk scores from 11 functional genetic variants proven to be associated with IBD in genes that are directly involved in the bacterial handling in the gut: NOD2, CARD9, ATG16L1, IRGM and FUT2. RESULTS Strikingly, we observed significant alterations of the gut microbiota of healthy individuals with a high genetic risk for IBD: the IBD genetic risk score was significantly associated with a decrease in the genus Roseburia in healthy controls (false discovery rate 0.017). Moreover, disease location was a major determinant of the gut microbiota: the gut microbiota of patients with colonic Crohn's disease (CD) is different from that of patients with ileal CD, with a decrease in alpha diversity associated to ileal disease (p=3.28×10-13). CONCLUSIONS We show for the first time that genetic risk variants associated with IBD influence the gut microbiota in healthy individuals. Roseburia spp are acetate-to-butyrate converters, and a decrease has already been observed in patients with IBD.
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Affiliation(s)
- Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Dirk Gevers
- Broad Institute of Harvard and MIT, Boston, USA
| | - Marijn C. Visschedijk
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lieke M. Spekhorst
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rudi Alberts
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Hendrik M. van Dullemen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Rinze W.F. Ter Steege
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Curtis Huttenhower
- Broad Institute of Harvard and MIT, Boston, USA,Biostatistics Department, Harvard School of Public Health, Boston, USA
| | - Gerard Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Ramnik J. Xavier
- Broad Institute of Harvard and MIT, Boston, USA,Massachusetts General Hospital, Boston, USA
| | - Eleonora A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rinse K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
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36
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Dos Santos JC, Damen MSMA, Oosting M, de Jong DJ, Heinhuis B, Gomes RS, Araújo CS, Netea MG, Ribeiro-Dias F, Joosten LAB. The NOD2 receptor is crucial for immune responses towards New World Leishmania species. Sci Rep 2017; 7:15219. [PMID: 29123157 PMCID: PMC5680260 DOI: 10.1038/s41598-017-15412-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/25/2017] [Indexed: 01/07/2023] Open
Abstract
American Tegumentary Leishmaniasis is a chronic infection caused by Leishmania protozoan. It is not known whether genetic variances in NOD-like receptor (NLR) family members influence the immune response towards Leishmania parasites and modulate intracellular killing. Using functional genomics, we investigated whether genetic variants in NOD1 or NOD2 influence the production of cytokines by human PBMCs exposed to Leishmania. In addition, we examined whether recognition of Leishmania by NOD2 contributes to intracellular killing. Polymorphisms in the NOD2 gene decreased monocyte- and lymphocyte-derived cytokine production after stimulation with L. amazonensis or L. braziliensis compared to individuals with a functional NOD2 receptor. The phagolysosome formation is important for Leishmania-induced cytokine production and upregulation of NOD2 mRNA expression. NOD2 is crucial to control intracellular infection caused by Leishmania spp. NOD2 receptor is important for Leishmania recognition, the control of intracellular killing, and the induction of innate and adaptive immune responses.
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Affiliation(s)
- Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Michelle S M A Damen
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dirk J de Jong
- Department of Gastroenterology and Hepatology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rodrigo Saar Gomes
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Carla Santos Araújo
- Universidade Federal do Vale do São Francisco, Petrolina, Pernambuco, Brazil
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Fátima Ribeiro-Dias
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands. .,Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
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37
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Aleva FE, van de Veerdonk FL, Li Y, Tunjungputri RN, Simons S, De Groot PG, Netea MM, Heijdra YF, de Mast Q, van der Ven AJAM. The effects of signal transducer and activator of transcription three mutations on human platelets. Platelets 2017; 29:602-609. [PMID: 28960117 DOI: 10.1080/09537104.2017.1349309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Involvement of signal transducer and activator of transcription 3 (STAT3) in inflammation is well known. Recently, a role for STAT3 in platelet activation and platelet production has been suggested. Platelets exhibit important immune functions and engagement of STAT3 in platelet physiology may link inflammation and hemostasis. This study investigated the effects of STAT3 loss-of-function mutations and single nucleotide polymorphisms (SNPs) in STAT3 on glycoprotein VI (GPVI)-mediated platelet activation and platelet numbers in humans. Two cohorts were studied. The first cohort concerned patients with STAT3 loss-of-function mutations. Platelet numbers were investigated in eight patients and GPVI-mediated platelet activation was functionally tested in four patients. Additional experiments were performed to investigate underlying mechanisms. The second cohort concerned 334 healthy volunteers and investigated the consequences of SNPs in STAT3 on GPVI-mediated platelet activation and platelet numbers. Platelet activation was lower in STAT3 loss-of-function patients at baseline and after stimulation of the GPVI receptor, reflected by decreased P-selectin expression. This was independent of gene transcription. Blockade of the adenosine di-phosphate (ADP) pathway resulted in a further decrease of P-selectin expression, particularly in STAT3 loss-of-function patients. In contrast, the SNPs in STAT3 did not influence GPVI-mediated platelet activation. Also, platelet numbers were not affected by STAT3 loss-of-function mutations, nor was there an association with the SNPs. In conclusion, STAT3 signaling does not seem to play a major role in thrombopoiesis. We confirm that STAT3 is involved in GPVI-mediated platelet activation in humans, independent of gene transcription. GPVI-mediated platelet activation is highly dependent on secondary ADP release. Our findings suggest that STAT3 modulation may affect inflammation, hemostasis, and their interaction.
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Affiliation(s)
- Floor E Aleva
- a Department of Respiratory Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Frank L van de Veerdonk
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Yang Li
- d Department of Genetics , University Medical Center Groningen , Nijmegen , the Netherlands
| | - Rahajeng N Tunjungputri
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Sami Simons
- a Department of Respiratory Medicine , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Philip G De Groot
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Mihai M Netea
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Yvonne F Heijdra
- a Department of Respiratory Medicine , Radboud University Medical Center , Nijmegen , the Netherlands
| | - Quirijn de Mast
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
| | - André J A M van der Ven
- b Department of Internal Medicine , Radboud University Medical Center , Nijmegen , the Netherlands.,c Radboud Center for Infectious Diseases , Radboud University Medical Center , Nijmegen , the Netherlands
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38
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Transancestral mapping and genetic load in systemic lupus erythematosus. Nat Commun 2017; 8:16021. [PMID: 28714469 PMCID: PMC5520018 DOI: 10.1038/ncomms16021] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (∼50% of these regions have multiple independent associations); these include 24 novel SLE regions (P<5 × 10−8), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE. Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong ethnic and gender bias. In a transancestral genetic association study, Langefeld et al. identify 24 novel regions associated with risk to lupus and propose a cumulative hits hypothesis for loci conferring risk to SLE.
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39
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Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KKH, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 2017; 547:173-178. [PMID: 28658209 PMCID: PMC5511510 DOI: 10.1038/nature22969] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 05/07/2017] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn's disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.
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Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Ming Fang
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Christ Church, University of Oxford, St Aldates OX1 1DP, UK
| | - Maša Umićević Mirkov
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Gabrielle Boucher
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vibeke Andersen
- Focused research unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland, Hospital of Southern Jutland, 6200 Åbenrå, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | | | - Adrian Cortes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - François Crins
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Gastrointestinal and Liver Diseases, BioDonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Valérie Deffontaine
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Julia Dmitrieva
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Elisa Docampo
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mahmoud Elansary
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Kyle Kai-How Farh
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Illumina, San Diego, California 92122, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Ann-Stephan Gori
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Philippe Goyette
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, SE-70182 Örebro, Sweden
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jo Knight
- Data Science Institute and Lancaster Medical School, Lancaster University, Lancaster LA1 4YG, UK
| | - Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco, Western Australia 6008, Australia.,Harry Perkins Institute for Medical Research, School of Medicine and Pharmacology, University of Western Australia, Murdoch, Western Australia 6150, Australia
| | - Charlie W Lees
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Edouard Louis
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Division of Gastroenterology, Centre Hospitalier Universitaire (CHU) de Liège, 4000 Liège, Belgium
| | - Rob Mariman
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Theo Meuwissen
- Institute of Livestock and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Myriam Mni
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Yukihide Momozawa
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Open Targets, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emilie Théâtre
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Gosia Trynka
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Severine Vermeire
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.,Division of Gastroenterology, University Hospital Gasthuisberg, 3000 Leuven, Belgium
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | | | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK.,Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Michel Georges
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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40
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Yang CH, Weng ZJ, Chuang LY, Yang CS. Identification of SNP-SNP interaction for chronic dialysis patients. Comput Biol Med 2017; 83:94-101. [DOI: 10.1016/j.compbiomed.2017.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 01/10/2023]
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41
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Westerlind H, Mellander MR, Bresso F, Munch A, Bonfiglio F, Assadi G, Rafter J, Hübenthal M, Lieb W, Källberg H, Brynedal B, Padyukov L, Halfvarson J, Törkvist L, Bjork J, Andreasson A, Agreus L, Almer S, Miehlke S, Madisch A, Ohlsson B, Löfberg R, Hultcrantz R, Franke A, D'Amato M. Dense genotyping of immune-related loci identifies HLA variants associated with increased risk of collagenous colitis. Gut 2017; 66:421-428. [PMID: 26525574 DOI: 10.1136/gutjnl-2015-309934] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/11/2015] [Accepted: 10/12/2015] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Collagenous colitis (CC) is a major cause of chronic non-bloody diarrhoea, particularly in the elderly female population. The aetiology of CC is unknown, and still poor is the understanding of its pathogenesis. This possibly involves dysregulated inflammation and immune-mediated reactions in genetically predisposed individuals, but the contribution of genetic factors to CC is underinvestigated. We systematically tested immune-related genes known to impact the risk of several autoimmune diseases for their potential CC-predisposing role. DESIGN Three independent cohorts of histologically confirmed CC cases (N=314) and controls (N=4299) from Sweden and Germany were included in a 2-step association analysis. Immunochip and targeted single nucleotide polymorphism (SNP) genotype data were produced, respectively, for discovery and replication purposes. Classical human leucocyte antigen (HLA) variants at 2-digit and 4-digit resolution were obtained via imputation from single marker genotypes. SNPs and HLA variants passing quality control filters were tested for association with CC with logistic regression adjusting for age, sex and country of origin. RESULTS Forty-two markers gave rise to genome-wide significant association signals, all contained within the HLA region on chromosome 6 (best p=4.2×10-10 for SNP rs4143332). Among the HLA variants, most pronounced risk effects were observed for 8.1 haplotype alleles including DQ2.5, which was targeted and confirmed in the replication data set (p=2.3×10-11; OR=2.06; 95% CI (1.67 to 2.55) in the combined analysis). CONCLUSIONS HLA genotype associates with CC, thus implicating HLA-related immune mechanisms in its pathogenesis.
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Affiliation(s)
- Helga Westerlind
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Marie-Rose Mellander
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Francesca Bresso
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Munch
- Department of Clinical and Experimental Medicine, Faculty of Health Science, Linköpings University, Linköping, Sweden
| | - Ferdinando Bonfiglio
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Joseph Rafter
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henrik Källberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Boel Brynedal
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Leif Törkvist
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Bjork
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Andreasson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Sven Almer
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Stephan Miehlke
- Center for Digestive Diseases, Internal Medicine Center Eppendorf, Hamburg, Germany
| | - Ahmed Madisch
- Clinic for Gastroenterology, Endoscopy and Interventional Diabetology, Siloah Hospital, Hannover, Germany
| | - Bodil Ohlsson
- Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Robert Löfberg
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Sophiahemmet Hospital, Stockholm, Sweden
| | - Rolf Hultcrantz
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- BioCruces Health Research Institute and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Munroe ME, Pezant N, Brown MA, Fife DA, Guthridge JM, Kelly JA, Wiley G, Gaffney PM, James JA, Montgomery CG. Association of IFIH1 and pro-inflammatory mediators: Potential new clues in SLE-associated pathogenesis. PLoS One 2017; 12:e0171193. [PMID: 28234905 PMCID: PMC5325200 DOI: 10.1371/journal.pone.0171193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 01/18/2017] [Indexed: 12/27/2022] Open
Abstract
Antiviral defenses are inappropriately activated in systemic lupus erythematosus (SLE) and association between SLE and the antiviral helicase gene, IFIH1, is well established. We sought to extend the previously reported association of pathogenic soluble mediators and autoantibodies with mouse Mda5 to its human ortholog, IFIH1. To better understand the role this gene plays in human lupus, we assessed association of IFIH1 variants with soluble mediators and autoantibodies in 357 European-American SLE patients, first-degree relatives, and unrelated, unaffected healthy controls. Association between each of 135 genotyped SNPs in IFIH1 and four lupus-associated plasma mediators, IL-6, TNF-α, IFN-β, and IP-10, were investigated via linear regression. No significant associations were found to SNPs orthologous to those identified in exon 13 of the mouse. However, outside of this region there were significant associations between IL-6 and rs76162067 (p = 0.008), as well as IP-10 and rs79711023 (p = 0.003), located in a region of IFIH1 previously shown to directly influence MDA-5 mediated IP-10 and IL-6 secretion. SLE patients and FDRs carrying the minor allele for rs79711023 demonstrated lower levels of IP-10, while only FDRs carrying the minor allele for rs76162067 demonstrated an increased level of IL-6. This would suggest that the change in IP-10 is genotypically driven, while the change in IL-6 may be reflective of SLE transition status. These data suggest that IFIH1 may contribute to SLE pathogenesis via altered inflammatory mechanisms.
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Affiliation(s)
- Melissa E. Munroe
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Nathan Pezant
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Michael A. Brown
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Dustin A. Fife
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Graham Wiley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
- Department of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
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43
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de Lange KM, Moutsianas L, Lee JC, Lamb CA, Luo Y, Kennedy NA, Jostins L, Rice DL, Gutierrez-Achury J, Ji SG, Heap G, Nimmo ER, Edwards C, Henderson P, Mowat C, Sanderson J, Satsangi J, Simmons A, Wilson DC, Tremelling M, Hart A, Mathew CG, Newman WG, Parkes M, Lees CW, Uhlig H, Hawkey C, Prescott NJ, Ahmad T, Mansfield JC, Anderson CA, Barrett JC. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat Genet 2017; 49:256-261. [PMID: 28067908 PMCID: PMC5289481 DOI: 10.1038/ng.3760] [Citation(s) in RCA: 763] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/07/2016] [Indexed: 02/07/2023]
Abstract
Genetic association studies have identified 215 risk loci for inflammatory bowel disease, thereby uncovering fundamental aspects of its molecular biology. We performed a genome-wide association study of 25,305 individuals and conducted a meta-analysis with published summary statistics, yielding a total sample size of 59,957 subjects. We identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease. The associated variants are correlated with expression changes in response to immune stimulus at two of these genes (ITGA4 and ITGB8) and at previously implicated loci (ITGAL and ICAM1). In all four cases, the expression-increasing allele also increases disease risk. We also identified likely causal missense variants in a gene implicated in primary immune deficiency, PLCG2, and a negative regulator of inflammation, SLAMF8. Our results demonstrate that new associations at common variants continue to identify genes relevant to therapeutic target identification and prioritization.
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Affiliation(s)
| | - Loukas Moutsianas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James C. Lee
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge, UK
| | | | - Yang Luo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Division of Genetics and Rheumatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nicholas A. Kennedy
- Precision Medicine Exeter, University of Exeter, Exeter, UK
- IBD Pharmacogenetics, Royal Devon and Exeter Foundation Trust, Exeter, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK
- Christ Church, University of Oxford, St Aldates, UK
| | - Daniel L. Rice
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Sun-Gou Ji
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Graham Heap
- Precision Medicine Exeter, University of Exeter, Exeter, UK
- IBD Pharmacogenetics, Royal Devon and Exeter Foundation Trust, Exeter, UK
| | - Elaine R. Nimmo
- Gastrointestinal Unit, Wester General Hospital University of Edinburgh, Edinburgh, UK
| | - Cathryn Edwards
- Department of Gastroenterology, Torbay Hospital, Torbay, Devon, UK
| | - Paul Henderson
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
- Department of Paediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children,Edinburgh, UK
| | - Craig Mowat
- Department of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Jeremy Sanderson
- Guy’s & St Thomas’ NHS Foundation Trust, St Thomas’ Hospital, Department of Gastroenterology, London, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Wester General Hospital University of Edinburgh, Edinburgh, UK
| | - Alison Simmons
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - David C. Wilson
- Paediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, Edinburgh, UK
- Child Life and Health, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mark Tremelling
- Gastroenterology & General Medicine, Norfolk and Norwich University Hospital, Norwich, UK
| | - Ailsa Hart
- Department of Medicine, St Mark's Hospital, Harrow, Middlesex, UK
| | - Christopher G. Mathew
- Department of Medical and Molecular Genetics, Faculty of Life Science and Medicine, King's College London, Guy's Hospital, London, UK
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of Witwatersrand, South Africa
| | - William G. Newman
- Genetic Medicine, Manchester Academic Health Science Centre, Manchester, UK
- The Manchester Centre for Genomic Medicine, University of Manchester, Manchester, UK
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge, UK
| | - Charlie W. Lees
- Gastrointestinal Unit, Wester General Hospital University of Edinburgh, Edinburgh, UK
| | - Holm Uhlig
- Translational Gastroenterology Unit and the Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Chris Hawkey
- Nottingham Digestive Diseases Centre, Queens Medical Centre, Nottingham, UK
| | - Natalie J. Prescott
- Department of Medical and Molecular Genetics, Faculty of Life Science and Medicine, King's College London, Guy's Hospital, London, UK
| | - Tariq Ahmad
- Precision Medicine Exeter, University of Exeter, Exeter, UK
- IBD Pharmacogenetics, Royal Devon and Exeter Foundation Trust, Exeter, UK
| | - John C. Mansfield
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, UK
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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44
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Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat Genet 2017. [PMID: 28067908 DOI: 10.1038/ng.3760.] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic association studies have identified 215 risk loci for inflammatory bowel disease, thereby uncovering fundamental aspects of its molecular biology. We performed a genome-wide association study of 25,305 individuals and conducted a meta-analysis with published summary statistics, yielding a total sample size of 59,957 subjects. We identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease. The associated variants are correlated with expression changes in response to immune stimulus at two of these genes (ITGA4 and ITGB8) and at previously implicated loci (ITGAL and ICAM1). In all four cases, the expression-increasing allele also increases disease risk. We also identified likely causal missense variants in a gene implicated in primary immune deficiency, PLCG2, and a negative regulator of inflammation, SLAMF8. Our results demonstrate that new associations at common variants continue to identify genes relevant to therapeutic target identification and prioritization.
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45
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Oosting M, Kerstholt M, Ter Horst R, Li Y, Deelen P, Smeekens S, Jaeger M, Lachmandas E, Vrijmoeth H, Lupse M, Flonta M, Cramer RA, Kullberg BJ, Kumar V, Xavier R, Wijmenga C, Netea MG, Joosten LAB. Functional and Genomic Architecture of Borrelia burgdorferi-Induced Cytokine Responses in Humans. Cell Host Microbe 2016; 20:822-833. [PMID: 27818078 DOI: 10.1016/j.chom.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/25/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022]
Abstract
Despite the importance of immune variation for the symptoms and outcome of Lyme disease, the factors influencing cytokine production during infection with the causal pathogen Borrelia burgdorferi remain poorly understood. Borrelia infection-induced monocyte- and T cell-derived cytokines were profiled in peripheral blood from two healthy human cohorts of Western Europeans from the Human Functional Genomics Project. Both non-genetic and genetic host factors were found to influence Borrelia-induced cytokine responses. Age strongly impaired IL-22 responses, and genetic studies identified several independent QTLs that impact Borrelia-induced cytokine production. Genetic, transcriptomic, and functional validation studies revealed an important role for HIF-1α-mediated glycolysis in the cytokine response to Borrelia. HIF-1α pathway activation and increase in glycolysis-derived lactate was confirmed in Lyme disease patients. In conclusion, functional genomics approaches reveal the architecture of cytokine production induced by Borrelia infection of human primary leukocytes and suggest a connection between cellular glucose metabolism and Borrelia-induced cytokine production.
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Affiliation(s)
- Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Mariska Kerstholt
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713GZ Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713GZ Groningen, the Netherlands; Genomics Coordination Center, University Medical Center Groningen, University of Groningen, 9713GZ Groningen, the Netherlands
| | - Sanne Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Ekta Lachmandas
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Hedwig Vrijmoeth
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Mihaela Lupse
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu," 400012 Cluj-Napoca, Romania
| | - Mirela Flonta
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu," 400012 Cluj-Napoca, Romania
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Dartmouth, NH 03755-1404, USA
| | - Bart Jan Kullberg
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713GZ Groningen, the Netherlands
| | - Ramnik Xavier
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, MA 02114, USA; Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713GZ Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA Nijmegen, the Netherlands.
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46
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Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG. A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell 2016; 167:1099-1110.e14. [DOI: 10.1016/j.cell.2016.10.017] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
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47
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Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AAM, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A. The effect of host genetics on the gut microbiome. Nat Genet 2016; 48:1407-1412. [PMID: 27694959 DOI: 10.1038/ng.3663] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/10/2016] [Indexed: 02/07/2023]
Abstract
The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified associations of 9 loci with microbial taxonomies and 33 loci with microbial pathways and gene ontology terms at P < 5 × 10-8. Additionally, in a targeted analysis of regions involved in complex diseases, innate and adaptive immunity, or food preferences, 32 loci were identified at the suggestive level of P < 5 × 10-6. Most of our reported associations are new, including genome-wide significance for the C-type lectin molecules CLEC4F-CD207 at 2p13.3 and CLEC4A-FAM90A1 at 12p13. We also identified association of a functional LCT SNP with the Bifidobacterium genus (P = 3.45 × 10-8) and provide evidence of a gene-diet interaction in the regulation of Bifidobacterium abundance. Our results demonstrate the importance of understanding host-microbe interactions to gain better insight into human health.
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Affiliation(s)
- Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Top Institute Food and Nutrition, Wageningen, the Netherlands
| | - Zlatan Mujagic
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Computer Science, Aalto University School of Science, Espoo, Finland
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sanne P Smeekens
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maria Carmen Cenit
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Vinod Kumar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Leo Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hermie Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marten H Hofker
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daisy Jonkers
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Top Institute Food and Nutrition, Wageningen, the Netherlands
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48
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Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nat Med 2016; 22:952-60. [PMID: 27376574 DOI: 10.1038/nm.4139] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/07/2016] [Indexed: 12/14/2022]
Abstract
Little is known about the inter-individual variation of cytokine responses to different pathogens in healthy individuals. To systematically describe cytokine responses elicited by distinct pathogens and to determine the effect of genetic variation on cytokine production, we profiled cytokines produced by peripheral blood mononuclear cells from 197 individuals of European origin from the 200 Functional Genomics (200FG) cohort in the Human Functional Genomics Project (http://www.humanfunctionalgenomics.org), obtained over three different years. We compared bacteria- and fungi-induced cytokine profiles and found that most cytokine responses were organized around a physiological response to specific pathogens, rather than around a particular immune pathway or cytokine. We then correlated genome-wide single-nucleotide polymorphism (SNP) genotypes with cytokine abundance and identified six cytokine quantitative trait loci (QTLs). Among them, a cytokine QTL at the NAA35-GOLM1 locus markedly modulated interleukin (IL)-6 production in response to multiple pathogens and was associated with susceptibility to candidemia. Furthermore, the cytokine QTLs that we identified were enriched among SNPs previously associated with infectious diseases and heart diseases. These data reveal and begin to explain the variability in cytokine production by human immune cells in response to pathogens.
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49
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Young KA, Munroe ME, Guthridge JM, Kamen DL, Niewold TB, Gilkeson GS, Weisman MH, Ishimori ML, Kelly J, Gaffney PM, Sivils KH, Lu R, Wallace DJ, Karp DR, Harley JB, James JA, Norris JM. Combined role of vitamin D status and CYP24A1 in the transition to systemic lupus erythematosus. Ann Rheum Dis 2016; 76:153-158. [PMID: 27283331 DOI: 10.1136/annrheumdis-2016-209157] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/06/2016] [Accepted: 05/14/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVE We examined whether measures of vitamin D were associated with transitioning to systemic lupus erythematosus (SLE) in individuals at risk for SLE. METHODS 436 individuals who reported having a relative with SLE but who did not have SLE themselves were evaluated at baseline and again an average of 6.3 (±3.9) years later. Fifty-six individuals transitioned to SLE (≥4 cumulative American College of Rheumatology criteria). 25-Hydroxyvitamin D (25[OH]D) levels were measured by ELISA. Six single-nucleotide polymorphisms in four vitamin D genes were genotyped. Generalised estimating equations, adjusting for correlation within families, were used to test associations between the vitamin D variables and the outcome of transitioning to SLE. RESULTS Mean baseline 25[OH]D levels (p=0.42) and vitamin D supplementation (p=0.65) were not different between those who did and did not transition to SLE. Vitamin D deficiency (25[OH]D <20 ng/mL) was greater in those who transitioned compared with those who did not transition to SLE (46% vs 33%, p=0.05). The association between 25[OH]D and SLE was modified by CYP24A1 rs4809959, where for each additional minor allele increased 25[OH]D was associated with decreased SLE risk: zero minor alleles (adjusted OR: 1.03, CI 0.98 to 1.09), one minor allele (adjusted OR: 1.01, CI 0.97 to 1.05) and two minor alleles (adjusted OR: 0.91, CI 0.84 to 0.98). Similarly, vitamin D deficiency significantly increased the risk of transitioning to SLE in those with two minor alleles at rs4809959 (adjusted OR: 4.90, CI 1.33 to 18.04). CONCLUSIONS Vitamin D status and CYP24A1 may have a combined role in the transition to SLE in individuals at increased genetic risk for SLE.
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Affiliation(s)
| | - Melissa E Munroe
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Diane L Kamen
- Medical University of South Carolina, Charleston, South Carolina, USA
| | | | - Gary S Gilkeson
- Medical University of South Carolina, Charleston, South Carolina, USA
| | | | | | - Jennifer Kelly
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | | | - Kathy H Sivils
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Rufei Lu
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - David R Karp
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Judith A James
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Oklahoma University Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jill M Norris
- Colorado School of Public Health, Aurora, Colorado, USA
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50
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Moons T, De Hert M, Gellens E, Gielen L, Sweers K, Jacqmaert S, van Winkel R, Vandekerckhove P, Claes S. Genetic Evaluation of Schizophrenia Using the Illumina HumanExome Chip. PLoS One 2016; 11:e0150464. [PMID: 27028512 PMCID: PMC4814136 DOI: 10.1371/journal.pone.0150464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Schizophrenia is a genetically heterogeneous disorder that is associated with several common and rare genetic variants. As technology involved, cost advantages of chip based genotyping was combined with information about rare variants, resulting in the Infinium HumanExome Beadchip. Using this chip, a sample of 493 patients with schizophrenia or schizoaffective disorder and 484 healthy controls was genotyped. RESULTS From the initial 242901 SNVs, 88306 had at least one minor allele and passed quality control. No variant reached genomewide-significant results (p<10(-8)). The SNP with the lowest p-value was rs1230345 in WISP3 (p = 3.05*10(-6)), followed by rs9311525 in CACNA2D3 (p = 1.03*10(-5)) and rs1558557 (p = 3.85*10(-05)) on chromosome 7. At the gene level, 3 genes were of interest: WISP3, on chromosome 6q21, a signally protein from the extracellular matrix. A second candidate gene is CACNA2D3, a regulator of the intracerebral calcium pathway. A third gene is TNFSF10, associated with p53 mediated apoptosis.
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Affiliation(s)
- Tim Moons
- GRASP research group, UPC KULeuven, Campus Leuven, Leuven, Belgium
| | - Marc De Hert
- UPC KULeuven, campus Kortenberg, Kortenberg, Belgium
| | - Edith Gellens
- GRASP research group, UPC KULeuven, Campus Leuven, Leuven, Belgium
| | - Leen Gielen
- UPC KULeuven, campus Kortenberg, Kortenberg, Belgium
| | - Kim Sweers
- UPC KULeuven, campus Kortenberg, Kortenberg, Belgium
| | | | - Ruud van Winkel
- KU Leuven—University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium
| | - Philippe Vandekerckhove
- Belgian Red Cross-Flanders, Mechelen, Belgium
- KU Leuven—University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium
| | - Stephan Claes
- GRASP research group, UPC KULeuven, Campus Leuven, Leuven, Belgium
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