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Mulder RH, Kraaij R, Schuurmans IK, Frances-Cuesta C, Sanz Y, Medina-Gomez C, Duijts L, Rivadeneira F, Tiemeier H, Jaddoe VWV, Felix JF, Cecil CAM. Early-life stress and the gut microbiome: A comprehensive population-based investigation. Brain Behav Immun 2024; 118:117-127. [PMID: 38402916 PMCID: PMC7615798 DOI: 10.1016/j.bbi.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
Early-life stress (ELS) has been robustly associated with a range of poor mental and physical health outcomes. Recent studies implicate the gut microbiome in stress-related mental, cardio-metabolic and immune health problems, but research on humans is scarce and thus far often based on small, selected samples, often using retrospective reports of ELS. We examined associations between ELS and the human gut microbiome in a large, population-based study of children. ELS was measured prospectively from birth to 10 years of age in 2,004 children from the Generation R Study. We studied overall ELS, as well as unique effects of five different ELS domains, including life events, contextual risk, parental risk, interpersonal risk, and direct victimization. Stool microbiome was assessed using 16S rRNA sequencing at age 10 years and data were analyzed at multiple levels (i.e. α- and β-diversity indices, individual genera and predicted functional pathways). In addition, we explored potential mediators of ELS-microbiome associations, including diet at age 8 and body mass index at 10 years. While no associations were observed between overall ELS (composite score of five domains) and the microbiome after multiple testing correction, contextual risk - a specific ELS domain related to socio-economic stress, including risk factors such as financial difficulties and low maternal education - was significantly associated with microbiome variability. This ELS domain was associated with lower α-diversity, with β-diversity, and with predicted functional pathways involved, amongst others, in tryptophan biosynthesis. These associations were in part mediated by overall diet quality, a pro-inflammatory diet, fiber intake, and body mass index (BMI). These results suggest that stress related to socio-economic adversity - but not overall early life stress - is associated with a less diverse microbiome in the general population, and that this association may in part be explained by poorer diet and higher BMI. Future research is needed to test causality and to establish whether modifiable factors such as diet could be used to mitigate the negative effects of socio-economic adversity on the microbiome and related health consequences.
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Affiliation(s)
- Rosa H Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Isabel K Schuurmans
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Carlos Frances-Cuesta
- Microbiome, Nutrition & Health Research Unit. Institute of Agrochemistry and Food Technology, Severo Ochoa Centre of Excellence, National Research Council (IATA-CSIC), Valencia, Spain.
| | - Yolanda Sanz
- Microbiome, Nutrition & Health Research Unit. Institute of Agrochemistry and Food Technology, Severo Ochoa Centre of Excellence, National Research Council (IATA-CSIC), Valencia, Spain.
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Neonatal and Pediatric Intensive Care, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Social and Behavioral Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
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Najjary S, Kros JM, Stricker BH, Ruiter R, Shuai Y, Kraaij R, Van Steen K, van der Spek P, Van Eijck CHJ, Ikram MA, Ahmad S. Association of blood cell-based inflammatory markers with gut microbiota and cancer incidence in the Rotterdam study. Cancer Med 2024; 13:e6860. [PMID: 38366800 PMCID: PMC10904974 DOI: 10.1002/cam4.6860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 02/18/2024] Open
Abstract
The immune response-gut microbiota interaction is implicated in various human diseases, including cancer. Identifying the link between the gut microbiota and systemic inflammatory markers and their association with cancer will be important for our understanding of cancer etiology. The current study was performed on 8090 participants from the population-based Rotterdam study. We found a significant association (false discovery rate [FDR] ≤0.05) between lymphocytes and three gut microbial taxa, namely the family Streptococcaceae, genus Streptococcus, and order Lactobacillales. In addition, we identified 95 gut microbial taxa that were associated with inflammatory markers (p < 0.05). Analyzing the cancer data, we observed a significant association between higher systemic immune-inflammation index (SII) levels at baseline (hazard ratio (HR): 1.65 [95% confidence interval (CI); 1.10-2.46, p ≤ 0.05]) and a higher count of lymphocytes (HR: 1.38 [95% CI: 1.15-1.65, p ≤ 0.05]) and granulocytes (HR: 1.69 [95% CI: 1.40-2.03, p ≤ 0.05]) with increased risk of lung cancer after adjusting for age, sex, body mass index (BMI), and study cohort. This association was lost for SII and lymphocytes after additional adjustment for smoking (SII = HR:1.46 [95% CI: 0.96-2.22, p = 0.07] and lymphocytes = HR: 1.19 [95% CI: 0.97-1.46, p = 0.08]). In the stratified analysis, higher count of lymphocyte and granulocytes at baseline were associated with an increased risk of lung cancer in smokers after adjusting for age, sex, BMI, and study cohort (HR: 1.33 [95% CI: 1.09-1.62, p ≤0.05] and HR: 1.57 [95% CI: 1.28-1.92, p ≤0.05], respectively). Our study revealed a positive association between gut microbiota, higher SII levels, and higher lymphocyte and granulocyte counts, with an increased risk of developing lung cancer.
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Affiliation(s)
- Shiva Najjary
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | - Johan M. Kros
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | - Bruno H. Stricker
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Rikje Ruiter
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Yu Shuai
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Robert Kraaij
- Department of Internal MedicineErasmus University Medical CenterRotterdamthe Netherlands
| | - Kristel Van Steen
- Department of Human Genetics, Laboratory for Systems MedicineCenter for Human Genetics, KU LeuvenLeuvenBelgium
| | - Peter van der Spek
- Department of Pathology and Clinical Bioinformatics, The Tumor Immuno‐Pathology LaboratoryErasmus University Medical CenterRotterdamthe Netherlands
| | | | - M. Arfan Ikram
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
| | - Shahzad Ahmad
- Department of EpidemiologyErasmus University Medical CenterRotterdamthe Netherlands
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Pardo LM, Wang C, Ardon CB, Kraaij R, Prens EP, Van Straalen KR. Bacterial Microbiota Composition in Hidradenitis Suppurativa Differs per Skin Layer. J Invest Dermatol 2024; 144:426-430.e5. [PMID: 37717935 DOI: 10.1016/j.jid.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Affiliation(s)
- Luba M Pardo
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Cong Wang
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Laboratory for Experimental Immunodermatology, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christine B Ardon
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Laboratory for Experimental Immunodermatology, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert Kraaij
- Laboratory of Population Genomics, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Errol P Prens
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Laboratory for Experimental Immunodermatology, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kelsey R Van Straalen
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands; Laboratory for Experimental Immunodermatology, Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Vergroesen JE, Jarrar ZA, Weiss S, Frost F, Ansari AS, Nguyen P, Kraaij R, Medina-Gomez C, Völzke H, Tost F, Amin N, van Duijn CM, Klaver CCW, Jürgens C, Hammond CJ, Ramdas WD. Glaucoma Patients Have a Lower Abundance of Butyrate-Producing Taxa in the Gut. Invest Ophthalmol Vis Sci 2024; 65:7. [PMID: 38315494 PMCID: PMC10851784 DOI: 10.1167/iovs.65.2.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Purpose Glaucoma is an eye disease that is the most common cause of irreversible blindness worldwide. It has been suggested that gut microbiota can produce reactive oxygen species and pro-inflammatory cytokines that may travel from the gastric mucosa to distal sites, for example, the optic nerve head or trabecular meshwork. There is evidence for a gut-eye axis, as microbial dysbiosis has been associated with retinal diseases. We investigated the microbial composition in patients with glaucoma and healthy controls. Moreover, we analyzed the association of the gut microbiome with intraocular pressure (IOP; risk factor of glaucoma) and vertical cup-to-disc ratio (VCDR; quantifying glaucoma severity). Methods The discovery analyses included participants of the Rotterdam Study and the Erasmus Glaucoma Cohort. A total of 225 patients with glaucoma and 1247 age- and sex-matched participants without glaucoma were included in our analyses. Stool samples were used to generate 16S rRNA gene profiles. We assessed associations with 233 genera and species. We used data from the TwinsUK and the Study of Health in Pomerania (SHIP) to replicate our findings. Results Several butyrate-producing taxa (e.g. Butyrivibrio, Caproiciproducens, Clostridium sensu stricto 1, Coprococcus 1, Ruminococcaceae UCG 007, and Shuttleworthia) were less abundant in people with glaucoma compared to healthy controls. The same taxa were also associated with lower IOP and smaller VCDR. The replication analyses confirmed the findings from the discovery analyses. Conclusions Large human studies exploring the link between the gut microbiome and glaucoma are lacking. Our results suggest that microbial dysbiosis plays a role in the pathophysiology of glaucoma.
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Affiliation(s)
- Joëlle E. Vergroesen
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Zakariya A. Jarrar
- Department of Ophthalmology, King's College London, London, United Kingdom
- Department of Twins Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Stefan Weiss
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Abdus S. Ansari
- Department of Ophthalmology, King's College London, London, United Kingdom
- Department of Twins Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Picard Nguyen
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Frank Tost
- Department of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Cornelia M. van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| | - Clemens Jürgens
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Chris J. Hammond
- Department of Ophthalmology, King's College London, London, United Kingdom
- Department of Twins Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Wishal D. Ramdas
- Department of Ophthalmology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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Mulders MCF, Audhoe AS, Van Koetsveld PM, Feelders RA, Hofland LJ, de Herder WW, Kraaij R, Hofland J. Midgut neuroendocrine tumor patients have a depleted gut microbiome with a discriminative signature. Eur J Cancer 2024; 197:113472. [PMID: 38100919 DOI: 10.1016/j.ejca.2023.113472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
RATIONALE When compared to other types of cancer, the prevalence of midgut neuroendocrine tumors (NET) has disproportionally increased over the past decades. To date, there has been very little progress in discovering (epi)genetic drivers and treatment options for these tumors. Recent microbiome research has revealed that enteroendocrine cells communicate with the intestinal microbiome and has provided novel treatment targets for various other cancer types. Hence, our aim was to analyze the role of the gut microbiome in midgut NET patients. METHODS Fecal samples, prospectively collected from patients and control subjects, were analyzed with next generation 16S sequencing. Patients with neuroendocrine carcinomas and recent antibiotics use were excluded. Relevant variables were extracted from questionnaires and electronic health records. Microbial composition was compared between patients and controls as well as between groups within the patient cohort. RESULTS 87 midgut NET patients and 95 controls were included. Midgut NET patients had a less rich and diverse gut microbiome than controls (p < 0.001). Moreover, we identified 31 differentially abundant species and a gut microbial signature consisting of 17 species that was predictive of midgut NET presence with an area under the receiver operating characteristic curve of 0.863. Gut microbial composition was not directly associated with the presence of the carcinoid syndrome, tumor grade or multifocality. Nonetheless, we did observe a potential link between microbial diversity and the presence of carcinoid syndrome symptoms within the subset of patients with elevated 5-hydroxyindolacetic acid levels. CONCLUSION Midgut NET patients have an altered gut microbiome which suggests a role in NET development and could provide novel targets for microbiome-based diagnostics and therapeutics.
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Affiliation(s)
- M C F Mulders
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands.
| | - A S Audhoe
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - P M Van Koetsveld
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - R A Feelders
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - L J Hofland
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - W W de Herder
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
| | - R Kraaij
- Laboratory of Population Genomics, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - J Hofland
- ENETS Center of Excellence, Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center and Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
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Bruijstens AL, Molenaar S, Wong YYM, Kraaij R, Neuteboom RF. Gut microbiota analysis in pediatric-onset multiple sclerosis compared to pediatric monophasic demyelinating syndromes and pediatric controls. Eur J Neurol 2023; 30:3507-3515. [PMID: 36209482 DOI: 10.1111/ene.15594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/23/2022] [Accepted: 09/15/2022] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND PURPOSE Gut microbiota dysbiosis may lead to proinflammatory conditions contributing to multiple sclerosis (MS) etiology. Pediatric-onset MS patients are close to biological disease onset and less exposed to confounders. Therefore, this study investigated gut microbiota composition and functional pathways in pediatric-onset MS, compared to monophasic acquired demyelinating syndromes (mADS) and healthy controls (HCs). METHODS Pediatric participants were selected from the Dutch national prospective cohort study including ADS patients and HCs <18 years old. Amplicon sequence variants (ASVs) were generated from sequencing the V3/4 regions of the 16S rRNA gene. Functional MetaCyc microbial pathways were predicted based on Enzyme Commission numbers. Gut microbiota composition (alpha/beta diversity and individual microbe abundance at ASV to phylum level) and predicted functional pathways were tested using nonparametric tests, permutational multivariate analysis of variance, and linear regression. RESULTS Twenty-six pediatric-onset MS (24 with disease-modifying therapy [DMT]), 25 mADS, and 24 HC subjects were included. Alpha/beta diversity, abundance of individual resident microbes, and microbial functional features were not different between these participant groups. Body mass index (BMI) showed significant differences, with obese children having a lower alpha diversity (Chao1 Index p = 0.015, Shannon/Simpson Diversity Index p = 0.014/p = 0.023), divergent beta diversity (R2 = 3.7%, p = 0.013), and higher abundance of numerous individual resident microbes and functional microbial pathways. CONCLUSIONS Previous results of gut microbiota composition and predicted functional features could not be validated in this Dutch pediatric-onset MS cohort using a more sensitive 16S pipeline, although it was limited by sample size and DMT use. Notably, several other host-related factors were found to associate with gut microbiota variation, especially BMI.
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Affiliation(s)
- Arlette L Bruijstens
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sandy Molenaar
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yu Yi M Wong
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rinze F Neuteboom
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
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Amin N, Liu J, Bonnechere B, MahmoudianDehkordi S, Arnold M, Batra R, Chiou YJ, Fernandes M, Ikram MA, Kraaij R, Krumsiek J, Newby D, Nho K, Radjabzadeh D, Saykin AJ, Shi L, Sproviero W, Winchester L, Yang Y, Nevado-Holgado AJ, Kastenmüller G, Kaddurah-Daouk R, van Duijn CM. Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals. JAMA Psychiatry 2023; 80:597-609. [PMID: 37074710 PMCID: PMC10116384 DOI: 10.1001/jamapsychiatry.2023.0685] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/07/2023] [Indexed: 04/20/2023]
Abstract
Importance Metabolomics reflect the net effect of genetic and environmental influences and thus provide a comprehensive approach to evaluating the pathogenesis of complex diseases, such as depression. Objective To identify the metabolic signatures of major depressive disorder (MDD), elucidate the direction of associations using mendelian randomization, and evaluate the interplay of the human gut microbiome and metabolome in the development of MDD. Design, Setting and Participants This cohort study used data from participants in the UK Biobank cohort (n = 500 000; aged 37 to 73 years; recruited from 2006 to 2010) whose blood was profiled for metabolomics. Replication was sought in the PREDICT and BBMRI-NL studies. Publicly available summary statistics from a 2019 genome-wide association study of depression were used for the mendelian randomization (individuals with MDD = 59 851; control individuals = 113 154). Summary statistics for the metabolites were obtained from OpenGWAS in MRbase (n = 118 000). To evaluate the interplay of the metabolome and the gut microbiome in the pathogenesis of depression, metabolic signatures of the gut microbiome were obtained from a 2019 study performed in Dutch cohorts. Data were analyzed from March to December 2021. Main Outcomes and Measures Outcomes were lifetime and recurrent MDD, with 249 metabolites profiled with nuclear magnetic resonance spectroscopy with the Nightingale platform. Results The study included 6811 individuals with lifetime MDD compared with 51 446 control individuals and 4370 individuals with recurrent MDD compared with 62 508 control individuals. Individuals with lifetime MDD were younger (median [IQR] age, 56 [49-62] years vs 58 [51-64] years) and more often female (4447 [65%] vs 2364 [35%]) than control individuals. Metabolic signatures of MDD consisted of 124 metabolites spanning the energy and lipid metabolism pathways. Novel findings included 49 metabolites, including those involved in the tricarboxylic acid cycle (ie, citrate and pyruvate). Citrate was significantly decreased (β [SE], -0.07 [0.02]; FDR = 4 × 10-04) and pyruvate was significantly increased (β [SE], 0.04 [0.02]; FDR = 0.02) in individuals with MDD. Changes observed in these metabolites, particularly lipoproteins, were consistent with the differential composition of gut microbiota belonging to the order Clostridiales and the phyla Proteobacteria/Pseudomonadota and Bacteroidetes/Bacteroidota. Mendelian randomization suggested that fatty acids and intermediate and very large density lipoproteins changed in association with the disease process but high-density lipoproteins and the metabolites in the tricarboxylic acid cycle did not. Conclusions and Relevance The study findings showed that energy metabolism was disturbed in individuals with MDD and that the interplay of the gut microbiome and blood metabolome may play a role in lipid metabolism in individuals with MDD.
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Affiliation(s)
- Najaf Amin
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Bruno Bonnechere
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- REVAL Rehabilitation Research Center, Faculty of Rehabilitation Sciences, Hasselt University, Hasselt, Belgium
- Technology-Supported and Data-Driven Rehabilitation, Data Sciences Institute, Hasselt University, Hasselt, Belgium
| | | | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Richa Batra
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Yu-Jie Chiou
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Marco Fernandes
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Danielle Newby
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Andrew J. Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis
| | - Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - William Sproviero
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Laura Winchester
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom
| | - Yang Yang
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | | | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina
| | - Cornelia M. van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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Chen J, Radjabzadeh D, Medina-Gomez C, Voortman T, van Meurs JBJ, Ikram MA, Uitterlinden AG, Kraaij R, Zillikens MC. Advanced Glycation End Products (AGEs) in Diet and Skin in Relation to Stool Microbiota: The Rotterdam Study. Nutrients 2023; 15:nu15112567. [PMID: 37299529 DOI: 10.3390/nu15112567] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/11/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Advanced glycation end products (AGEs) are involved in age-related diseases, but the interaction of gut microbiota with dietary AGEs (dAGEs) and tissue AGEs in the population is unknown. OBJECTIVE Our objective was to investigate the association of dietary and tissue AGEs with gut microbiota in the population-based Rotterdam Study, using skin AGEs as a marker for tissue accumulation and stool microbiota as a surrogate for gut microbiota. DESIGN Dietary intake of three AGEs (dAGEs), namely carboxymethyl-lysine (CML), N-(5-hydro-5-methyl-4-imidazolon-2-yl)-ornithine (MGH1), and carboxyethyl-lysine (CEL), was quantified at baseline from food frequency questionnaires. Following up after a median of 5.7 years, skin AGEs were measured using skin autofluorescence (SAF), and stool microbiota samples were sequenced (16S rRNA) to measure microbial composition (including alpha-diversity, beta-dissimilarity, and taxonomic abundances) as well as predict microbial metabolic pathways. Associations of both dAGEs and SAF with microbial measures were investigated using multiple linear regression models in 1052 and 718 participants, respectively. RESULTS dAGEs and SAF were not associated with either the alpha-diversity or beta-dissimilarity of the stool microbiota. After multiple-testing correction, dAGEs were not associated with any of the 188 genera tested, but were nominally inversely associated with the abundance of Barnesiella, Colidextribacter, Oscillospiraceae UCG-005, and Terrisporobacter, in addition to being positively associated with Coprococcus, Dorea, and Blautia. A higher abundance of Lactobacillus was associated with a higher SAF, along with several nominally significantly associated genera. dAGEs and SAF were nominally associated with several microbial pathways, but none were statistically significant after multiple-testing correction. CONCLUSIONS Our findings did not solidify a link between habitual dAGEs, skin AGEs, and overall stool microbiota composition. Nominally significant associations with several genera and functional pathways suggested a potential interaction between gut microbiota and AGE metabolism, but validation is required. Future studies are warranted, to investigate whether gut microbiota modifies the potential impact of dAGEs on health.
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Affiliation(s)
- Jinluan Chen
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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9
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Kraaij R, Schuurmans IK, Radjabzadeh D, Tiemeier H, Dinan TG, Uitterlinden AG, Hillegers M, Jaddoe VW, Duijts L, Moll H, Rivadeneira F, Medina-Gomez C, Jansen PW, Cecil CA. The gut microbiome and child mental health: A population-based study. Brain Behav Immun 2023; 108:188-196. [PMID: 36494050 PMCID: PMC7614161 DOI: 10.1016/j.bbi.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
The link between the gut microbiome and the brain has gained increasing scientific and public interest for its potential to explain psychiatric risk. While differences in gut microbiome composition have been associated with several mental health problems, evidence to date has been largely based on animal models and human studies with modest sample sizes. In this cross-sectional study in 1,784 ten-year-old children from the multi-ethnic, population-based Generation R Study, we aimed to characterize associations of the gut microbiome with child mental health problems. Gut microbiome was assessed from stool samples using 16S rRNA sequencing. We focused on overall psychiatric symptoms as well as with specific domains of emotional and behavioral problems, assessed via the maternally rated Child Behavior Checklist. While we observed lower gut microbiome diversity in relation to higher overall and specific mental health problems, associations were not significant. Likewise, we did not identify any taxonomic feature associated with mental health problems after multiple testing correction, although suggestive findings indicated depletion of genera previously associated with psychiatric disorders, including Hungatella, Anaerotruncus and Oscillospiraceae. The identified compositional abundance differences were found to be similar across all mental health problems. Finally, we did not find significant enrichment for specific microbial functions in relation to mental health problems. In conclusion, based on the largest sample examined to date, we do not find clear evidence of associations between gut microbiome diversity, taxonomies or functions and mental health problems in the general pediatric population. In future, the use of longitudinal designs with repeated measurements of microbiome and psychiatric outcomes will be critical to identify whether and when associations between the gut microbiome and mental health emerge across development and into adulthood.
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Affiliation(s)
- Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Isabel K. Schuurmans
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,The Generation R Study Group, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Social and Behavioral Sciences, Harvard. T.H. Chan School of Public Health, Boston, MA, USA
| | - Timothy G. Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Manon Hillegers
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vincent W.V. Jaddoe
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Pediatrics, Divisions of Respiratory Medicine and Allergology, and Neonatology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Henriette Moll
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pauline W. Jansen
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Charlotte A.M. Cecil
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, The Netherlands,Corresponding authors at: Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, Rotterdam, The Netherlands (C. Cecil). addresses: (R. Kraaij), (C.A.M. Cecil)
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10
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Young KL, Fisher V, Deng X, Brody JA, Graff M, Lim E, Lin BM, Xu H, Amin N, An P, Aslibekyan S, Fohner AE, Hidalgo B, Lenzini P, Kraaij R, Medina-Gomez C, Prokić I, Rivadeneira F, Sitlani C, Tao R, van Rooij J, Zhang D, Broome JG, Buth EJ, Heavner BD, Jain D, Smith AV, Barnes K, Boorgula MP, Chavan S, Darbar D, De Andrade M, Guo X, Haessler J, Irvin MR, Kalyani RR, Kardia SLR, Kooperberg C, Kim W, Mathias RA, McDonald ML, Mitchell BD, Peyser PA, Regan EA, Redline S, Reiner AP, Rich SS, Rotter JI, Smith JA, Weiss S, Wiggins KL, Yanek LR, Arnett D, Heard-Costa NL, Leal S, Lin D, McKnight B, Province M, van Duijn CM, North KE, Cupples LA, Liu CT. Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants. HGG Adv 2023; 4:100163. [PMID: 36568030 PMCID: PMC9772568 DOI: 10.1016/j.xhgg.2022.100163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Anthropometric traits, measuring body size and shape, are highly heritable and significant clinical risk factors for cardiometabolic disorders. These traits have been extensively studied in genome-wide association studies (GWASs), with hundreds of genome-wide significant loci identified. We performed a whole-exome sequence analysis of the genetics of height, body mass index (BMI) and waist/hip ratio (WHR). We meta-analyzed single-variant and gene-based associations of whole-exome sequence variation with height, BMI, and WHR in up to 22,004 individuals, and we assessed replication of our findings in up to 16,418 individuals from 10 independent cohorts from Trans-Omics for Precision Medicine (TOPMed). We identified four trait associations with single-nucleotide variants (SNVs; two for height and two for BMI) and replicated the LECT2 gene association with height. Our expression quantitative trait locus (eQTL) analysis within previously reported GWAS loci implicated CEP63 and RFT1 as potential functional genes for known height loci. We further assessed enrichment of SNVs, which were monogenic or syndromic variants within loci associated with our three traits. This led to the significant enrichment results for height, whereas we observed no Bonferroni-corrected significance for all SNVs. With a sample size of ∼20,000 whole-exome sequences in our discovery dataset, our findings demonstrate the importance of genomic sequencing in genetic association studies, yet they also illustrate the challenges in identifying effects of rare genetic variants.
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Affiliation(s)
- Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Virginia Fisher
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Xuan Deng
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Elise Lim
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ping An
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Institute for Public Health Genetics, University of Washington, Seattle, WA 98101, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Petra Lenzini
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ivana Prokić
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Di Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Benjamin D Heavner
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Tempus Labs, Chicago, IL 60654, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza De Andrade
- Health Quantitative Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rita R Kalyani
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Merry-Lynn McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Susan Redline
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Suzanne Leal
- Department of Neurology, Columbia University, New York City, NY, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Michael Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
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11
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Holstege H, Hulsman M, Charbonnier C, Grenier-Boley B, Quenez O, Grozeva D, van Rooij JGJ, Sims R, Ahmad S, Amin N, Norsworthy PJ, Dols-Icardo O, Hummerich H, Kawalia A, Amouyel P, Beecham GW, Berr C, Bis JC, Boland A, Bossù P, Bouwman F, Bras J, Campion D, Cochran JN, Daniele A, Dartigues JF, Debette S, Deleuze JF, Denning N, DeStefano AL, Farrer LA, Fernández MV, Fox NC, Galimberti D, Genin E, Gille JJP, Le Guen Y, Guerreiro R, Haines JL, Holmes C, Ikram MA, Ikram MK, Jansen IE, Kraaij R, Lathrop M, Lemstra AW, Lleó A, Luckcuck L, Mannens MMAM, Marshall R, Martin ER, Masullo C, Mayeux R, Mecocci P, Meggy A, Mol MO, Morgan K, Myers RM, Nacmias B, Naj AC, Napolioni V, Pasquier F, Pastor P, Pericak-Vance MA, Raybould R, Redon R, Reinders MJT, Richard AC, Riedel-Heller SG, Rivadeneira F, Rousseau S, Ryan NS, Saad S, Sanchez-Juan P, Schellenberg GD, Scheltens P, Schott JM, Seripa D, Seshadri S, Sie D, Sistermans EA, Sorbi S, van Spaendonk R, Spalletta G, Tesi N, Tijms B, Uitterlinden AG, van der Lee SJ, Visser PJ, Wagner M, Wallon D, Wang LS, Zarea A, Clarimon J, van Swieten JC, Greicius MD, Yokoyama JS, Cruchaga C, Hardy J, Ramirez A, Mead S, van der Flier WM, van Duijn CM, Williams J, Nicolas G, Bellenguez C, Lambert JC. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's disease. Nat Genet 2022; 54:1786-1794. [PMID: 36411364 PMCID: PMC9729101 DOI: 10.1038/s41588-022-01208-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals-16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-β precursor protein processing, amyloid-β aggregation, lipid metabolism and microglial function in AD.
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Affiliation(s)
- Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Marc Hulsman
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Camille Charbonnier
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Benjamin Grenier-Boley
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Olivier Quenez
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Detelina Grozeva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeroen G J van Rooij
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Rebecca Sims
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Penny J Norsworthy
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Oriol Dols-Icardo
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Holger Hummerich
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Amit Kawalia
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Philippe Amouyel
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Claudine Berr
- Université Montpellier, INSERM, Institute for Neurosciences of Montpellier, Montpellier, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anne Boland
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Paola Bossù
- Experimental Neuro-psychobiology Laboratory, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Femke Bouwman
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Dominique Campion
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | | | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | | | - Stéphanie Debette
- Université Bordeaux, INSERM, Bordeaux Population Health Research Center, Bordeaux, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Nicola Denning
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Boston, MA, USA
| | - Maria Victoria Fernández
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Nick C Fox
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Daniela Galimberti
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda, Ospedale Policlinico, Milan, Italy
- University of Milan, Milan, Italy
| | - Emmanuelle Genin
- Université Brest, INSERM, Etablissement Français du Sang, Centre Hospitalier Universitaire Brest, Unité Mixte de Recherche 1078, GGB, Brest, France
| | - Johan J P Gille
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Clive Holmes
- Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije University, Amsterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marc Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Alberto Lleó
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Lauren Luckcuck
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
| | - Rachel Marshall
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Carlo Masullo
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Alun Meggy
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Adam C Naj
- Penn Neurodegeneration Genomics Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Genomic and Molecular Epidemiology Laboratory, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Florence Pasquier
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, UMR1172, Resources and Research Memory Center (MRRC) of Distalz, Licend, Lille, France
| | - Pau Pastor
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Barcelona, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Rachel Raybould
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Richard Redon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Centre National de la Recherche Scientifique, INSERM, l'institut du Thorax, Nantes, France
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Anne-Claire Richard
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Steffi G Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Stéphane Rousseau
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Natalie S Ryan
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Salha Saad
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Pascual Sanchez-Juan
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jonathan M Schott
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Davide Seripa
- Laboratory for Advanced Hematological Diagnostics, Department of Hematology and Stem Cell Transplant, Lecce, Italy
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
| | - Daoud Sie
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Erik A Sistermans
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Resie van Spaendonk
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Niccolo' Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Betty Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Sven J van der Lee
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - David Wallon
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aline Zarea
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Jordi Clarimon
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Simon Mead
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Julie Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Gaël Nicolas
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France.
| | - Céline Bellenguez
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Jean-Charles Lambert
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
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12
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van Duijn CM, Amin N, Liu J, Bonnechere B, MahmoudianDehkordi S, Arnold M, Batra R, Chiou Y, Fernandes M, Ikram MA, Kraaij R, Krumsiek J, Newby D, Nho K, Radjabzadeh D, Saykin AJ, Shi L, Sproviero W, Winchester LM, Yang Y, Nevado‐Holgado AJ, Kastenmüller G, Kaddurah‐Daouk R. Interplay of the human exposome, metabolome and gut microbiome in dementia and major depression. Alzheimers Dement 2022. [DOI: 10.1002/alz.067261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cornelia M van Duijn
- Nuffield Department of Population Health, University of Oxford Oxford United Kingdom
| | - Najaf Amin
- University of Oxford Oxford United Kingdom
| | - Jun Liu
- University of Oxford Oxford United Kingdom
| | | | - Siamak MahmoudianDehkordi
- Bioinformatics Research Center, Department of Statistics, North Carolina State University Raleigh NC USA
| | | | - Richa Batra
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine New York NY USA
| | - Yu‐Jie Chiou
- Nuffield Department of Population Health, Oxford University Oxford United Kingdom
| | | | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC Rotterdam Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine New York NY USA
| | | | - Kwangsik Nho
- Indiana Alzheimer’s Disease Research Center Indianapolis IN USA
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Andrew J. Saykin
- Department of Radiology and Imaging Services, Indiana University School of Medicine Indianapolis IN USA
| | - Liu Shi
- Department of Psychiatry, University of Oxford Oxford United Kingdom
| | | | | | - Yang Yang
- Department of Computer Science and Engineering Shanghai China
| | | | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
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13
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Pankratz N, Wei P, Brody JA, Chen MH, de Vries PS, Huffman JE, Stimson MR, Auer PL, Boerwinkle E, Cushman M, de Maat MPM, Folsom AR, Franco OH, Gibbs RA, Haagenson KK, Hofman A, Johnsen JM, Kovar CL, Kraaij R, McKnight B, Metcalf GA, Muzny D, Psaty BM, Tang W, Uitterlinden AG, van Rooij JGJ, Dehghan A, O'Donnell CJ, Reiner AP, Morrison AC, Smith NL. Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors. Hum Mol Genet 2022; 31:3120-3132. [PMID: 35552711 PMCID: PMC9476613 DOI: 10.1093/hmg/ddac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 11/12/2022] Open
Abstract
Plasma levels of fibrinogen, coagulation factors VII and VIII and von Willebrand factor (vWF) are four intermediate phenotypes that are heritable and have been associated with the risk of clinical thrombotic events. To identify rare and low-frequency variants associated with these hemostatic factors, we conducted whole-exome sequencing in 10 860 individuals of European ancestry (EA) and 3529 African Americans (AAs) from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and the National Heart, Lung and Blood Institute's Exome Sequencing Project. Gene-based tests demonstrated significant associations with rare variation (minor allele frequency < 5%) in fibrinogen gamma chain (FGG) (with fibrinogen, P = 9.1 × 10-13), coagulation factor VII (F7) (with factor VII, P = 1.3 × 10-72; seven novel variants) and VWF (with factor VIII and vWF; P = 3.2 × 10-14; one novel variant). These eight novel rare variant associations were independent of the known common variants at these loci and tended to have much larger effect sizes. In addition, one of the rare novel variants in F7 was significantly associated with an increased risk of venous thromboembolism in AAs (Ile200Ser; rs141219108; P = 4.2 × 10-5). After restricting gene-based analyses to only loss-of-function variants, a novel significant association was detected and replicated between factor VIII levels and a stop-gain mutation exclusive to AAs (rs3211938) in CD36 molecule (CD36). This variant has previously been linked to dyslipidemia but not with the levels of a hemostatic factor. These efforts represent the largest integration of whole-exome sequence data from two national projects to identify genetic variation associated with plasma hemostatic factors.
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Affiliation(s)
- Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Peng Wei
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jennifer E Huffman
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Center for Population Genomics, MAVERIC, VA Boston Healthcare System, Boston, MA, USA
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont, Colchester, VT, USA
| | - Moniek P M de Maat
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kelly K Haagenson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill M Johnsen
- Research Institute Bloodworks, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christopher J O'Donnell
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Cardiology Section, Department of Medicine, Boston Veterans Administration Healthcare, Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA, USA
- Seattle Epidemiologic Research and Information Center, Veterans Administration Office of Research and Development, Seattle, WA, USA
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14
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Li R, Ahmadizar F, Koromani F, Ghatan S, Roshchupkin G, Zillikens MC, Oei L, Uitterlinden AG, Kraaij R, Kavousi M, Rivadeneira F, Medina-Gomez C. Gut microbiome profiles identified by a machine learning algorithm are correlated with T2D and muscle strength: the Rotterdam Study. Bone Rep 2022. [DOI: 10.1016/j.bonr.2022.101207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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15
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Li Y, van Houten CB, Boers SA, Jansen R, Cohen A, Engelhard D, Kraaij R, Hiltemann SD, Ju J, Fernández D, Mankoc C, González E, de Waal WJ, de Winter-de Groot KM, Wolfs TFW, Meijers P, Luijk B, Oosterheert JJ, Sankatsing SUC, Bossink AWJ, Stein M, Klein A, Ashkar J, Bamberger E, Srugo I, Odeh M, Dotan Y, Boico O, Etshtein L, Paz M, Navon R, Friedman T, Simon E, Gottlieb TM, Pri-Or E, Kronenfeld G, Oved K, Eden E, Stubbs AP, Bont LJ, Hays JP. The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections. PLoS One 2022; 17:e0267140. [PMID: 35436301 PMCID: PMC9015155 DOI: 10.1371/journal.pone.0267140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background The ability to accurately distinguish bacterial from viral infection would help clinicians better target antimicrobial therapy during suspected lower respiratory tract infections (LRTI). Although technological developments make it feasible to rapidly generate patient-specific microbiota profiles, evidence is required to show the clinical value of using microbiota data for infection diagnosis. In this study, we investigated whether adding nasal cavity microbiota profiles to readily available clinical information could improve machine learning classifiers to distinguish bacterial from viral infection in patients with LRTI. Results Various multi-parametric Random Forests classifiers were evaluated on the clinical and microbiota data of 293 LRTI patients for their prediction accuracies to differentiate bacterial from viral infection. The most predictive variable was C-reactive protein (CRP). We observed a marginal prediction improvement when 7 most prevalent nasal microbiota genera were added to the CRP model. In contrast, adding three clinical variables, absolute neutrophil count, consolidation on X-ray, and age group to the CRP model significantly improved the prediction. The best model correctly predicted 85% of the ‘bacterial’ patients and 82% of the ‘viral’ patients using 13 clinical and 3 nasal cavity microbiota genera (Staphylococcus, Moraxella, and Streptococcus). Conclusions We developed high-accuracy multi-parametric machine learning classifiers to differentiate bacterial from viral infections in LRTI patients of various ages. We demonstrated the predictive value of four easy-to-collect clinical variables which facilitate personalized and accurate clinical decision-making. We observed that nasal cavity microbiota correlate with the clinical variables and thus may not add significant value to diagnostic algorithms that aim to differentiate bacterial from viral infections.
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Affiliation(s)
- Yunlei Li
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chantal B. van Houten
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Dan Engelhard
- Division of Paediatric Infectious Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Saskia D. Hiltemann
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jie Ju
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | | | - Wouter J. de Waal
- Department of Paediatrics, Diakonessenhuis, Utrecht, The Netherlands
| | - Karin M. de Winter-de Groot
- Department of Paediatric Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom F. W. Wolfs
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter Meijers
- Department of Paediatrics, Gelderse Vallei Hospital, Ede, The Netherlands
| | - Bart Luijk
- Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Jelrik Oosterheert
- Department of Internal Medicine and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Aik W. J. Bossink
- Department of Respiratory Medicine, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Michal Stein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Adi Klein
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Jalal Ashkar
- Department of Paediatrics, Hillel Yaffe Medical Centre, Hadera, Israel
| | - Ellen Bamberger
- MeMed, Tirat Carmel, Israel
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Isaac Srugo
- Department of Paediatrics, Bnai Zion Medical Centre, Haifa, Israel
| | - Majed Odeh
- Department of Internal Medicine A, Bnai Zion Medical Centre, Haifa, Israel
| | - Yaniv Dotan
- Pulmonary Division, Rambam Health Care Campus, Haifa, Israel
| | | | | | | | | | | | | | | | | | | | | | | | - Andrew P. Stubbs
- Department of Pathology & Clinical Bioinformatics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Louis J. Bont
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - John P. Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
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Verhaar BJH, Hendriksen HMA, de Leeuw FA, Doorduijn AS, van Leeuwenstijn M, Teunissen CE, Barkhof F, Scheltens P, Kraaij R, van Duijn CM, Nieuwdorp M, Muller M, van der Flier WM. Gut Microbiota Composition Is Related to AD Pathology. Front Immunol 2022; 12:794519. [PMID: 35173707 PMCID: PMC8843078 DOI: 10.3389/fimmu.2021.794519] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/31/2021] [Indexed: 12/26/2022] Open
Abstract
IntroductionSeveral studies have reported alterations in gut microbiota composition of Alzheimer’s disease (AD) patients. However, the observed differences are not consistent across studies. We aimed to investigate associations between gut microbiota composition and AD biomarkers using machine learning models in patients with AD dementia, mild cognitive impairment (MCI) and subjective cognitive decline (SCD).Materials and MethodsWe included 170 patients from the Amsterdam Dementia Cohort, comprising 33 with AD dementia (66 ± 8 years, 46%F, mini-mental state examination (MMSE) 21[19-24]), 21 with MCI (64 ± 8 years, 43%F, MMSE 27[25-29]) and 116 with SCD (62 ± 8 years, 44%F, MMSE 29[28-30]). Fecal samples were collected and gut microbiome composition was determined using 16S rRNA sequencing. Biomarkers of AD included cerebrospinal fluid (CSF) amyloid-beta 1-42 (amyloid) and phosphorylated tau (p-tau), and MRI visual scores (medial temporal atrophy, global cortical atrophy, white matter hyperintensities). Associations between gut microbiota composition and dichotomized AD biomarkers were assessed with machine learning classification models. The two models with the highest area under the curve (AUC) were selected for logistic regression, to assess associations between the 20 best predicting microbes and the outcome measures from these machine learning models while adjusting for age, sex, BMI, diabetes, medication use, and MMSE.ResultsThe machine learning prediction for amyloid and p-tau from microbiota composition performed best with AUCs of 0.64 and 0.63. Highest ranked microbes included several short chain fatty acid (SCFA)-producing species. Higher abundance of [Clostridium] leptum and lower abundance of [Eubacterium] ventriosum group spp., Lachnospiraceae spp., Marvinbryantia spp., Monoglobus spp., [Ruminococcus] torques group spp., Roseburia hominis, and Christensenellaceae R-7 spp., was associated with higher odds of amyloid positivity. We found associations between lower abundance of Lachnospiraceae spp., Lachnoclostridium spp., Roseburia hominis and Bilophila wadsworthia and higher odds of positive p-tau status.ConclusionsGut microbiota composition was associated with amyloid and p-tau status. We extend on recent studies that observed associations between SCFA levels and AD CSF biomarkers by showing that lower abundances of SCFA-producing microbes were associated with higher odds of positive amyloid and p-tau status.
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Affiliation(s)
- Barbara J. H. Verhaar
- Department of Internal Medicine - Geriatrics, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Internal and Vascular Medicine, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- *Correspondence: Barbara J. H. Verhaar,
| | - Heleen M. A. Hendriksen
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Francisca A. de Leeuw
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Astrid S. Doorduijn
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Mardou van Leeuwenstijn
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Charlotte E. Teunissen
- Department of Clinical Chemistry, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- University College London (UCL) Institutes of Neurology, Faculty of Brain Sciences, London, United Kingdom
| | - Philip Scheltens
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center (MC), Rotterdam, Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam, Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Majon Muller
- Department of Internal Medicine - Geriatrics, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
| | - Wiesje M. van der Flier
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center (UMC), Amsterdam, Netherlands
- Department of Epidemiology and Data Science, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Verhaar BJ, Hendriksen HM, Leeuw FA, Doorduijn AS, Leeuwenstijn M, Teunissen CE, Berckel BN, Barkhof F, Scheltens P, Kraaij R, Duijn CM, Nieuwdorp M, Muller M, Flier WM. Associations between gut microbiota composition and AD biomarkers. Alzheimers Dement 2021. [DOI: 10.1002/alz.057781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Barbara J.H. Verhaar
- Department of Internal‐Geriatric Medicine Amsterdam UMC location VUMC Amsterdam Cardiovascular Sciences Institute Amsterdam Netherlands
- Department of Internal and Vascular Medicine Amsterdam UMC Amsterdam Netherlands
| | - Heleen M.A. Hendriksen
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Francisca A. Leeuw
- Alzheimer Center Amsterdam Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Astrid S. Doorduijn
- Alzheimer Center Amsterdam Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Mardou Leeuwenstijn
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory Department of Clinical Chemistry Amsterdam Neuroscience Amsterdam UMC VU University Amsterdam Netherlands
| | - Bart N.M. Berckel
- Department of Radiology & Nuclear Medicine Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam Netherlands
| | - Frederik Barkhof
- Institutes of Neurology and Healthcare Engineering University College London London United Kingdom
- Amsterdam UMC VU University Medical Center Amsterdam Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam University Medical Center Amsterdam Amsterdam Netherlands
| | - Robert Kraaij
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
| | - Cornelia M. Duijn
- Nuffield Department of Population Health University of Oxford Oxford United Kingdom
- Department of Epidemiology Erasmus Medical Center Rotterdam Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine Amsterdam UMC Amsterdam Netherlands
| | - Majon Muller
- Department of Internal‐Geriatric Medicine Amsterdam UMC location VUMC Amsterdam Cardiovascular Sciences Institute Amsterdam Netherlands
| | - Wiesje M. Flier
- Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience VU University Medical Center Amsterdam UMC Amsterdam Netherlands
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Ahmad S, Arnold M, Hankemeier T, Ghanbari M, Uitterlinden AG, Kraaij R, Van Duijn CM, Kaddurah‐Daouk RF, Kastenmüller G, Ikram MA. Gut microbiome‐related metabolites in plasma are associated with general cognition. Alzheimers Dement 2021. [DOI: 10.1002/alz.056142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research Leiden Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus Medical Centre Rotterdam Netherlands
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam Netherlands
| | - Cornelia M. Van Duijn
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford United Kingdom
| | - Rima F. Kaddurah‐Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Duke Institute for Brain Sciences, Duke University Durham NC USA
- Department of Medicine, Duke University Durham NC USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
- German Center for Diabetes Research (DZD) Neuherberg Germany
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center Rotterdam Netherlands
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Chen Z, Radjabzadeh D, Chen L, Kurilshikov A, Kavousi M, Ahmadizar F, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, Voortman T. Association of Insulin Resistance and Type 2 Diabetes With Gut Microbial Diversity: A Microbiome-Wide Analysis From Population Studies. JAMA Netw Open 2021; 4:e2118811. [PMID: 34323983 PMCID: PMC8322996 DOI: 10.1001/jamanetworkopen.2021.18811] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
IMPORTANCE Previous studies have indicated that gut microbiome may be associated with development of type 2 diabetes. However, these studies are limited by small sample size and insufficient for confounding. Furthermore, which specific taxa play a role in the development of type 2 diabetes remains unclear. OBJECTIVE To examine associations of gut microbiome composition with insulin resistance and type 2 diabetes in a large population-based setting controlling for various sociodemographic and lifestyle factors. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional analysis included 2166 participants from 2 Dutch population-based prospective cohorts: the Rotterdam Study and the LifeLines-DEEP study. EXPOSURES The 16S ribosomal RNA method was used to measure microbiome composition in stool samples collected between January 1, 2012, and December 31, 2013. The α diversity (Shannon, richness, and Inverse Simpson indexes), β diversity (Bray-Curtis dissimilarity matrix), and taxa (from domain to genus level) were identified to reflect gut microbiome composition. MAIN OUTCOMES AND MEASURES Associations among α diversity, β diversity, and taxa with the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and with type 2 diabetes were examined. Glucose and insulin were measured to calculate the HOMA-IR. Type 2 diabetes cases were identified based on glucose levels and medical records from January 2012 to December 2013. Analyses were adjusted for technical covariates, lifestyle, sociodemographic, and medical factors. Data analysis was performed from January 1, 2018, to December 31, 2020. RESULTS There were 2166 participants in this study: 1418 from the Rotterdam Study (mean [SD] age, 62.4 [5.9] years; 815 [57.5%] male) and 748 from the LifeLines-DEEP study (mean [SD] age, 44.7 [13.4] years; 431 [57.6%] male); from this total, 193 type 2 diabetes cases were identified. Lower microbiome Shannon index and richness were associated with higher HOMA-IR (eg, Shannon index, -0.06; 95% CI, -0.10 to -0.02), and patients with type 2 diabetes had a lower richness than participants without diabetes (odds ratio [OR], 0.93; 95% CI, 0.88-0.99). The β diversity (Bray-Curtis dissimilarity matrix) was associated with insulin resistance (R2 = 0.004, P = .001 in the Rotterdam Study and R2 = 0.005, P = .002 in the LifeLines-DEEP study). A total of 12 groups of bacteria were associated with HOMA-IR or type 2 diabetes. Specifically, a higher abundance of Christensenellaceae (β = -0.08; 95% CI, -0.12 to -0.03: P < .001), Christensenellaceae R7 group (β = -0.07; 95% CI, -0.12 to -0.03; P < .001), Marvinbryantia (β = -0.07; 95% CI, -0.11 to -0.03; P < .001), Ruminococcaceae UCG005 (β = -0.09; 95% CI, -0.13 to -0.05; P < .001), Ruminococcaceae UCG008 (β = -0.07; 95% CI, -0.11 to -0.03; P < .001), Ruminococcaceae UCG010 (β = -0.08; 95% CI, -0.12 to -0.04; P < .001), or Ruminococcaceae NK4A214 group (β = -0.09; 95% CI, -0.13 to -0.05; P < .001) was associated with lower HOMA-IR. A higher abundance of Clostridiaceae 1 (OR, 0.51; 95% CI, 0.41-0.65; P < .001), Peptostreptococcaceae (OR, 0.56; 95% CI, 0.45-0.70; P < .001), C sensu stricto 1 (OR, 0.51; 95% CI, 0.40-0.65; P < .001), Intestinibacter (OR, 0.60; 95% CI, 0.48-0.76; P < .001), or Romboutsia (OR, 0.55; 95% CI, 0.44-0.70; P < .001) was associated with less type 2 diabetes. These bacteria are all known to produce butyrate. CONCLUSIONS AND RELEVANCE In this cross-sectional study, higher microbiome α diversity, along with more butyrate-producing gut bacteria, was associated with less type 2 diabetes and with lower insulin resistance among individuals without diabetes. These findings could help provide insight into the etiology, pathogenesis, and treatment of type 2 diabetes.
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Affiliation(s)
- Zhangling Chen
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Andre G. Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
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Mulder M, Arp PP, Kiefte-de Jong JC, Uitterlinden AG, Klaassen CHW, Kraaij R, Goessens WHF, Verbon A, Stricker BH. Prevalence of and risk factors for extended-spectrum beta-lactamase genes carriership in a population-based cohort of middle-aged and elderly. Int J Antimicrob Agents 2021; 58:106388. [PMID: 34161788 DOI: 10.1016/j.ijantimicag.2021.106388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 05/17/2021] [Accepted: 06/13/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Increasing resistance to beta-lactam antibiotics is an alarming development worldwide. Fecal carriership of TEM, SHV, CTX-M and CMY was studied in a community-dwelling population of middle-aged and elderly individuals. PATIENTS AND METHODS Feces was obtained from individuals of the Rotterdam Study. Carriership of the TEM, SHV, CTX-M and CMY genes was determined using real-time polymerase chain reaction (qPCR). Possible associations were investigated between carriership of these genes and several risk factors, such as the use of antimicrobial drugs, diabetes mellitus, protein pump inhibitor (PPI) use, travelling, the composition of the gut microbiota, and intake of certain foods. RESULTS The most prevalent gene was TEM (53.0%), followed by SHV (18.4%), CTX-M (5.4%) and CMY (3.6%). Use of penicillins with extended spectrum was associated with TEM carriership, whereas use of macrolides and lincosamides was associated with TEM and SHV carriership. Interestingly, use of PPIs was associated with a higher prevalence of carriership of TEM, SHV and CMY (TEM: odds ratio [OR] 1.34; 95% confidence interval [CI] 1.05-1.77; SHV: OR 2.17; 95%CI 1.55-2.87; CMY: OR 2.26; 95%CI 1.23-4.11). Furthermore, associations were found between the richness and composition of the gut microbiota and TEM and SHV carriership. CONCLUSIONS The prevalence of carriership of TEM was substantial, but the prevalence of carriership of the extended-spectrum β-lactamase gene, CTX-M and the AmpC β-lactamase gene, CMY was relatively low in this community-dwelling, population-based cohort. The composition of the microbiota might play a role in the retention of resistance genes, but future studies are necessary to further elucidate this relationship.
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Affiliation(s)
- M Mulder
- Department of Epidemiology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Medical Microbiology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - P P Arp
- Department of Internal Medicine, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - J C Kiefte-de Jong
- Department of Epidemiology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Public Health and Primary Care/LUMC Campus, The Hague, Leiden University Medical Center, The Netherlands
| | - A G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - C H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - R Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - W H F Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - A Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - B H Stricker
- Department of Epidemiology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Department of Internal Medicine, Erasmus MC University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands; Inspectorate of Health Care, PO Box 2518, 6401 DA Heerlen, The Netherlands.
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21
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Sanders MGH, Nijsten T, Verlouw J, Kraaij R, Pardo LM. Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study. PLoS One 2021; 16:e0251136. [PMID: 34029350 PMCID: PMC8143393 DOI: 10.1371/journal.pone.0251136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/20/2021] [Indexed: 12/26/2022] Open
Abstract
Background Seborrheic dermatitis (SD) is a chronic inflammatory skin disease with a multifactorial aetiology. Malassezia yeasts have been associated with the disease but the role of bacterial composition in SD has not been thoroughly investigated. Objectives To profile the bacterial microbiome of SD patients and compare this with the microbiome of individuals with no inflammatory skin disease (controls). Methods This was a cross sectional study embedded in a population-based study. Skin swabs were taken from naso-labial fold from patients with seborrheic dermatitis (lesional skin: n = 22; non-lesional skin SD: n = 75) and controls (n = 465). Sample collection began in 2016 at the research facility and is still ongoing. Shannon and Chao1 α- diversity metrics were calculated per group. Associations between the microbiome composition of cases and controls was calculated using multivariate statistics (permANOVA) and univariate statistics. Results We found an increased α-diversity between SD lesional cases versus controls (Shannon diversity: Kruskal-Wallis rank sum: Chi-squared: 19.06; global p-value = 7.7x10-5). Multivariate statistical analysis showed significant associations in microbiome composition when comparing lesional SD skin to controls (p-value = 0.03;R2 = 0.1%). Seven out of 13 amplicon sequence variants (ASVs) that were significantly different between controls and lesional cases were members of the genus Staphylococcus, most of which showed increased composition in lesional cases, and were closely related to S. capitis S. caprae and S. epidermidis. Conclusion Microbiome composition differs in patients with seborrheic dermatitis and individuals without diseases. Differences were mainly found in the genus Staphylococcus.
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Affiliation(s)
| | - Tamar Nijsten
- Department of Dermatology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Joost Verlouw
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Luba M. Pardo
- Department of Dermatology, Erasmus Medical Centre, Rotterdam, The Netherlands
- * E-mail:
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Hu C, van Meel ER, Medina-Gomez C, Kraaij R, Barroso M, Kiefte-de Jong J, Radjabzadeh D, Pasmans SGMA, de Jong NW, de Jongste JC, Moll HA, Nijsten T, Rivadeneira F, Pardo LM, Duijts L. A population-based study on associations of stool microbiota with atopic diseases in school-age children. J Allergy Clin Immunol 2021; 148:612-620. [PMID: 33862008 DOI: 10.1016/j.jaci.2021.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Infants with less diverse gut microbiota seem to have higher risks of atopic diseases in early life, but any associations at school age are unclear. OBJECTIVES This study sought to examine the associations of diversity, relative abundance, and functional pathways of stool microbiota with atopic diseases in school-age children. METHODS We performed a cross-sectional study within an existing population-based prospective cohort among 1440 children 10 years of age. On stool samples, 16S ribosomal RNA gene sequencing was performed, and taxonomic and functional tables were produced. Physician-diagnosed eczema, allergy, and asthma were measured by questionnaires, allergic sensitization by skin prick tests, and lung function by spirometry. RESULTS The α-diversity of stool microbiota was associated with a decreased risk of eczema (odds ratio [OR], 0.98; 95% CI, 0.97, 1.00), and β-diversity was associated with physician-diagnosed inhalant allergy (R2 = 0.001; P = .047). Lachnospiraceae, Ruminococcaceae_UCG-005, and Christensenellaceae_R-7_group species were associated with decreased risks of eczema, inhalant allergic sensitization, and physician-diagnosed inhalant allergy (OR range, 0.88-0.94; 95% CI range, 0.79-0.96 to 0.88-0.98), while Agathobacter species were associated with an increased risk of physician-diagnosed inhalant allergy (OR, 1.23; 95% CI, 1.08-1.42). Functional pathways related to heme and terpenoid biosynthesis were associated with decreased risks of physician-diagnosed inhalant allergy and asthma (OR range, 0.89-0.86; 95% CI range, 0.80-0.99 to 0.73-1.02). No associations of stool microbiota with lung function were observed. CONCLUSIONS The diversity, relative abundance and functional pathways of stool microbiota were most consistently associated with physician-diagnosed inhalant allergy in school-age children and less consistently with other atopic diseases.
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Affiliation(s)
- Chen Hu
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Evelien R van Meel
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Division of Respiratory Medicine and Allergolog, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Monica Barroso
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jessica Kiefte-de Jong
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Public Health and Primary Care/Leiden University Medical Center Campus The Hague, Leiden University Medical Center, Leiden, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Suzanne G M A Pasmans
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicolette W de Jong
- Divison of Allergy and Clinical Immunology, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Division of Respiratory Medicine and Allergolog, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luba M Pardo
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Division of Respiratory Medicine and Allergolog, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Alferink LJM, Radjabzadeh D, Erler NS, Vojinovic D, Medina-Gomez C, Uitterlinden AG, de Knegt RJ, Amin N, Ikram MA, Janssen HLA, Kiefte-de Jong JC, Metselaar HJ, van Duijn CM, Kraaij R, Darwish Murad S. Microbiomics, Metabolomics, Predicted Metagenomics, and Hepatic Steatosis in a Population-Based Study of 1,355 Adults. Hepatology 2021; 73:968-982. [PMID: 32530501 DOI: 10.1002/hep.31417] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/15/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Previous small studies have appraised the gut microbiome (GM) in steatosis, but large-scale studies are lacking. We studied the association of the GM diversity and composition, plasma metabolites, predicted functional metagenomics, and steatosis. APPROACH AND RESULTS This is a cross-sectional analysis of the prospective population-based Rotterdam Study. We used 16S ribosomal RNA gene sequencing and determined taxonomy using the SILVA reference database. Alpha diversity and beta diversity were calculated using the Shannon diversity index and Bray-Curtis dissimilarities. Differences were tested across steatosis using permutational multivariate analysis of variance. Hepatic steatosis was diagnosed by ultrasonography. We subsequently selected genera using regularized regression. The functional metagenome was predicted based on the GM using Kyoto Encyclopedia of Genes and Genomes pathways. Serum metabolomics were assessed using high-throughput proton nuclear magnetic resonance. All analyses were adjusted for age, sex, body mass index, alcohol, diet, and proton-pump inhibitors. We included 1,355 participants, of whom 472 had steatosis. Alpha diversity was lower in steatosis (P = 1.1∙10-9 ), and beta diversity varied across steatosis strata (P = 0.001). Lasso selected 37 genera of which three remained significantly associated after adjustment (Coprococcus3: β = -65; Ruminococcus Gauvreauiigroup: β = 62; and Ruminococcus Gnavusgroup: β = 45, Q-value = 0.037). Predicted metagenome analyses revealed that pathways of secondary bile-acid synthesis and biotin metabolism were present, and D-alanine metabolism was absent in steatosis. Metabolic profiles showed positive associations for aromatic and branched chain amino acids and glycoprotein acetyls with steatosis and R. Gnavusgroup, whereas these metabolites were inversely associated with alpha diversity and Coprococcus3. CONCLUSIONS We confirmed, on a large-scale, the lower microbial diversity and association of Coprococcus and Ruminococcus Gnavus with steatosis. We additionally showed that steatosis and alpha diversity share opposite metabolic profiles.
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Affiliation(s)
- Louise J M Alferink
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamthe Netherlands
| | - Djawad Radjabzadeh
- Department of Internal MedicineErasmus Medical CenterRotterdamthe Netherlands
| | - Nicole S Erler
- Department of BiostatisticsErasmus Medical CenterRotterdamthe Netherlands
| | - Dina Vojinovic
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | | | - André G Uitterlinden
- Department of Internal MedicineErasmus Medical CenterRotterdamthe Netherlands.,Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamthe Netherlands
| | - Najaf Amin
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands
| | - Harry L A Janssen
- Toronto Center of Liver DiseaseToronto General HospitalUniversity Health NetworkTorontoOntarioCanada
| | - Jessica C Kiefte-de Jong
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands.,Department of Public Health and Primary Care/LUMC Campus The HagueLeiden University Medical CenterLeidenthe Netherlands
| | - Herold J Metselaar
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamthe Netherlands
| | - Cornelia M van Duijn
- Department of EpidemiologyErasmus Medical CenterRotterdamthe Netherlands.,Nuffield Department of Population HealthUniversity of OxfordOxfordUnited Kingdom
| | - Robert Kraaij
- Department of Internal MedicineErasmus Medical CenterRotterdamthe Netherlands
| | - Sarwa Darwish Murad
- Department of Gastroenterology and HepatologyErasmus Medical CenterRotterdamthe Netherlands
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24
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Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet 2021; 53:156-165. [PMID: 33462485 PMCID: PMC8515199 DOI: 10.1038/s41588-020-00763-1] [Citation(s) in RCA: 566] [Impact Index Per Article: 188.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10-8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10-20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10-10 < P < 5 × 10-8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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Affiliation(s)
- Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ayse Demirkan
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Section of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey, Guildford, UK
| | - Caroline I Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Juan Antonio Raygoza Garay
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Casey T Finnicum
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
| | - Xingrong Liu
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Williams Turpin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kreete Lüll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Elad Barkan
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Myriam Fornage
- Institute of Molecular Medicine McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanna Szopinska-Tokov
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Larbi Bedrani
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Hans Bisgaard
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kenneth Croitoru
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gareth E Davies
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liesbeth Duijts
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Richard G Ijzerman
- Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Vincent W V Jaddoe
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Torben Jørgensen
- Centre for Clinical Research and Prevention, Bispebjerg/Frederiksberg Hospital, Capital Region of Copenhagen and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Keszthelyi
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation and Department of Bioengeering, University of California, San Diego, La Jolla, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matthias Laudes
- Department of Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Bethesda, MD, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Aldons J Lusis
- Departments of Microbiology, Immunology and Molecular Genetics, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Zlatan Mujagic
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Qi Qibin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daphna Rothschild
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hocheol Shin
- Department of Family Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Raul Y Tito
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Susanna Walter
- Department of Biomedical and Clinical Sciences, University of Linköping, Linköping, Sweden
- Department of Gastroenterology, County Council of Östergötland, Linköping, Sweden
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, the Netherlands
| | - Stefan Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank U Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Omer Weissbrod
- School of Public Health, Harvard University, Boston, MA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gonneke Willemsen
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daisy M A E Jonkers
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Alejandro Arias Vasquez
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam UMC, Amsterdam, the Netherlands
| | - Katie A Meyer
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Jakob Stokholm
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eran Segal
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elin Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica, National Research Council, Monserrato, Italy
| | - Mauro D'Amato
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Science Foundation, Bilbao, Spain
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew D Paterson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Lam SY, Radjabzadeh D, Eppinga H, Nossent YRA, van der Zee HH, Kraaij R, Konstantinov SR, Fuhler GM, Prens EP, Thio HB, Peppelenbosch MP. A microbiome study to explore the gut-skin axis in hidradenitis suppurativa. J Dermatol Sci 2021; 101:218-220. [PMID: 33423845 DOI: 10.1016/j.jdermsci.2020.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Suk Yee Lam
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Hester Eppinga
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, The Netherlands; Department of Dermatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Yoena Roos Anna Nossent
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | | | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, The Netherlands
| | | | - Gwenny Manel Fuhler
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Errol Prospero Prens
- Department of Dermatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Hok Bing Thio
- Department of Dermatology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Maikel Petrus Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, The Netherlands.
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26
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Bonnechère B, Karamujić‐Čomić H, Radjabzadeh D, Ahmad S, Ikram MA, Hankemeier T, Kaddurah‐Daouk RF, Uitterlinden AG, Amin N, Kraaij R, van Duijn CM. The role of the gut microbiome in cognitive function and Alzheimer’s disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.043197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Djawad Radjabzadeh
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
| | - Shahzad Ahmad
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Thomas Hankemeier
- Erasmus University Medical Center Rotterdam Netherlands
- Leiden University Leiden Netherlands
| | | | - André G. Uitterlinden
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
| | - Najaf Amin
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Robert Kraaij
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
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27
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Karamujić‐Čomić H, Ahmad S, Radjabzadeh D, Bonnechere B, Kaddurah‐Daouk RF, Kraaij R, Ikram MA, Amin N, van Duijn CM. Clostridium
shows a higher abundance in less neurovascular and neurodegenerative changes: A microbiome‐wide association study. Alzheimers Dement 2020. [DOI: 10.1002/alz.044743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hata Karamujić‐Čomić
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Shahzad Ahmad
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
| | - Bruno Bonnechere
- Nuffield Department of Population Health University of Oxford Oxford United Kingdom
| | - Rima F. Kaddurah‐Daouk
- Department of Medicine Duke University Durham NC USA
- Department of Psychiatry and Behavioral Sciences Duke University Durham NC USA
| | - Robert Kraaij
- Department of Internal Medicine Erasmus University Medical Center Rotterdam Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Najaf Amin
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology Erasmus University Medical Center Rotterdam Netherlands
- Nuffield Department of Population Health University of Oxford Oxford United Kingdom
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Mulder M, Radjabzadeh D, Kiefte-de Jong JC, Uitterlinden AG, Kraaij R, Stricker BH, Verbon A. Long-term effects of antimicrobial drugs on the composition of the human gut microbiota. Gut Microbes 2020; 12:1795492. [PMID: 32991820 PMCID: PMC7781642 DOI: 10.1080/19490976.2020.1791677] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Antimicrobial drugs are known to have effects on the human gut microbiota. We studied the long-term temporal relationship between several antimicrobial drug groups and the composition of the human gut microbiota determined in feces samples. METHODS Feces samples were obtained from a community-dwelling cohort of middle-aged and elderly individuals (Rotterdam Study). Bacterial DNA was isolated and sequenced using V3/V4 16 S ribosomal RNA sequencing (Illumina MiSeq). The time between the last prescription of several antimicrobial drug groups and the day of sampling was categorized into 0-12, 12-24, 24-48 and >48 months. The effects of the antimicrobial drug groups on the Shannon alpha-diversity (diversity), the Bray-Curtis beta-diversity (community structure), the Firmicutes/Bacteroidetes (F/B) ratio and individual genera were determined. RESULTS We studied the gut microbiota of 1413 individuals (57.5% female, median age 62.6 years). The alpha-diversity was significantly lower up to 4 years after prescriptions of macrolides and lincosamides. It was also lower in the first year after the use of beta-lactams. The community structure (beta-diversity) of the microbiota was significantly different up to 4 years for macrolides and lincosamides, the first year for beta-lactams and at least the first year for quinolones. For the F/B ratio, drugs with a high anaerobic activity shifted the ratio toward Firmicutes in the first year whereas other antimicrobial drugs shifted the ratio toward Bacteroidetes. CONCLUSION Use of antimicrobial drugs is associated with a shift in the composition of the gut microbiota.These effects differ in strength and duration, depending on the antimicrobial drug group used. These findings should be considered when prescribing antimicrobial drugs.
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Affiliation(s)
- M. Mulder
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands,Youth and Healthcare Inspectorate, Heerlen, The Netherlands
| | - D. Radjabzadeh
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - J. C. Kiefte-de Jong
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands,Department of Public Health and Primary Care, LUMC, The Hague, The Netherlands
| | - A. G. Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - R. Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - B. H. Stricker
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands,Youth and Healthcare Inspectorate, Heerlen, The Netherlands,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands,CONTACT B. H. Stricker Department of Epidemiology, Erasmus MC Rotterdam, PO Box 2040, Rotterdam, CA 3000, The Netherlands
| | - A. Verbon
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands,Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
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29
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Dijkstra-de Neijs L, Leenen PJM, Hays JP, van der Valk ES, Kraaij R, van Rossum EFC, Ester WA. Biological Consequences of Psychological Distress in Caregivers of Children with Autism Spectrum Disorder and its Potential Relevance to Other Chronic Diseases Including Cancer. CURR EPIDEMIOL REP 2020. [DOI: 10.1007/s40471-020-00237-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abstract
Purpose of Review
Caregivers of children with a chronic illness are a neglected group in medical research and patient care, and are frequently confronted with chronic psychological distress. The biological consequences of this chronic distress are unclear but highly relevant, as these caregivers have a lifelong task in caring for their child. In this review, the authors specifically describe caregiver distress related to autism spectrum disorder (ASD), but the review may be relevant to other chronic diseases, including cancer.
Recent Findings
Epidemiological evidence illustrates the increased mortality risk in caregivers of children with ASD although some individual factors appear to diminish these risks. Biological studies demonstrate that caregiver distress can lead to dysregulation of the hypothalamic-pituitary-adrenal-axis, a pro-inflammatory state of the immune and central nervous system, and gut microbiome imbalance.
Summary
Caregivers of children with a chronic illness like ASD deserve more health-related attention with respect to their psychological and physical well-being. Such attention would benefit individual caregivers, as well as their children, as both are highly interconnected. Structural psychological and physical screening of caregivers can be considered.
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30
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Chen Z, Radjabzadeh D, Ikram A, Uitterlinden A, Kraaij R, Voortman T. Dietary Patterns and Gut Microbiome Composition in a Large Population-Based Cohort. Curr Dev Nutr 2020. [DOI: 10.1093/cdn/nzaa046_014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
Effects of diet on health and disease risk may be mediated by changes in gut microbiome composition. Our aim was to examine associations between intake of food groups and overall diet quality with gut microbiome composition in a large population-based cohort.
Methods
We analyzed data of 1130 participants (median age 57 years) from the Rotterdam Study, a population-based cohort study in the Netherlands. We measured dietary intake using a 389-item FFQ, and assessed adherence to dietary guidelines for 14 food groups and combined into a diet quality score. We assessed gut microbiome composition using 16S rRNA gene sequencing. Data were available for 11 phyla, 19 classes, 25 orders, 44 families, and 184 genera. Alpha diversity was quantified by Shannon index and Richness, and beta diversity was qualified by Bray-Curtis distance. We used linear models to examine associations with Shannon index and Richness, Adonis function to examine variations of Bray-Curtis distance, and Multivariate Association with Linear Models to examine associations with gut microbial communities. Models were adjusted for technical covariates, energy intake, age, sex, physical activity, education, smoking and BMI.
Results
After adjustment, higher diet quality was associated with more alpha diversity and explained part of the variation in beta diversity (P < 0.001). Overall diet quality was associated with relative abundance of four families (Erysipelotrichaceae, Ruminococcaceae, Lachnospiraceae, Christensenellaceae), and 15 genera (Torques group, RuminococcaceaeUCG002, RuminococcaceaeUCG003, RuminococcaceaeUCG005, RuminococcaceaeUCG010, Xylanophilum group, Blautia, RuminococcaceaeNK4A214 group, Eligens group, Coprococcus3, Senegalimassilia, Lachnospira, Halliigroup, ChristensenellaceaeR7 group, Ventriosum group) (adjusted p: q < 0.05). Results were not explained by any single food group. Higher intake of fruits, vegetables, whole grains, and tea, and lower intake of red meat and alcohol were all related to microbiome composition. Replication analyses are ongoing.
Conclusions
Better overall diet quality may improve overall gut microbial diversity. Furthermore, diet quality may influence abundance of certain gut microbial communities, several of which have previously been linked to lower risk of metabolic and inflammatory diseases.
Funding Sources
N/A.
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Affiliation(s)
- Zhangling Chen
- Department of Epidemiology, Erasmus University Medical Center Rotterdam
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam
| | - Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center Rotterdam
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center Rotterdam
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31
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van der Spek A, Warner SC, Broer L, Nelson CP, Vojinovic D, Ahmad S, Arp PP, Brouwer RWW, Denniff M, van den Hout MCGN, van Rooij JGJ, Kraaij R, van IJcken WFJ, Samani NJ, Ikram MA, Uitterlinden AG, Codd V, Amin N, van Duijn CM. Exome Sequencing Analysis Identifies Rare Variants in ATM and RPL8 That Are Associated With Shorter Telomere Length. Front Genet 2020; 11:337. [PMID: 32425970 PMCID: PMC7204400 DOI: 10.3389/fgene.2020.00337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/20/2020] [Indexed: 01/04/2023] Open
Abstract
Telomeres are important for maintaining genomic stability. Telomere length has been associated with aging, disease, and mortality and is highly heritable (∼82%). In this study, we aimed to identify rare genetic variants associated with telomere length using whole-exome sequence data. We studied 1,303 participants of the Erasmus Rucphen Family (ERF) study, 1,259 of the Rotterdam Study (RS), and 674 of the British Heart Foundation Family Heart Study (BHF-FHS). We conducted two analyses, first we analyzed the family-based ERF study and used the RS and BHF-FHS for replication. Second, we combined the summary data of the three studies in a meta-analysis. Telomere length was measured by quantitative polymerase chain reaction in blood. We identified nine rare variants significantly associated with telomere length (p-value < 1.42 × 10–7, minor allele frequency of 0.2–0.5%) in the ERF study. Eight of these variants (in C11orf65, ACAT1, NPAT, ATM, KDELC2, and EXPH5) were located on chromosome 11q22.3 that contains ATM, a gene involved in telomere maintenance. Although we were unable to replicate the variants in the RS and BHF-FHS (p-value ≥ 0.21), segregation analysis showed that all variants segregate with shorter telomere length in a family. In the meta-analysis of all studies, a nominally significant association with LTL was observed with a rare variant in RPL8 (p-value = 1.48 × 10−6), which has previously been associated with age. Additionally, a novel rare variant in the known RTEL1 locus showed suggestive evidence for association (p-value = 1.18 × 10–4) with LTL. To conclude, we identified novel rare variants associated with telomere length. Larger samples size are needed to confirm these findings and to identify additional variants.
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Affiliation(s)
- Ashley van der Spek
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,SkylineDx B.V., Rotterdam, Netherlands
| | - Sophie C Warner
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Pascal P Arp
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Jeroen G J van Rooij
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Neurology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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32
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Giacco A, delli Paoli G, Simiele R, Caterino M, Ruoppolo M, Bloch W, Kraaij R, Uitterlinden AG, Santillo A, Senese R, Cioffi F, Silvestri E, Iervolino S, Lombardi A, Moreno M, Goglia F, Lanni A, de Lange P. Exercise with food withdrawal at thermoneutrality impacts fuel use, the microbiome, AMPK phosphorylation, muscle fibers, and thyroid hormone levels in rats. Physiol Rep 2020; 8:e14354. [PMID: 32034884 PMCID: PMC7007447 DOI: 10.14814/phy2.14354] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/06/2023] Open
Abstract
Exercise under fasting conditions induces a switch to lipid metabolism, eliciting beneficial metabolic effects. Knowledge of signaling responses underlying metabolic adjustments in such conditions may help to identify therapeutic strategies. Therefore, we studied the effect of mild exercise on rats submitted to food withdrawal at thermoneutrality (28°C) for 3 days. Animals were housed at thermoneutrality rather than the standard housing temperature (22°C) to avoid beta-adrenergic signaling responses that themselves affect metabolism and well-being. Quantitative analysis of multi-organ mRNA levels, myofibers, and serum metabolites shows that this protocol (a) boosts fat oxidation in muscle and liver, (b) reduces lipogenesis and increases gluconeogenesis in liver, (c) increases serum acylcarnitines (especially C4 OH) and ketone bodies and the use of the latter as fuel in muscle, (d) increases Type I myofibers, and (e) is associated with an increased thyroid hormone uptake and metabolism in muscle. In addition, stool microbiome DNA analysis revealed that food withdrawal dramatically alters the presence of bacterial genera associated with ketone metabolism. Taken together, this protocol induces a drastic switch toward increased lipid and ketone metabolism compared to exercise or food withdrawal alone, which may prove beneficial and may involve local thyroid hormones, which may be regarded as exercise mimetics.
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Affiliation(s)
- Antonia Giacco
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Giuseppe delli Paoli
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
| | - Roberta Simiele
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
| | - Marianna Caterino
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico IINaplesItaly
- Ceinge–Biotecnologie AvanzateNaplesItaly
- Divulgazione Scientifica Multidisciplinare per la Sostenibilità Ricerca, FormazioneCultura (DiSciMuS RCF)NaplesItaly
| | - Margherita Ruoppolo
- Dipartimento di Medicina Molecolare e Biotecnologie MedicheUniversità degli Studi di Napoli Federico IINaplesItaly
- Ceinge–Biotecnologie AvanzateNaplesItaly
- Divulgazione Scientifica Multidisciplinare per la Sostenibilità Ricerca, FormazioneCultura (DiSciMuS RCF)NaplesItaly
| | - Wilhelm Bloch
- Department of Molecular and Cellular Sport MedicineInstitute of Cardiovascular Research and Sport MedicineGerman Sport University CologneCologneGermany
| | - Robert Kraaij
- Genetic LaboratoryDepartment of Internal MedicineErasmus Medical CenterRotterdamThe Netherlands
| | - André G. Uitterlinden
- Genetic LaboratoryDepartment of Internal MedicineErasmus Medical CenterRotterdamThe Netherlands
| | - Alessandra Santillo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
| | - Rosalba Senese
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
| | - Federica Cioffi
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Elena Silvestri
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Stefania Iervolino
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Assunta Lombardi
- Dipartimento di BiologiaUniversità degli Studi di Napoli "Federico II"NaplesItaly
| | - Maria Moreno
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Fernando Goglia
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
| | - Antonia Lanni
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
| | - Pieter de Lange
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e FarmaceuticheUniversità degli Studi della Campania Luigi VanvitelliCasertaItaly
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33
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Liu J, Lahousse L, Nivard MG, Bot M, Chen L, van Klinken JB, Thesing CS, Beekman M, van den Akker EB, Slieker RC, Waterham E, van der Kallen CJH, de Boer I, Li-Gao R, Vojinovic D, Amin N, Radjabzadeh D, Kraaij R, Alferink LJM, Murad SD, Uitterlinden AG, Willemsen G, Pool R, Milaneschi Y, van Heemst D, Suchiman HED, Rutters F, Elders PJM, Beulens JWJ, van der Heijden AAWA, van Greevenbroek MMJ, Arts ICW, Onderwater GLJ, van den Maagdenberg AMJM, Mook-Kanamori DO, Hankemeier T, Terwindt GM, Stehouwer CDA, Geleijnse JM, 't Hart LM, Slagboom PE, van Dijk KW, Zhernakova A, Fu J, Penninx BWJH, Boomsma DI, Demirkan A, Stricker BHC, van Duijn CM. Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug-metabolite atlas. Nat Med 2020; 26:110-117. [PMID: 31932804 DOI: 10.1038/s41591-019-0722-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022]
Abstract
Progress in high-throughput metabolic profiling provides unprecedented opportunities to obtain insights into the effects of drugs on human metabolism. The Biobanking BioMolecular Research Infrastructure of the Netherlands has constructed an atlas of drug-metabolite associations for 87 commonly prescribed drugs and 150 clinically relevant plasma-based metabolites assessed by proton nuclear magnetic resonance. The atlas includes a meta-analysis of ten cohorts (18,873 persons) and uncovers 1,071 drug-metabolite associations after evaluation of confounders including co-treatment. We show that the effect estimates of statins on metabolites from the cross-sectional study are comparable to those from intervention and genetic observational studies. Further data integration links proton pump inhibitors to circulating metabolites, liver function, hepatic steatosis and the gut microbiome. Our atlas provides a tool for targeted experimental pharmaceutical research and clinical trials to improve drug efficacy, safety and repurposing. We provide a web-based resource for visualization of the atlas (http://bbmri.researchlumc.nl/atlas/).
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Affiliation(s)
- Jun Liu
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands. .,Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Lies Lahousse
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Michel G Nivard
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Mariska Bot
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Bert van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands.,Department of Clinical Chemistry, Laboratory Genetic Metabolic Disease, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Carisha S Thesing
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Marian Beekman
- Department of Biomedical Data Sciences, section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik Ben van den Akker
- Department of Biomedical Data Sciences, section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, the Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Roderick C Slieker
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eveline Waterham
- Division of Human Nutrition and Health, Wageningen University, Wageningen, the Netherlands
| | - Carla J H van der Kallen
- Department of Internal Medicine, Maastricht University, Maastricht, the Netherlands.,School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Irene de Boer
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Louise J M Alferink
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Rene Pool
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Yuri Milaneschi
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - H Eka D Suchiman
- Department of Biomedical Data Sciences, section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Femke Rutters
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Petra J M Elders
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of General Practice and Elderly Care Medicine, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Joline W J Beulens
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Amber A W A van der Heijden
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of General Practice and Elderly Care Medicine, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine, Maastricht University, Maastricht, the Netherlands.,School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Ilja C W Arts
- School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands.,Department of Epidemiology, Maastricht University, Maastricht, the Netherlands.,Maastricht Center for Systems Biology, Maastricht University, Maastricht, the Netherlands
| | | | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas Hankemeier
- Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands.,Netherlands Metabolomics Center, Leiden, the Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Coen D A Stehouwer
- Department of Internal Medicine, Maastricht University, Maastricht, the Netherlands.,School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Johanna M Geleijnse
- Division of Human Nutrition and Health, Wageningen University, Wageningen, the Netherlands
| | - Leen M 't Hart
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.,Department of Biomedical Data Sciences, section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands.,Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Brenda W J H Penninx
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands.,Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Ayşe Demirkan
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands.,Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Bruno H C Stricker
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.,Inspectorate of Healthcare, The Hague, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands. .,Nuffield Department of Population Health, University of Oxford, Oxford, UK. .,Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands.
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Vojinovic D, Radjabzadeh D, Kurilshikov A, Amin N, Wijmenga C, Franke L, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, van Duijn CM. Relationship between gut microbiota and circulating metabolites in population-based cohorts. Nat Commun 2019; 10:5813. [PMID: 31862950 PMCID: PMC6925111 DOI: 10.1038/s41467-019-13721-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022] Open
Abstract
Gut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. Recent development in metabolomics allows classifying the lipoprotein particles into more details. Here, we examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance technology in 2309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort. We assess the relationship between gut microbiota and metabolites by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. We report an association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, and acute-phase reaction markers. These observations provide insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.
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Affiliation(s)
- Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cisca Wijmenga
- 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
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexandra Zhernakova
- 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
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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35
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Díez López C, Vidaki A, Ralf A, Montiel González D, Radjabzadeh D, Kraaij R, Uitterlinden AG, Haas C, Lao O, Kayser M. Novel taxonomy-independent deep learning microbiome approach allows for accurate classification of different forensically relevant human epithelial materials. Forensic Sci Int Genet 2019; 41:72-82. [PMID: 31003081 DOI: 10.1016/j.fsigen.2019.03.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and identification when using previously proposed human cell biomarkers, while their microbiota composition largely differs. By using validated 16S rRNA gene massively parallel sequencing data from the Human Microbiome Project of 1636 skin, oral and vaginal samples, 50 taxonomy-independent deep learning networks were trained to classify these three tissues. Validation testing was performed in de-novo generated high-throughput 16S rRNA gene sequencing data using the Ion Torrent™ Personal Genome Machine from 110 test samples: 56 hand skin, 31 saliva and 23 vaginal secretion specimens. Body-site classification accuracy of these test samples was very high as indicated by AUC values of 0.99 for skin, 0.99 for oral, and 1 for vaginal secretion. Misclassifications were limited to 3 (5%) skin samples. Additional forensic validation testing was performed in mock casework samples by de-novo high-throughput sequencing of 19 freshly-prepared samples and 22 samples aged for 1 up to 7.6 years. All of the 19 fresh and 20 (91%) of the 22 aged mock casework samples were correctly tissue-type classified. Moreover, comparing the microbiome results with outcomes from previous human mRNA-based tissue identification testing in the same 16 aged mock casework samples reveals that our microbiome approach performs better in 12 (75%), similarly in 2 (12.5%), and less good in 2 (12.5%) of the samples. Our results demonstrate that this new microbiome approach allows for accurate tissue-type classification of three human epithelial materials of skin, oral and vaginal origin, which is highly relevant for future forensic investigations.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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36
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Grosserichter-Wagener C, Radjabzadeh D, van der Weide H, Smit KN, Kraaij R, Hays JP, van Zelm MC. Differences in Systemic IgA Reactivity and Circulating Th Subsets in Healthy Volunteers With Specific Microbiota Enterotypes. Front Immunol 2019; 10:341. [PMID: 30899257 PMCID: PMC6417458 DOI: 10.3389/fimmu.2019.00341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/08/2019] [Indexed: 12/24/2022] Open
Abstract
Changes in the intestinal microbiota have been associated with the development of immune-mediated diseases in humans. Additionally, the introduction of defined bacterial species into the mouse intestinal microbiota has been shown to impact on the adaptive immune response. However, how much impact the intestinal microbiota composition actually has on regulating adaptive immunity remains poorly understood. Therefore, we studied aspects of the adaptive immunity in healthy adults possessing distinct intestinal microbiota profiles. The intestinal microbiota composition was determined via Illumina sequencing of bacterial 16S rRNA genes extracted from the feces of 35 individuals. Blood B-cell and T-cell subsets from the same individuals were studied using flow cytometry. Finally, the binding of fecal and plasma Immunoglobulin A (IgA) to intestinal bacteria (associated with health and disease) Bacteroides fragilis, Prevotella copri, Bifidobacterium longum, Clostridium difficile, and Escherichia coli was analyzed using ELISA. Unsupervised clustering of microbiota composition revealed the presence of three clusters within the cohort. Cluster 1 and 2 were similar to previously-described enterotypes with a predominance of Bacteroides in Cluster 1 and Prevotella in Cluster 2. The bacterial diversity (Shannon index) and bacterial richness of Cluster 3 was significantly higher than observed in Clusters 1 and 2, with the Ruminococacceae tending to predominate. Within circulating B- and T-cell subsets, only Th subsets were significantly different between groups of distinct intestinal microbiota. Individuals of Cluster 3 have significantly fewer Th17 and Th22 circulating cells, while Th17.1 cell numbers were increased in individuals of Cluster 1. IgA reactivity to intestinal bacteria was higher in plasma than feces, and individuals of Cluster 1 had significant higher plasma IgA reactivity against B. longum than individuals of Cluster 2. In conclusion, we identified three distinct fecal microbiota clusters, of which two clusters resembled previously-described "enterotypes". Global T-cell and B-cell immunity seemed unaffected, however, circulating Th subsets and plasma IgA reactivity were significantly different between Clusters. Hence, the impact of intestinal bacteria composition on human B cells, T cells and IgA reactivity appears limited in genetically-diverse and environmentally-exposed humans, but can skew antibody reactivity and Th cell subsets.
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Affiliation(s)
| | - Djawad Radjabzadeh
- Department Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Hessel van der Weide
- Department Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Kyra N Smit
- Department Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Robert Kraaij
- Department Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - John P Hays
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Menno C van Zelm
- Department Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Immunology and Pathology, Central Clinical School, Monash University and The Alfred Hospital, Melbourne, VIC, Australia
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37
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Mulder M, Radjabzadeh D, Hassing RJ, Heeringa J, Uitterlinden AG, Kraaij R, Stricker BH, Verbon A. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC Microbiol 2019; 19:9. [PMID: 30626324 PMCID: PMC6327605 DOI: 10.1186/s12866-018-1379-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The urinary tract is inhabited by a diversity of microorganisms, known as the genitourinary microbiota. Here, we investigated the association between the use of antimicrobial drugs and the composition of the genitourinary microbiota. RESULTS Clean-catch urinary samples were collected from 27 participants of the Rotterdam Study. Bacterial DNA was extracted and the 16S ribosomal RNA gene variable regions V3 and V4 were analyzed using Illumina sequencing. 23 of the 27 participants were included in the analysis. The population consisted of 10 men and 13 women with a mean age of 75 ± 3 years. The time between the last prescription of an antimicrobial drug and sampling was determined and categorized. The use of antimicrobial drugs prior to urine sampling was associated with statistically significant differences in the beta-diversity of the genitourinary microbiota. No association was found between antimicrobial drug use and the alpha-diversity of the genitourinary microbiota. Operational Taxonomic Units (OTUs) that were lowest in participants who used antimicrobial drug belonged to Lactobacillus and Finegoldia. In contrast, an OTU belonging to the genus Parabacteroides had higher abundances. Also, an OTU belonging to the species E.coli was higher in the participants who used antimicrobial drugs. CONCLUSION Prior use of antimicrobial drugs is associated with a different composition of the genitourinary microbiota. Our results might indicate a persisting effect of antimicrobial drugs on the composition of the microbiota, but reverse causality cannot be ruled out. Future studies are needed to differentiate between two possibilities. Genitourinary dysbiosis could be the result of antimicrobial drug use or genitourinary dysbiosis could be a risk factor for urinary tract infections resulting in increased use of antimicrobial drugs. This may have important implications for treatment and prevention of (recurrent) UTIs.
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Affiliation(s)
- M Mulder
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands.,Inspectorate of Health Care, PO Box 2518, 6401, DA, Heerlen, The Netherlands
| | - D Radjabzadeh
- Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
| | - R J Hassing
- Department of Internal Medicine, Rijnstate Hospital, PO Box 9555, 6800, TA, Arnhem, The Netherlands
| | - J Heeringa
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
| | - R Kraaij
- Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
| | - B H Stricker
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands.
| | - A Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, PO Box 2040, 3000, CA, Rotterdam, The Netherlands
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38
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Vojinovic D, Kavousi M, Ghanbari M, Brouwer RWW, van Rooij JGJ, van den Hout MCGN, Kraaij R, van Ijcken WFJ, Uitterlinden AG, van Duijn CM, Amin N. Whole-Genome Linkage Scan Combined With Exome Sequencing Identifies Novel Candidate Genes for Carotid Intima-Media Thickness. Front Genet 2018; 9:420. [PMID: 30356672 PMCID: PMC6189289 DOI: 10.3389/fgene.2018.00420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/10/2018] [Indexed: 01/06/2023] Open
Abstract
Carotid intima-media thickness (cIMT) is an established heritable marker for subclinical atherosclerosis. In this study, we aim to identify rare variants with large effects driving differences in cIMT by performing genome-wide linkage analysis of individuals in the extremes of cIMT trait distribution (>90th percentile) in a large family-based study from a genetically isolated population in the Netherlands. Linked regions were subsequently explored by fine-mapping using exome sequencing. We observed significant evidence of linkage on chromosomes 2p16.3 [rs1017418, heterogeneity LOD (HLOD) = 3.35], 19q13.43 (rs3499, HLOD = 9.09), 20p13 (rs1434789, HLOD = 4.10), and 21q22.12 (rs2834949, HLOD = 3.59). Fine-mapping using exome sequencing data identified a non-coding variant (rs62165235) in PNPT1 gene under the linkage peak at chromosome 2 that is likely to have a regulatory function. The variant was associated with quantitative cIMT in the family-based study population (effect = 0.27, p-value = 0.013). Furthermore, we identified several genes under the linkage peak at chromosome 21 highly expressed in tissues relevant for atherosclerosis. To conclude, our linkage analysis identified four genomic regions significantly linked to cIMT. Further analyses are needed to demonstrate involvement of identified candidate genes in development of atherosclerosis.
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Affiliation(s)
- Dina Vojinovic
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rutger W W Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Jeroen G J van Rooij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Mirjam C G N van den Hout
- Department of Cell Biology, Center for Biomics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Wilfred F J van Ijcken
- Department of Cell Biology, Center for Biomics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Jabbari K, Bobbili DR, Lal D, Reinthaler EM, Schubert J, Wolking S, Sinha V, Motameny S, Thiele H, Kawalia A, Altmüller J, Toliat MR, Kraaij R, van Rooij J, Uitterlinden AG, Ikram MA, Zara F, Lehesjoki AE, Krause R, Zimprich F, Sander T, Neubauer BA, May P, Lerche H, Nürnberg P. Rare gene deletions in genetic generalized and Rolandic epilepsies. PLoS One 2018; 13:e0202022. [PMID: 30148849 PMCID: PMC6110470 DOI: 10.1371/journal.pone.0202022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed a systematic survey of rare deletions affecting protein-coding genes derived from exome data of patients with common forms of genetic epilepsies. We analysed exomes from 390 European patients (196 GGE and 194 RE) and 572 population controls to identify low-frequency genic deletions. We found that 75 (32 GGE and 43 RE) patients out of 390, i.e. ~19%, carried rare genic deletions. In particular, large deletions (>400 kb) represent a higher burden in both GGE and RE syndromes as compared to controls. The detected low-frequency deletions (1) share genes with brain-expressed exons that are under negative selection, (2) overlap with known autism and epilepsy-associated candidate genes, (3) are enriched for CNV intolerant genes recorded by the Exome Aggregation Consortium (ExAC) and (4) coincide with likely disruptive de novo mutations from the NPdenovo database. Employing several knowledge databases, we discuss the most prominent epilepsy candidate genes and their protein-protein networks for GGE and RE.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Biocenter, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Dheeraj R. Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stefan Wolking
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Vishal Sinha
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - M. Arfan Ikram
- Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Neuroscience Center and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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van Houten CB, Oved K, Eden E, Cohen A, Engelhard D, Boers S, Kraaij R, Karlsson R, Fernandez D, Gonzalez E, Li Y, Stubbs A, Moore ERB, Hays JP, Bont LJ. Observational multi-centre, prospective study to characterize novel pathogen-and host-related factors in hospitalized patients with lower respiratory tract infections and/or sepsis - the "TAILORED-Treatment" study. BMC Infect Dis 2018; 18:377. [PMID: 30086729 PMCID: PMC6081806 DOI: 10.1186/s12879-018-3300-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/01/2018] [Indexed: 12/29/2022] Open
Abstract
Background The emergence and spread of antibiotic resistant micro-organisms is a global concern, which is largely attributable to inaccurate prescribing of antibiotics to patients presenting with non-bacterial infections. The use of ‘omics’ technologies for discovery of novel infection related biomarkers combined with novel treatment algorithms offers possibilities for rapidly distinguishing between bacterial and viral infections. This distinction can be particularly important for patients suffering from lower respiratory tract infections (LRTI) and/or sepsis as they represent a significant burden to healthcare systems. Here we present the study details of the TAILORED-Treatment study, an observational, prospective, multi-centre study aiming to generate a multi-parametric model, combining host and pathogen data, for distinguishing between bacterial and viral aetiologies in children and adults with LRTI and/or sepsis. Methods A total number of 1200 paediatric and adult patients aged 1 month and older with LRTI and/or sepsis or a non-infectious disease are recruited from Emergency Departments and hospital wards of seven Dutch and Israeli medical centres. A panel of three experienced physicians adjudicate a reference standard diagnosis for all patients (i.e., bacterial or viral infection) using all available clinical and laboratory information, including a 28-day follow-up assessment. Nasal swabs and blood samples are collected for multi-omics investigations including host RNA and protein biomarkers, nasal microbiota profiling, host genomic profiling and bacterial proteomics. Simplified data is entered into a custom-built database in order to develop a multi-parametric model and diagnostic tools for differentiating between bacterial and viral infections. The predictions from the model will be compared with the consensus diagnosis in order to determine its accuracy. Discussion The TAILORED-Treatment study will provide new insights into the interplay between the host and micro-organisms. New host- or pathogen-related biomarkers will be used to generate a multi-parametric model for distinguishing between bacterial and viral infections. This model will be helpful to better guide antimicrobial therapy for patients with LRTI and sepsis. This study has the potential to improve patient care, reduce unnecessary antibiotic prescribing and will contribute positively to institutional, national and international healthcare economics. Trial Registration NCT02025699. Registration Date: January, 1, 2014. Electronic supplementary material The online version of this article (10.1186/s12879-018-3300-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C B van Houten
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Office KC.03.063.0, P.O. Box 85090, 3508 AB, Utrecht, The Netherlands
| | - K Oved
- MeMed, Tirat Carmel, Israel
| | - E Eden
- MeMed, Tirat Carmel, Israel
| | | | - D Engelhard
- Division of Paediatric Infectious Disease Unit, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - S Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, the Netherlands
| | - R Kraaij
- Department of Internal Medicine, Erasmus University Medical Centre (Erasmus MC), Rotterdam, the Netherlands
| | - R Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Y Li
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre (Erasmus MC), Rotterdam, the Netherlands
| | - A Stubbs
- Department of Pathology, Clinical Bioinformatics Unit, Erasmus University Medical Centre (Erasmus MC), Rotterdam, the Netherlands
| | - E R B Moore
- University of Gothenburg, Gothenburg, Sweden
| | - J P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, the Netherlands
| | - L J Bont
- Division of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht University, Office KC.03.063.0, P.O. Box 85090, 3508 AB, Utrecht, The Netherlands.
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41
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Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN, Spector TD, Bell JT, Steves CJ, Timpson N, Franke A, Wijmenga C, Meyer K, Kacprowski T, Franke L, Paterson AD, Raes J, Kraaij R, Zhernakova A. Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative. Microbiome 2018; 6:101. [PMID: 29880062 PMCID: PMC5992867 DOI: 10.1186/s40168-018-0479-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/10/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. RESULTS Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. CONCLUSION We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Department of Microbiology and Immunology, Rega Institute. KU Leuven - University of Leuven, Leuven, Belgium.
- VIB Center for Microbiology, Leuven, Belgium.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Williams Turpin
- Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Matthew A Jackson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, 3000, CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, 3000, CA, Rotterdam, The Netherlands
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - David Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, South Korea
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicolas Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katie Meyer
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute. KU Leuven - University of Leuven, Leuven, Belgium.
- VIB Center for Microbiology, Leuven, Belgium.
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Corominas J, Colijn JM, Geerlings MJ, Pauper M, Bakker B, Amin N, Lores Motta L, Kersten E, Garanto A, Verlouw JAM, van Rooij JGJ, Kraaij R, de Jong PTVM, Hofman A, Vingerling JR, Schick T, Fauser S, de Jong EK, van Duijn CM, Hoyng CB, Klaver CCW, den Hollander AI. Whole-Exome Sequencing in Age-Related Macular Degeneration Identifies Rare Variants in COL8A1, a Component of Bruch's Membrane. Ophthalmology 2018; 125:1433-1443. [PMID: 29706360 PMCID: PMC6104593 DOI: 10.1016/j.ophtha.2018.03.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/19/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Genome-wide association studies and targeted sequencing studies of candidate genes have identified common and rare variants that are associated with age-related macular degeneration (AMD). Whole-exome sequencing (WES) studies allow a more comprehensive analysis of rare coding variants across all genes of the genome and will contribute to a better understanding of the underlying disease mechanisms. To date, the number of WES studies in AMD case-control cohorts remains scarce and sample sizes are limited. To scrutinize the role of rare protein-altering variants in AMD cause, we performed the largest WES study in AMD to date in a large European cohort consisting of 1125 AMD patients and 1361 control participants. DESIGN Genome-wide case-control association study of WES data. PARTICIPANTS One thousand one hundred twenty-five AMD patients and 1361 control participants. METHODS A single variant association test of WES data was performed to detect variants that are associated individually with AMD. The cumulative effect of multiple rare variants with 1 gene was analyzed using a gene-based CMC burden test. Immunohistochemistry was performed to determine the localization of the Col8a1 protein in mouse eyes. MAIN OUTCOME MEASURES Genetic variants associated with AMD. RESULTS We detected significantly more rare protein-altering variants in the COL8A1 gene in patients (22/2250 alleles [1.0%]) than in control participants (11/2722 alleles [0.4%]; P = 7.07×10-5). The association of rare variants in the COL8A1 gene is independent of the common intergenic variant (rs140647181) near the COL8A1 gene previously associated with AMD. We demonstrated that the Col8a1 protein localizes at Bruch's membrane. CONCLUSIONS This study supported a role for protein-altering variants in the COL8A1 gene in AMD pathogenesis. We demonstrated the presence of Col8a1 in Bruch's membrane, further supporting the role of COL8A1 variants in AMD pathogenesis. Protein-altering variants in COL8A1 may alter the integrity of Bruch's membrane, contributing to the accumulation of drusen and the development of AMD.
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Affiliation(s)
- Jordi Corominas
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johanna M Colijn
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maartje J Geerlings
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marc Pauper
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bjorn Bakker
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Najaf Amin
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Laura Lores Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline Kersten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost A M Verlouw
- Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, The Netherlands
| | - Paulus T V M de Jong
- Netherlands Institute of Neurosciences (NIN), Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), Departments of Ophthalmology, Amsterdam Medical Center, Amsterdam, and Leiden University Medical Center, Leiden, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany; Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelia M van Duijn
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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Radjabzadeh D, Uitterlinden AG, Kraaij R. Microbiome measurement: Possibilities and pitfalls. Best Pract Res Clin Gastroenterol 2017; 31:619-623. [PMID: 29566904 DOI: 10.1016/j.bpg.2017.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/29/2017] [Indexed: 01/31/2023]
Abstract
Microbiome research is an emerging field in medical sciences. Several studies have made headways in understanding the influence of microbes on our health and disease states. Further progress in mapping microbiome populations across different body sites and understanding the underlying mechanisms of microbiome-host interactions depends critically on study design, collection protocols, analytical genetic techniques, and reference databases. In particular, a shift has appeared going from small sample collections to large-scale population studies (with extensive phenotypic information including disease status) which calls for some adaptions. In this review we will focus on gut microbiome profiling using the 16S ribosomal RNA approach in the setting of large-scale population studies, and discuss some novel developments.
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Affiliation(s)
| | - André G Uitterlinden
- Dept. Internal Medicine, Erasmus MC, Rotterdam, The Netherlands; Dept. Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert Kraaij
- Dept. Internal Medicine, Erasmus MC, Rotterdam, The Netherlands; Dept. Epidemiology, Erasmus MC, Rotterdam, The Netherlands.
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44
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Robak LA, Jansen IE, van Rooij J, Uitterlinden AG, Kraaij R, Jankovic J, Heutink P, Shulman JM. Excessive burden of lysosomal storage disorder gene variants in Parkinson's disease. Brain 2017; 140:3191-3203. [PMID: 29140481 PMCID: PMC5841393 DOI: 10.1093/brain/awx285] [Citation(s) in RCA: 275] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/15/2017] [Accepted: 09/10/2017] [Indexed: 12/19/2022] Open
Abstract
Mutations in the glucocerebrosidase gene (GBA), which cause Gaucher disease, are also potent risk factors for Parkinson's disease. We examined whether a genetic burden of variants in other lysosomal storage disorder genes is more broadly associated with Parkinson's disease susceptibility. The sequence kernel association test was used to interrogate variant burden among 54 lysosomal storage disorder genes, leveraging whole exome sequencing data from 1156 Parkinson's disease cases and 1679 control subjects. We discovered a significant burden of rare, likely damaging lysosomal storage disorder gene variants in association with Parkinson's disease risk. The association signal was robust to the exclusion of GBA, and consistent results were obtained in two independent replication cohorts, including 436 cases and 169 controls with whole exome sequencing and an additional 6713 cases and 5964 controls with exome-wide genotyping. In secondary analyses designed to highlight the specific genes driving the aggregate signal, we confirmed associations at the GBA and SMPD1 loci and newly implicate CTSD, SLC17A5, and ASAH1 as candidate Parkinson's disease susceptibility genes. In our discovery cohort, the majority of Parkinson's disease cases (56%) have at least one putative damaging variant in a lysosomal storage disorder gene, and 21% carry multiple alleles. Our results highlight several promising new susceptibility loci and reinforce the importance of lysosomal mechanisms in Parkinson's disease pathogenesis. We suggest that multiple genetic hits may act in combination to degrade lysosomal function, enhancing Parkinson's disease susceptibility.
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Affiliation(s)
- Laurie A Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX USA
- Jan and Dan Duncan Neurologic Research Institute, Texas Children’s Hospital, Houston TX USA
| | - Iris E Jansen
- German Center for Neurodegenerative Diseases (DZNE) and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen 72076, Germany
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1081HZ, The Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, The Netherlands
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE) and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen 72076, Germany
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX USA
- Jan and Dan Duncan Neurologic Research Institute, Texas Children’s Hospital, Houston TX USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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45
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Jansen IE, Gibbs JR, Nalls MA, Price TR, Lubbe S, van Rooij J, Uitterlinden AG, Kraaij R, Williams NM, Brice A, Hardy J, Wood NW, Morris HR, Gasser T, Singleton AB, Heutink P, Sharma M. Establishing the role of rare coding variants in known Parkinson's disease risk loci. Neurobiol Aging 2017; 59:220.e11-220.e18. [DOI: 10.1016/j.neurobiolaging.2017.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/13/2017] [Accepted: 07/22/2017] [Indexed: 10/19/2022]
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van der Spek A, Luik AI, Kocevska D, Liu C, Brouwer RWW, van Rooij JGJ, van den Hout MCGN, Kraaij R, Hofman A, Uitterlinden AG, van IJcken WFJ, Gottlieb DJ, Tiemeier H, van Duijn CM, Amin N. Exome-Wide Meta-Analysis Identifies Rare 3'-UTR Variant in ERCC1/CD3EAP Associated with Symptoms of Sleep Apnea. Front Genet 2017; 8:151. [PMID: 29093733 PMCID: PMC5651235 DOI: 10.3389/fgene.2017.00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/28/2017] [Indexed: 12/30/2022] Open
Abstract
Obstructive sleep apnea (OSA) is a common sleep breathing disorder associated with an increased risk of cardiovascular and cerebrovascular diseases and mortality. Although OSA is fairly heritable (~40%), there have been only few studies looking into the genetics of OSA. In the present study, we aimed to identify genetic variants associated with symptoms of sleep apnea by performing a whole-exome sequence meta-analysis of symptoms of sleep apnea in 1,475 individuals of European descent. We identified 17 rare genetic variants with at least suggestive evidence of significance. Replication in an independent dataset confirmed the association of a rare genetic variant (rs2229918; minor allele frequency = 0.3%) with symptoms of sleep apnea (p-valuemeta = 6.98 × 10−9, βmeta = 0.99). Rs2229918 overlaps with the 3′ untranslated regions of ERCC1 and CD3EAP genes on chromosome 19q13. Both genes are expressed in tissues in the neck area, such as the tongue, muscles, cartilage and the trachea. Further, CD3EAP is localized in the nucleus and mitochondria and involved in the tumor necrosis factor-alpha/nuclear factor kappa B signaling pathway. Our results and biological functions of CD3EAP/ERCC1 genes suggest that the 19q13 locus is interesting for further OSA research.
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Affiliation(s)
| | - Annemarie I Luik
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Desana Kocevska
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, Netherlands
| | - Chunyu Liu
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA, United States.,Population Sciences Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, United States.,Department of Biostatistics, School of Public Health, Boston University, Boston, MA, United States
| | | | - Jeroen G J van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands.,Netherlands Consortium for Healthy Ageing, Rotterdam, Netherlands.,Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Robert Kraaij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands.,Netherlands Consortium for Healthy Ageing, Rotterdam, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands.,Netherlands Consortium for Healthy Ageing, Rotterdam, Netherlands
| | | | - Daniel J Gottlieb
- VA Boston Healthcare System, Boston, MA, United States.,Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, MA, United States.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands.,Department of Psychiatry, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
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47
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van Rooij JGJ, Jhamai M, Arp PP, Nouwens SCA, Verkerk M, Hofman A, Ikram MA, Verkerk AJ, van Meurs JBJ, Rivadeneira F, Uitterlinden AG, Kraaij R. Population-specific genetic variation in large sequencing data sets: why more data is still better. Eur J Hum Genet 2017; 25:1173-1175. [PMID: 28905877 DOI: 10.1038/ejhg.2017.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 04/25/2017] [Accepted: 06/13/2017] [Indexed: 11/09/2022] Open
Abstract
We have generated a next-generation whole-exome sequencing data set of 2628 participants of the population-based Rotterdam Study cohort, comprising 669 737 single-nucleotide variants and 24 019 short insertions and deletions. Because of broad and deep longitudinal phenotyping of the Rotterdam Study, this data set permits extensive interpretation of genetic variants on a range of clinically relevant outcomes, and is accessible as a control data set. We show that next-generation sequencing data sets yield a large degree of population-specific variants, which are not captured by other available large sequencing efforts, being ExAC, ESP, 1000G, UK10K, GoNL and DECODE.
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Affiliation(s)
- Jeroen G J van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Neurology, Erasmus MC, Rotterdam, Netherlands
| | - Mila Jhamai
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Pascal P Arp
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
| | | | - Marijn Verkerk
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, Netherlands.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - M Arfan Ikram
- Department of Neurology, Erasmus MC, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC, Rotterdam, Netherlands
| | | | | | | | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands.,Department of Neurology, Erasmus MC, Rotterdam, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
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48
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Amin N, Belonogova NM, Jovanova O, Brouwer RWW, van Rooij JGJ, van den Hout MCGN, Svishcheva GR, Kraaij R, Zorkoltseva IV, Kirichenko AV, Hofman A, Uitterlinden AG, van IJcken WFJ, Tiemeier H, Axenovich TI, van Duijn CM. Nonsynonymous Variation in NKPD1 Increases Depressive Symptoms in European Populations. Biol Psychiatry 2017; 81:702-707. [PMID: 27745872 DOI: 10.1016/j.biopsych.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 07/28/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Despite high heritability, little success was achieved in mapping genetic determinants of depression-related traits by means of genome-wide association studies. METHODS To identify genes associated with depressive symptomology, we performed a gene-based association analysis of nonsynonymous variation captured using exome-sequencing and exome-chip genotyping in a genetically isolated population from the Netherlands (n = 1999). Finally, we reproduced our significant findings in an independent population-based cohort (n = 1604). RESULTS We detected significant association of depressive symptoms with a gene NKPD1 (p = 3.7 × 10-08). Nonsynonymous variants in the gene explained 0.9% of sex- and age-adjusted variance of depressive symptoms in the discovery study, which is translated into 3.8% of the total estimated heritability (h2 = 0.24). Significant association of depressive symptoms with NKPD1 was also observed (n = 1604; p = 1.5 × 10-03) in the independent replication sample despite little overlap with the discovery cohort in the set of nonsynonymous genetic variants observed in the NKPD1 gene. Meta-analysis of the discovery and replication studies improved the association signal (p = 1.0 × 10-09). CONCLUSIONS Our study suggests that nonsynonymous variation in the gene NKPD1 affects depressive symptoms in the general population. NKPD1 is predicted to be involved in the de novo synthesis of sphingolipids, which have been implicated in the pathogenesis of depression.
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Affiliation(s)
- Najaf Amin
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | | | - Olivera Jovanova
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen G J van Rooij
- Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Gulnara R Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Robert Kraaij
- Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Irina V Zorkoltseva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly V Kirichenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Albert Hofman
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - André G Uitterlinden
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Henning Tiemeier
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tatiana I Axenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Cornelia M van Duijn
- Departments of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
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49
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Amin N, Jovanova O, Adams HHH, Dehghan A, Kavousi M, Vernooij MW, Peeters RP, de Vrij FMS, van der Lee SJ, van Rooij JGJ, van Leeuwen EM, Chaker L, Demirkan A, Hofman A, Brouwer RWW, Kraaij R, Willems van Dijk K, Hankemeier T, van Ijcken WFJ, Uitterlinden AG, Niessen WJ, Franco OH, Kushner SA, Ikram MA, Tiemeier H, van Duijn CM. Exome-sequencing in a large population-based study reveals a rare Asn396Ser variant in the LIPG gene associated with depressive symptoms. Mol Psychiatry 2017; 22:537-543. [PMID: 27431295 DOI: 10.1038/mp.2016.101] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 11/09/2022]
Abstract
Despite a substantial genetic component, efforts to identify common genetic variation underlying depression have largely been unsuccessful. In the current study we aimed to identify rare genetic variants that might have large effects on depression in the general population. Using high-coverage exome-sequencing, we studied the exonic variants in 1265 individuals from the Rotterdam study (RS), who were assessed for depressive symptoms. We identified a missense Asn396Ser mutation (rs77960347) in the endothelial lipase (LIPG) gene, occurring with an allele frequency of 1% in the general population, which was significantly associated with depressive symptoms (P-value=5.2 × 10-08, β=7.2). Replication in three independent data sets (N=3612) confirmed the association of Asn396Ser (P-value=7.1 × 10-03, β=2.55) with depressive symptoms. LIPG is predicted to have enzymatic function in steroid biosynthesis, cholesterol biosynthesis and thyroid hormone metabolic processes. The Asn396Ser variant is predicted to have a damaging effect on the function of LIPG. Within the discovery population, carriers also showed an increased burden of white matter lesions (P-value=3.3 × 10-02) and a higher risk of Alzheimer's disease (odds ratio=2.01; P-value=2.8 × 10-02) compared with the non-carriers. Together, these findings implicate the Asn396Ser variant of LIPG in the pathogenesis of depressive symptoms in the general population.
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Affiliation(s)
- N Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - O Jovanova
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - H H H Adams
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Radiology, Erasmus MC, Rotterdam, The Netherlands
| | - A Dehghan
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - M Kavousi
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - M W Vernooij
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Radiology, Erasmus MC, Rotterdam, The Netherlands
| | - R P Peeters
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Rotterdam Thyroid Center, Erasmus MC, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - F M S de Vrij
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - S J van der Lee
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - J G J van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - E M van Leeuwen
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - L Chaker
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Rotterdam Thyroid Center, Erasmus MC, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - A Demirkan
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, RC Leiden, The Netherlands
| | - A Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - R W W Brouwer
- Center for Biomics, Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - R Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - K Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, RC Leiden, The Netherlands.,Division of Endocrinology, Department of Medicine, Leiden University Medical Center, RC Leiden, The Netherlands
| | - T Hankemeier
- Leiden Academic Center for Drug Research, Division of Analytical Biosciences, Leiden University, Leiden, The Netherlands.,The Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | - W F J van Ijcken
- Center for Biomics, Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - W J Niessen
- Departments of Radiology and Medical Informatics, Erasmus MC, Rotterdam, The Netherlands.,Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - O H Franco
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - S A Kushner
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - M A Ikram
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Radiology, Erasmus MC, Rotterdam, The Netherlands
| | - H Tiemeier
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - C M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
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50
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Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LPC, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TFJ, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JGJ, Ikram MA, Uitterlinden AG, van Duijn CM, Daly MJ, MacArthur DG. Quantifying prion disease penetrance using large population control cohorts. Sci Transl Med 2016; 8:322ra9. [PMID: 26791950 DOI: 10.1126/scitranslmed.aad5169] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.
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Affiliation(s)
- Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA.
| | - Sonia M Vallabh
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karol Estrada
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Cory Y McLean
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Joyce Y Tung
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Linda P C Yu
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Pierluigi Gambetti
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Janis Blevins
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Shulin Zhang
- University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Yvonne Cohen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Wei Chen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Tsuyoshi Hamaguchi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Nobuo Sanjo
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hidehiro Mizusawa
- National Center Hospital, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Yosikazu Nakamura
- Department of Public Health, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Steven J Collins
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Boyd
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert G Will
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard Knight
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Claudia Ponto
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Inga Zerr
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Sabina Eigenbrod
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Miguel Calero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Jesús de Pedro-Cuesta
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Stéphane Haïk
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Jean-Louis Laplanche
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Elodie Bouaziz-Amar
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Jean-Philippe Brandel
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Sabina Capellari
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Piero Parchi
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Anna Poleggi
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anna Ladogana
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jamie L Marshall
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio 70210, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Anna Kähler
- Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA. Karolinska Institutet, Stockholm SE-171 77, Sweden
| | | | - Shaun M Purcell
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Annemieke Rozemuller
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Casper Jansen
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | | | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands. Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | | | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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