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Sinnott-Armstrong N, Fields S, Roth F, Starita LM, Trapnell C, Villen J, Fowler DM, Queitsch C. Understanding genetic variants in context. eLife 2024; 13:e88231. [PMID: 39625477 PMCID: PMC11614383 DOI: 10.7554/elife.88231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/15/2024] [Indexed: 12/06/2024] Open
Abstract
Over the last three decades, human genetics has gone from dissecting high-penetrance Mendelian diseases to discovering the vast and complex genetic etiology of common human diseases. In tackling this complexity, scientists have discovered the importance of numerous genetic processes - most notably functional regulatory elements - in the development and progression of these diseases. Simultaneously, scientists have increasingly used multiplex assays of variant effect to systematically phenotype the cellular consequences of millions of genetic variants. In this article, we argue that the context of genetic variants - at all scales, from other genetic variants and gene regulation to cell biology to organismal environment - are critical components of how we can employ genomics to interpret these variants, and ultimately treat these diseases. We describe approaches to extend existing experimental assays and computational approaches to examine and quantify the importance of this context, including through causal analytic approaches. Having a unified understanding of the molecular, physiological, and environmental processes governing the interpretation of genetic variants is sorely needed for the field, and this perspective argues for feasible approaches by which the combined interpretation of cellular, animal, and epidemiological data can yield that knowledge.
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Affiliation(s)
- Nasa Sinnott-Armstrong
- Herbold Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
| | - Stanley Fields
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Medicine, University of WashingtonSeattleUnited States
| | - Frederick Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of TorontoTorontoCanada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai HospitalTorontoCanada
- Department of Computational and Systems Biology, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Lea M Starita
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
| | - Cole Trapnell
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
| | - Judit Villen
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
| | - Christine Queitsch
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Brotman Baty Institute for Precision MedicineSeattleUnited States
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Hakola L, Lund-Blix NA, Takkinen HM, Tapanainen H, Niinistö S, Korhonen TE, Stene LC, Hyöty H, Toppari J, Ilonen J, Knip M, Veijola R, Virtanen SM. Maternal gluten, cereal, and dietary fiber intake during pregnancy and lactation and the risk of islet autoimmunity and type 1 diabetes in the child. Clin Nutr ESPEN 2024; 62:22-27. [PMID: 38901945 DOI: 10.1016/j.clnesp.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND & AIMS Maternal gluten intake in relation to child's risk of type 1 diabetes has been studied in few prospective studies considering the diet during pregnancy but none during lactation. Our aim was to study whether gluten, cereals, or dietary fiber in maternal diet during pregnancy and lactation is associated with the risk of islet autoimmunity or type 1 diabetes in the offspring. METHODS We included 4943 children with genetic susceptibility to type 1 diabetes from the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) Study, born between 1996 and 2004. Maternal intake of gluten, different types of cereals, and dietary fiber were derived from a semi-quantitative validated food frequency questionnaire covering the eighth month of pregnancy and the third month of lactation. Children were monitored for islet autoantibodies up to age of 15 years and type 1 diabetes until year 2017. Risk of islet autoimmunity and clinical type 1 diabetes were estimated using Cox regression model, adjusted for energy intake, child's sex, HLA genotype, and familial diabetes. RESULTS Altogether 312 children (6.4%) developed islet autoimmunity at median age of 3.5 (IQR 1.7, 6.6) years and 178 children (3.6%) developed type 1 diabetes at median age of 7.1 (IQR 4.3, 10.6) years. Gluten intake during pregnancy was not associated with islet autoimmunity (HR 0.96; 95% CI 0.68, 1.35), per 1 g/MJ increase in intake nor type 1 diabetes (HR 0.96; 95% CI 0.62, 1.50) in the offspring. Higher barley consumption during lactation was associated with increased risk of type 1 diabetes (HR 3.25; 95% CI 1.21, 8.70) per 1 g/MJ increase in intake. Maternal intake of other cereals or dietary fiber was not associated with the offspring outcomes. CONCLUSIONS We observed no association between maternal intake of gluten, most consumed cereals, or dietary fiber during pregnancy or lactation and the risk of islet autoimmunity or type 1 diabetes in children from a high-risk population.
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Affiliation(s)
- Leena Hakola
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland; Tampere University Hospital, Wellbeing Services County of Pirkanmaa, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.
| | - Nicolai A Lund-Blix
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Norwegian Institute of Public Health, Oslo, Norway; Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Norway
| | - Hanna-Mari Takkinen
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland; Tampere University Hospital, Wellbeing Services County of Pirkanmaa, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Heli Tapanainen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sari Niinistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tuuli E Korhonen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lars C Stene
- Norwegian Institute of Public Health, Oslo, Norway
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland; Tampere University Hospital, Department of Pediatrics, Tampere, Finland
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Centre for Population Health Research, University of Turku, Turku, Finland; Turku University Hospital, Department of Pediatrics, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mikael Knip
- Tampere University Hospital, Department of Pediatrics, Tampere, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riitta Veijola
- Department of Paediatrics, Research Unit of Clinical Medicine, Medical Research Centre, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Suvi M Virtanen
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland; Tampere University Hospital, Wellbeing Services County of Pirkanmaa, Finland; Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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Karthikeyan BS, Hyötyläinen T, Ghaffarzadegan T, Triplett E, Orešič M, Ludvigsson J. Prenatal exposure to environmental contaminants and cord serum metabolite profiles in future immune-mediated diseases. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2024; 34:647-658. [PMID: 38678133 PMCID: PMC11303251 DOI: 10.1038/s41370-024-00680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Prenatal exposure to environmental contaminants is a significant health concern because it has the potential to interfere with host metabolism, leading to adverse health effects in early childhood and later in life. Growing evidence suggests that genetic and environmental factors, as well as their interactions, play a significant role in the development of autoimmune diseases. OBJECTIVE In this study, we hypothesized that prenatal exposure to environmental contaminants impacts cord serum metabolome and contributes to the development of autoimmune diseases. METHODS We selected cord serum samples from All Babies in Southeast Sweden (ABIS) general population cohort, from infants who later developed one or more autoimmune-mediated and inflammatory diseases: celiac disease (CD), Crohn's disease (IBD), hypothyroidism (HT), juvenile idiopathic arthritis (JIA), and type 1 diabetes (T1D) (all cases, N = 62), along with matched controls (N = 268). Using integrated exposomics and metabolomics mass spectrometry (MS) based platforms, we determined the levels of environmental contaminants and metabolites. RESULTS Differences in exposure levels were found between the controls and those who later developed various diseases. High contaminant exposure levels were associated with changes in metabolome, including amino acids and free fatty acids. Specifically, we identified marked associations between metabolite profiles and exposure levels of deoxynivalenol (DON), bisphenol S (BPS), and specific per- and polyfluorinated substances (PFAS). IMPACT STATEMENT Abnormal metabolism is a common feature preceding several autoimmune and inflammatory diseases. However, few studies compared common and specific metabolic patterns preceding these diseases. Here we hypothesized that exposure to environmental contaminants impacts cord serum metabolome, which may contribute to the development of autoimmune diseases. We found differences in exposure levels between the controls and those who later developed various diseases, and importantly, on the metabolic changes associated with the exposures. High contaminant exposure levels were associated with specific changes in metabolome. Our study suggests that prenatal exposure to specific environmental contaminants alters the cord serum metabolomes, which, in turn, might increase the risk of various immune-mediated diseases.
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Affiliation(s)
- Bagavathy Shanmugam Karthikeyan
- School of Science and Technology, Örebro University, SE-702 81, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-702 81, Örebro, Sweden
| | - Tuulia Hyötyläinen
- School of Science and Technology, Örebro University, SE-702 81, Örebro, Sweden
| | | | - Eric Triplett
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences University of Florida, Gainesville, 32611-0700, FL, USA
| | - Matej Orešič
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-702 81, Örebro, Sweden.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, FI-20520, Finland.
| | - Johnny Ludvigsson
- Crown Princess Victoria's Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, SE-581 85, Sweden
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Lund-Blix NA, Bjerregaard AA, Tapia G, Størdal K, Brantsæter AL, Strøm M, Halldorsson TI, Granstrøm C, Svensson J, Joner G, Skrivarhaug T, Njølstad PR, Olsen SF, Stene LC. No association between long-chain n-3 fatty acid intake during pregnancy and risk of type 1 diabetes in offspring in two large Scandinavian pregnancy cohorts. Diabetologia 2024; 67:1023-1028. [PMID: 38502240 PMCID: PMC11058590 DOI: 10.1007/s00125-024-06125-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024]
Abstract
AIMS/HYPOTHESIS The aim of this study was to investigate whether higher dietary intake of marine n-3 fatty acids during pregnancy is associated with a lower risk of type 1 diabetes in children. METHODS The Danish National Birth Cohort (DNBC) and the Norwegian Mother, Father and Child Cohort Study (MoBa) together include 153,843 mother-child pairs with prospectively collected data on eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake during pregnancy from validated food frequency questionnaires. Type 1 diabetes diagnosis in children (n=634) was ascertained from national diabetes registries. RESULTS There was no association between the sum of EPA and DHA intake during pregnancy and risk of type 1 diabetes in offspring (pooled HR per g/day of intake: 1.00, 95% CI 0.88, 1.14), with consistent results for both the MoBa and the DNBC. Robustness analyses gave very similar results. CONCLUSIONS/INTERPRETATION Initiation of a trial of EPA and DHA during pregnancy to prevent type 1 diabetes in offspring should not be prioritised.
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Affiliation(s)
| | - Anne A Bjerregaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Centre for Clinical Research and Prevention, Copenhagen University Hospitals - Bispebjerg and Frederiksberg, Frederiksberg, Denmark
| | - German Tapia
- Norwegian Institute of Public Health, Oslo, Norway
| | - Ketil Størdal
- Norwegian Institute of Public Health, Oslo, Norway
- Faculty of Medicine, Division of Paediatric and Adolescent Medicine, University of Oslo, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Marin Strøm
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- University of the Faroe Islands, Torshavn, Faroe Islands
| | - Thorhallur I Halldorsson
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | - Charlotta Granstrøm
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jannet Svensson
- Steno Diabetes Center Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Geir Joner
- Faculty of Medicine, Division of Paediatric and Adolescent Medicine, University of Oslo, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Torild Skrivarhaug
- Faculty of Medicine, Division of Paediatric and Adolescent Medicine, University of Oslo, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Pål R Njølstad
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Sjurdur F Olsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- University of the Faroe Islands, Torshavn, Faroe Islands
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lars C Stene
- Norwegian Institute of Public Health, Oslo, Norway.
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Mønsted MØ, Holm LJ, Buschard K, Haupt-Jorgensen M. Failure to replicate the diabetes alleviating effect of a maternal gluten-free diet in non-obese diabetic mice. PLoS One 2023; 18:e0289258. [PMID: 37682921 PMCID: PMC10490983 DOI: 10.1371/journal.pone.0289258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/13/2023] [Indexed: 09/10/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease with an unexplained rising incidence for which environmental factors like gluten may play a role. Previously, we showed that a gluten-free (GF) diet provided strictly in utero reduces the autoimmune diabetes incidence in Non-Obese Diabetic (NOD) mice compared to a gluten-containing standard (STD) diet. The current study was initiated to elucidate possible mechanisms behind the diabetes-alleviating effect of the same diet intervention. NOD mice received either a GF Altromin diet or a STD Altromin diet during pregnancy. Female offspring from both groups were fed a STD diet throughout life and their diabetes incidence was recorded for 200 days. The following parameters were measured in 13-week-old female offspring: insulitis degree, glucose and insulin tolerance, and plasma insulin autoantibody titer. The diet intervention showed no reduction in autoimmune diabetes incidence, insulitis degree, glucose nor insulin tolerance and plasma insulin autoantibody titer. In conclusion, this study could not replicate the previously observed diabetes alleviative effects of a maternal gluten-free diet in NOD mouse offspring and could therefore not further elucidate potential mechanisms.
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Affiliation(s)
- Mia Øgaard Mønsted
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Laurits Juulskov Holm
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Karsten Buschard
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
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Beeinflusst die maternale Nahrung das Risiko für Typ-1-Diabetes beim Kind? DIABETOL STOFFWECHS 2021. [DOI: 10.1055/a-1503-8479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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