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Hewitt JK. Announcement of the Editors' Choice Award (Formerly the Fulker Award) for a Paper Published in Behavior Genetics, Volume 53, 2023. Behav Genet 2024:10.1007/s10519-024-10199-6. [PMID: 39368007 DOI: 10.1007/s10519-024-10199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Affiliation(s)
- John K Hewitt
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
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Drouard G, Wang Z, Heikkinen A, Foraster M, Julvez J, Kanninen KM, van Kamp I, Pirinen M, Ollikainen M, Kaprio J. Lifestyle differences between co-twins are associated with decreased similarity in their internal and external exposome profiles. Sci Rep 2024; 14:21261. [PMID: 39261679 PMCID: PMC11390871 DOI: 10.1038/s41598-024-72354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024] Open
Abstract
Whether differences in lifestyle between co-twins are reflected in differences in their internal or external exposome profiles remains largely underexplored. We therefore investigated whether within-pair differences in lifestyle were associated with within-pair differences in exposome profiles across four domains: the external exposome, proteome, metabolome and epigenetic age acceleration (EAA). For each domain, we assessed the similarity of co-twin profiles using Gaussian similarities in up to 257 young adult same-sex twin pairs (54% monozygotic). We additionally tested whether similarity in one domain translated into greater similarity in another. Results suggest that a lower degree of similarity in co-twins' exposome profiles was associated with greater differences in their behavior and substance use. The strongest association was identified between excessive drinking behavior and the external exposome. Overall, our study demonstrates how social behavior and especially substance use are connected to the internal and external exposomes, while controlling for familial confounders.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Zhiyang Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Foraster
- PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull (URL), Barcelona, Spain
| | - Jordi Julvez
- Clinical and Epidemiological Neuroscience (NeuroÈpia), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- ISGlobal, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irene van Kamp
- Centre for Sustainability, Environment and Health, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
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3
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Hubers N, Hagenbeek FA, Pool R, Déjean S, Harms AC, Roetman PJ, van Beijsterveldt CEM, Fanos V, Ehli EA, Vermeiren RRJM, Bartels M, Hottenga JJ, Hankemeier T, van Dongen J, Boomsma DI. Integrative multi-omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention-Deficit/Hyperactivity Disorder. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32955. [PMID: 37534875 DOI: 10.1002/ajmg.b.32955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The evolving field of multi-omics combines data and provides methods for simultaneous analysis across several omics levels. Here, we integrated genomics (transmitted and non-transmitted polygenic scores [PGSs]), epigenomics, and metabolomics data in a multi-omics framework to identify biomarkers for Attention-Deficit/Hyperactivity Disorder (ADHD) and investigated the connections among the three omics levels. We first trained single- and next multi-omics models to differentiate between cases and controls in 596 twins (cases = 14.8%) from the Netherlands Twin Register (NTR) demonstrating reasonable in-sample prediction through cross-validation. The multi-omics model selected 30 PGSs, 143 CpGs, and 90 metabolites. We confirmed previous associations of ADHD with glucocorticoid exposure and the transmembrane protein family TMEM, show that the DNA methylation of the MAD1L1 gene associated with ADHD has a relation with parental smoking behavior, and present novel findings including associations between indirect genetic effects and CpGs of the STAP2 gene. However, out-of-sample prediction in NTR participants (N = 258, cases = 14.3%) and in a clinical sample (N = 145, cases = 51%) did not perform well (range misclassification was [0.40, 0.57]). The results highlighted connections between omics levels, with the strongest connections between non-transmitted PGSs, CpGs, and amino acid levels and show that multi-omics designs considering interrelated omics levels can help unravel the complex biology underlying ADHD.
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Affiliation(s)
- Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219, University of Toulouse, CNRS, Toulouse, France
| | - Amy C Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Peter J Roetman
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, USA
| | - Robert R J M Vermeiren
- LUMC-Curium, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Leiden, the Netherlands
- Youz, Parnassia Group, the Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, the Netherlands
- The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
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Niehues A, de Visser C, Hagenbeek FA, Kulkarni P, Pool R, Karu N, Kindt ASD, Singh G, Vermeiren RRJM, Boomsma DI, van Dongen J, ’t Hoen PAC, van Gool AJ. A multi-omics data analysis workflow packaged as a FAIR Digital Object. Gigascience 2024; 13:giad115. [PMID: 38217405 PMCID: PMC10787363 DOI: 10.1093/gigascience/giad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/14/2023] [Accepted: 12/10/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Applying good data management and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines. Practical examples can help promote the adoption of FAIR practices for computational workflows in the research community. We developed a multi-omics data analysis workflow implementing FAIR practices to share it as a FAIR Digital Object. FINDINGS We conducted a case study investigating shared patterns between multi-omics data and childhood externalizing behavior. The analysis workflow was implemented as a modular pipeline in the workflow manager Nextflow, including containers with software dependencies. We adhered to software development practices like version control, documentation, and licensing. Finally, the workflow was described with rich semantic metadata, packaged as a Research Object Crate, and shared via WorkflowHub. CONCLUSIONS Along with the packaged multi-omics data analysis workflow, we share our experiences adopting various FAIR practices and creating a FAIR Digital Object. We hope our experiences can help other researchers who develop omics data analysis workflows to turn FAIR principles into practice.
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Affiliation(s)
- Anna Niehues
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Casper de Visser
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Purva Kulkarni
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Alida S D Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Gurnoor Singh
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Robert R J M Vermeiren
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, 2342 AK Oegstgeest, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Peter A C ’t Hoen
- Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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Drouard G, Wang Z, Heikkinen A, Foraster M, Julvez J, Kanninen KM, van Kamp I, Pirinen M, Ollikainen M, Kaprio J. Lifestyle differences between co-twins are associated with decreased similarity in their internal and external exposome profiles. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.12.23299868. [PMID: 38168348 PMCID: PMC10760270 DOI: 10.1101/2023.12.12.23299868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Whether differences in lifestyle between co-twins are reflected in differences in their internal or external exposome profiles remains largely underexplored. We therefore investigated whether within-pair differences in lifestyle were associated with within-pair differences in exposome profiles across four domains: the external exposome, proteome, metabolome and epigenetic age acceleration (EAA). For each domain, we assessed the similarity of co-twin profiles using Gaussian similarities in up to 257 young adult same-sex twin pairs (54% monozygotic). We additionally tested whether similarity in one domain translated into greater similarity in another. Results suggest that a lower degree of similarity in co-twins' exposome profiles was associated with greater differences in their behavior and substance use. The strongest association was identified between excessive drinking behavior and the external exposome. Overall, our study demonstrates how social behavior and especially substance use are connected to the internal and external exposomes, while controlling for familial confounders.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Zhiyang Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Maria Foraster
- PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull (URL), Barcelona, Spain
| | - Jordi Julvez
- Clinical and epidemiological Neuroscience (NeuroÈpia), Institut d’Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- ISGlobal, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Katja M. Kanninen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irene van Kamp
- National Institute for Public Health and the Environment, centre for Sustainability, Environment and Health, Netherlands
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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Kuś J, Saramowicz K, Czerniawska M, Wiese W, Siwecka N, Rozpędek-Kamińska W, Kucharska-Lusina A, Strzelecki D, Majsterek I. Molecular Mechanisms Underlying NMDARs Dysfunction and Their Role in ADHD Pathogenesis. Int J Mol Sci 2023; 24:12983. [PMID: 37629164 PMCID: PMC10454781 DOI: 10.3390/ijms241612983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorders, although the aetiology of ADHD is not yet understood. One proposed theory for developing ADHD is N-methyl-D-aspartate receptors (NMDARs) dysfunction. NMDARs are involved in regulating synaptic plasticity and memory function in the brain. Abnormal expression or polymorphism of some genes associated with ADHD results in NMDAR dysfunction. Correspondingly, NMDAR malfunction in animal models results in ADHD-like symptoms, such as impulsivity and hyperactivity. Currently, there are no drugs for ADHD that specifically target NMDARs. However, NMDAR-stabilizing drugs have shown promise in improving ADHD symptoms with fewer side effects than the currently most widely used psychostimulant in ADHD treatment, methylphenidate. In this review, we outline the molecular and genetic basis of NMDAR malfunction and how it affects the course of ADHD. We also present new therapeutic options related to treating ADHD by targeting NMDAR.
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Affiliation(s)
- Justyna Kuś
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Kamil Saramowicz
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Maria Czerniawska
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Wojciech Wiese
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Natalia Siwecka
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Wioletta Rozpędek-Kamińska
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
| | - Dominik Strzelecki
- Department of Affective and Psychotic Disorders, Medical University of Lodz, Czechoslowacka 8/10, 92-216 Lodz, Poland;
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland; (J.K.); (K.S.); (M.C.); (W.W.); (N.S.); (W.R.-K.); (A.K.-L.)
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