1
|
Wesseltoft JB, Danielsen CD, Andersen AM, de Jonge N, Olsen A, Rohde PD, Kristensen TN. Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome. Sci Rep 2024; 14:7799. [PMID: 38565609 PMCID: PMC10987527 DOI: 10.1038/s41598-024-58500-1] [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: 01/10/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024] Open
Abstract
It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of our study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting our working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable.
Collapse
Affiliation(s)
| | | | | | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | |
Collapse
|
2
|
Møller PL, Rohde PD, Dahl JN, Rasmussen LD, Nissen L, Schmidt SE, McGilligan V, Gudbjartsson DF, Stefansson K, Holm H, Bentzon JF, Bøttcher M, Winther S, Nyegaard M. Predicting the presence of coronary plaques featuring high-risk characteristics using polygenic risk scores and targeted proteomics in patients with suspected coronary artery disease. Genome Med 2024; 16:40. [PMID: 38509622 PMCID: PMC10953133 DOI: 10.1186/s13073-024-01313-8] [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: 08/29/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The presence of coronary plaques with high-risk characteristics is strongly associated with adverse cardiac events beyond the identification of coronary stenosis. Testing by coronary computed tomography angiography (CCTA) enables the identification of high-risk plaques (HRP). Referral for CCTA is presently based on pre-test probability estimates including clinical risk factors (CRFs); however, proteomics and/or genetic information could potentially improve patient selection for CCTA and, hence, identification of HRP. We aimed to (1) identify proteomic and genetic features associated with HRP presence and (2) investigate the effect of combining CRFs, proteomics, and genetics to predict HRP presence. METHODS Consecutive chest pain patients (n = 1462) undergoing CCTA to diagnose obstructive coronary artery disease (CAD) were included. Coronary plaques were assessed using a semi-automatic plaque analysis tool. Measurements of 368 circulating proteins were obtained with targeted Olink panels, and DNA genotyping was performed in all patients. Imputed genetic variants were used to compute a multi-trait multi-ancestry genome-wide polygenic score (GPSMult). HRP presence was defined as plaques with two or more high-risk characteristics (low attenuation, spotty calcification, positive remodeling, and napkin ring sign). Prediction of HRP presence was performed using the glmnet algorithm with repeated fivefold cross-validation, using CRFs, proteomics, and GPSMult as input features. RESULTS HRPs were detected in 165 (11%) patients, and 15 input features were associated with HRP presence. Prediction of HRP presence based on CRFs yielded a mean area under the receiver operating curve (AUC) ± standard error of 73.2 ± 0.1, versus 69.0 ± 0.1 for proteomics and 60.1 ± 0.1 for GPSMult. Combining CRFs with GPSMult increased prediction accuracy (AUC 74.8 ± 0.1 (P = 0.004)), while the inclusion of proteomics provided no significant improvement to either the CRF (AUC 73.2 ± 0.1, P = 1.00) or the CRF + GPSMult (AUC 74.6 ± 0.1, P = 1.00) models, respectively. CONCLUSIONS In patients with suspected CAD, incorporating genetic data with either clinical or proteomic data improves the prediction of high-risk plaque presence. TRIAL REGISTRATION https://clinicaltrials.gov/ct2/show/NCT02264717 (September 2014).
Collapse
Affiliation(s)
- Peter Loof Møller
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jonathan Nørtoft Dahl
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Laust Dupont Rasmussen
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Louise Nissen
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Samuel Emil Schmidt
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Victoria McGilligan
- Personalized Medicine Centre, School of Medicine, Ulster University, Derry, Northern Ireland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc, Reykjavik, Iceland
| | - Jacob Fog Bentzon
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Morten Bøttcher
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Simon Winther
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
3
|
Paina C, Fois M, Asp T, Jensen J, Hansen PB, Rohde PD. The soil microbiome of Lolium perenne L. depends on host genotype, is modified by nitrogen level and varies across season. Sci Rep 2024; 14:5767. [PMID: 38459164 PMCID: PMC10923896 DOI: 10.1038/s41598-024-56353-2] [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: 06/01/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Genotype by environment interactions (G × E) are frequently observed in herbage production. Understanding the underlying biological mechanisms is important for achieving stable and predictive outputs across production environments. The microbiome is gaining increasing attention as a significant contributing factor to G × E. Here, we focused on the soil microbiome of perennial ryegrass (Lolium perenne L.) grown under field conditions and investigated the soil microbiome variation across different ryegrass varieties to assess whether environmental factors, such as seasonality and nitrogen levels, affect the microbial community. We identified bacteria, archaea, and fungi operational taxonomic units (OTUs) and showed that seasonality and ryegrass variety were the two factors explaining the largest fraction of the soil microbiome diversity. The strong and significant variety-by-treatment-by-seasonal cut interaction for ryegrass dry matter was associated with the number of unique OTUs within each sample. We identified seven OTUs associated with ryegrass dry matter variation. An OTU belonging to the Solirubrobacterales (Thermoleophilales) order was associated with increased plant biomass, supporting the possibility of developing engineered microbiomes for increased plant yield. Our results indicate the importance of incorporating different layers of biological data, such as genomic and soil microbiome data to improve the prediction accuracy of plant phenotypes grown across heterogeneous environments.
Collapse
Affiliation(s)
- Cristiana Paina
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, C. F. Møllers Allé 3, Bldg. 1130, 8000, Aarhus, Denmark.
| | - Pernille Bjarup Hansen
- Center for Quantitative Genetics and Genomics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Palle Duun Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Selma Lagerløfs Vej 249, 9260, Gistrup, Denmark
| |
Collapse
|
4
|
Noer NK, Rohde PD, Sørensen P, Bahrndorff S, Kristensen TN. Diurnal variation in genetic parameters for locomotor activity in Drosophila melanogaster assessed under natural thermal conditions. J Evol Biol 2024; 37:336-345. [PMID: 38320319 DOI: 10.1093/jeb/voae020] [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: 05/19/2023] [Revised: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 02/08/2024]
Abstract
In nature, organisms are exposed to variable and occasionally stressful environmental conditions. Responses to diurnal and seasonal fluctuations, such as temperature and food accessibility, involve adaptive behavioural and physiological changes. While much work has been done on understanding the genetic architecture and evolutionary potential of stress tolerance traits under constant thermal conditions, there has been less focus on the quantitative genetic background in variable environments. In this study, we use the Drosophila Genetic Reference Panel (DGRP) to investigate the locomotor activity, a key behavioural trait, under variable natural thermal conditions during the summer in a temperate environment. Male flies from 100 DGRP lines were exposed to natural thermal and light conditions in Drosophila activity monitors across three experimental days. We found that activity was highly temperature and time dependent and varied between lines both within and between days. Furthermore, we observed variation in genetic and environmental variance components, with low to moderate estimates of the heritability for locomotor activity, consistently peaking in the afternoons. Moreover, we showed that the estimated genetic correlations of locomotor activity between two time points decreased, as the absolute differences in ambient temperature increased. In conclusion, we find that the genetic background for locomotor activity is environment specific, and we conclude that more variable and unpredictable future temperatures will likely have a strong impact on the evolutionary trajectories of behavioural traits in ectotherms.
Collapse
Affiliation(s)
- Natasja Krog Noer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Peter Sørensen
- Centre for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Simon Bahrndorff
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | |
Collapse
|
5
|
Sequeros CB, Hansen TF, Westergaard D, Louloudis I, Kalamajski S, Röder T, Rohde PD, Schwinn M, Clemmensen LH, Didriksen M, Nyegaard M, Hjalgrim H, Nielsen KR, Bruun MT, Ostrowski SR, Erikstrup C, Mikkelsen S, Sørensen E, Pedersen OBV, Brunak S, Banasik K, Giordano GN. A genome-wide association study of social trust in 33,882 Danish blood donors. Sci Rep 2024; 14:1402. [PMID: 38228779 PMCID: PMC10792163 DOI: 10.1038/s41598-024-51636-0] [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: 10/19/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024] Open
Abstract
Social trust is a heritable trait that has been linked with physical health and longevity. In this study, we performed genome-wide association studies of self-reported social trust in n = 33,882 Danish blood donors. We observed genome-wide and local evidence of genetic similarity with other brain-related phenotypes and estimated the single nucleotide polymorphism-based heritability of trust to be 6% (95% confidence interval = (2.1, 9.9)). In our discovery cohort (n = 25,819), we identified one significantly associated locus (lead variant: rs12776883) in an intronic enhancer region of PLPP4, a gene highly expressed in brain, kidneys, and testes. However, we could not replicate the signal in an independent set of donors who were phenotyped a year later (n = 8063). In the subsequent meta-analysis, we found a second significantly associated variant (rs71543507) in an intergenic enhancer region. Overall, our work confirms that social trust is heritable, and provides an initial look into the genetic factors that influence it.
Collapse
Affiliation(s)
- Celia Burgos Sequeros
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Danish Headache Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - David Westergaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
- Department of Gynecology and Obstetrics, Copenhagen University Hospital Hvidovre, Copenhagen, Denmark
| | - Ioannis Louloudis
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, CRC, Lund University Diabetes Centre, Malmö, Sweden
| | - Timo Röder
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Palle Duun Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Line Harder Clemmensen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Mette Nyegaard
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Henrik Hjalgrim
- The Danish Cancer Institute, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kaspar René Nielsen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Mie Topholm Bruun
- Clinical Immunology Research Unit, Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Ole Birger Vestager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Gynecology and Obstetrics, Copenhagen University Hospital Hvidovre, Copenhagen, Denmark.
| | - Giuseppe Nicola Giordano
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, CRC, Lund University Diabetes Centre, Malmö, Sweden
| |
Collapse
|
6
|
Bak NK, Rohde PD, Kristensen TN. Strong Sex-Dependent Effects of Malnutrition on Life- and Healthspan in Drosophila melanogaster. Insects 2023; 15:9. [PMID: 38249015 PMCID: PMC10816799 DOI: 10.3390/insects15010009] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024]
Abstract
Insufficient intake of essential nutrients, malnutrition is a major issue for millions of people and has a strong impact on the distribution and abundance of species in nature. In this study, we investigated the effect of malnutrition on several fitness components in the vinegar fly Drosophila melanogaster. Four diets with different nutritional values, including three diluted diets of an optimal nutritional balanced diet, were used as feed sources. The effect of malnutrition on fitness components linked to healthspan, the period of life spent in good health conditions, was evaluated by quantifying the flies' lifespan, locomotor activity, heat stress tolerance, lipid content, and dry weight. The results showed that malnutrition had severe negative impact, such as reduced lifespan, locomotor activity, heat stress tolerance, fat content, and dry weight. The negative phenotypic effects were highly sex-dependent, with males being more negatively impacted by malnutrition compared to females. These findings highlight important detrimental and sex-specific effects of malnutrition not only on lifespan but also on traits related to healthspan.
Collapse
Affiliation(s)
- Nikolaj Klausholt Bak
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK 9220 Aalborg, Denmark;
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Selma Lagerløfs Vej 249, DK 9260 Gistrup, Denmark
| | - Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK 9220 Aalborg, Denmark;
| |
Collapse
|
7
|
Rohde PD, Fourie Sørensen I, Sørensen P. Expanded utility of the R package, qgg, with applications within genomic medicine. Bioinformatics 2023; 39:btad656. [PMID: 37882742 PMCID: PMC10627350 DOI: 10.1093/bioinformatics/btad656] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/17/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023] Open
Abstract
SUMMARY Here, we present an expanded utility of the R package qgg for genetic analyses of complex traits and diseases. One of the major updates of the package is, that it now includes Bayesian linear regression modeling procedures, which provide a unified framework for mapping of genetic variants, estimation of heritability and genomic prediction from either individual level data or from genome-wide association study summary data. With this release, the qgg package now provides a wealth of the commonly used methods in analysis of complex traits and diseases, without the need to switch between software and data formats. AVAILABILITY AND IMPLEMENTATION The methodologies are implemented in the publicly available R software package, qgg, using fast and memory efficient algorithms in C++ and is available on CRAN or as a developer version at our GitHub page (https://github.com/psoerensen/qgg). Notes on the implemented statistical genetic models, tutorials and example scripts are available at our GitHub page https://psoerensen.github.io/qgg/.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, 9260 Gistrup, Denmark
| | - Izel Fourie Sørensen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus, Denmark
| |
Collapse
|
8
|
Therkildsen J, Rohde PD, Nissen L, Thygesen J, Hauge EM, Langdahl BL, Boettcher M, Nyegaard M, Winther S. A genome-wide genomic score added to standard recommended stratification tools does not improve the identification of patients with very low bone mineral density. Osteoporos Int 2023; 34:1893-1906. [PMID: 37495683 PMCID: PMC10579117 DOI: 10.1007/s00198-023-06857-w] [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: 01/11/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
The role of integrating genomic scores (GSs) needs to be assessed. Adding a GS to recommended stratification tools does not improve the prediction of very low bone mineral density. However, we noticed that the GS performed equally or above individual risk factors in discrimination. PURPOSE We aimed to investigate whether adding a genomic score (GS) to recommended stratification tools improves the discrimination of participants with very low bone mineral density (BMD). METHODS BMD was measured in three thoracic vertebrae using CT. All participants provided information on standard osteoporosis risk factors. GSs and FRAX scores were calculated. Participants were grouped according to mean BMD into very low (<80 mg/cm3), low (80-120 mg/cm3), and normal (>120 mg/cm3) and according to the Bone Health and Osteoporosis Foundation recommendations for BMD testing into an "indication for BMD testing" and "no indication for BMD testing" group. Different models were assessed using the area under the receiver operating characteristics curves (AUC) and reclassification analyses. RESULTS In the total cohort (n=1421), the AUC for the GS was 0.57 (95% CI 0.52-0.61) corresponding to AUCs for osteoporosis risk factors. In participants without indication for BMD testing, the AUC was 0.60 (95% CI 0.52-0.69) above or equal to AUCs for osteoporosis risk factors. Adding the GS to a clinical risk factor (CRF) model resulted in AUCs not statistically significant from the CRF model. Using probability cutoff values of 6, 12, and 24%, we found no improved reclassification or risk discrimination using the CRF-GS model compared to the CRF model. CONCLUSION Our results suggest adding a GS to a CRF model does not improve prediction. However, we noticed that the GS performed equally or above individual risk factors in discrimination. Clinical risk factors combined showed superior discrimination to individual risk factors and the GS, underlining the value of combined CRFs in routine clinics as a stratification tool.
Collapse
Affiliation(s)
- J Therkildsen
- Department of Rheumatology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark.
| | - P D Rohde
- Department of Health Science & Technology, Aalborg University, Selma Lagerløfs Vej 24, 9269, Gistrup, Denmark
| | - L Nissen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
- Department of Cardiology, Gødstrup Hospital, Hospitalsparken 15, 7400, Herning, Denmark
| | - J Thygesen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
- Department of Clinical Engineering, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus, Denmark
| | - E-M Hauge
- Department of Rheumatology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
| | - B L Langdahl
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus, Denmark
| | - M Boettcher
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
- Department of Cardiology, Gødstrup Hospital, Hospitalsparken 15, 7400, Herning, Denmark
| | - M Nyegaard
- Department of Health Science & Technology, Aalborg University, Selma Lagerløfs Vej 24, 9269, Gistrup, Denmark
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus, Denmark
| | - S Winther
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
- Department of Cardiology, Gødstrup Hospital, Hospitalsparken 15, 7400, Herning, Denmark
| |
Collapse
|
9
|
Møller PL, Rohde PD, Dahl JN, Rasmussen LD, Schmidt SE, Nissen L, McGilligan V, Bentzon JF, Gudbjartsson DF, Stefansson K, Holm H, Winther S, Bøttcher M, Nyegaard M. Combining Polygenic and Proteomic Risk Scores With Clinical Risk Factors to Improve Performance for Diagnosing Absence of Coronary Artery Disease in Patients With de novo Chest Pain. Circ Genom Precis Med 2023; 16:442-451. [PMID: 37753640 DOI: 10.1161/circgen.123.004053] [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] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND Patients with de novo chest pain, referred for evaluation of possible coronary artery disease (CAD), frequently have an absence of CAD resulting in millions of tests not having any clinical impact. The objective of this study was to investigate whether polygenic risk scores and targeted proteomics improve the prediction of absence of CAD in patients with suspected CAD, when added to the PROMISE (Prospective Multicenter Imaging Study for Evaluation of Chest Pain) minimal risk score (PMRS). METHODS Genotyping and targeted plasma proteomics (N=368 proteins) were performed in 1440 patients with symptoms suspected to be caused by CAD undergoing coronary computed tomography angiography. Based on individual genotypes, a polygenic risk score for CAD (PRSCAD) was calculated. The prediction was performed using combinations of PRSCAD, proteins, and PMRS as features in models using stability selection and machine learning. RESULTS Prediction of absence of CAD yielded an area under the curve of PRSCAD-model, 0.64±0.03; proteomic-model, 0.58±0.03; and PMRS model, 0.76±0.02. No significant correlation was found between the genetic and proteomic risk scores (Pearson correlation coefficient, -0.04; P=0.13). Optimal predictive ability was achieved by the full model (PRSCAD+protein+PMRS) yielding an area under the curve of 0.80±0.02 for absence of CAD, significantly better than the PMRS model alone (P<0.001). For reclassification purpose, the full model enabled down-classification of 49% (324 of 661) of the 5% to 15% pretest probability patients and 18% (113 of 611) of >15% pretest probability patients. CONCLUSIONS For patients with chest pain and low-intermediate CAD risk, incorporating targeted proteomics and polygenic risk scores into the risk assessment substantially improved the ability to predict the absence of CAD. Genetics and proteomics seem to add complementary information to the clinical risk factors and improve risk stratification in this large patient group. REGISTRATION URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT02264717.
Collapse
Affiliation(s)
- Peter Loof Møller
- Department of Biomedicine (P.L.M., M.N.), Aarhus University
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Jonathan Nørtoft Dahl
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Laust Dupont Rasmussen
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Samuel Emil Schmidt
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| | - Louise Nissen
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Victoria McGilligan
- Personalized Medicine Centre, Ulster University, Derry, Northern Ireland (V.M.)
| | - Jacob F Bentzon
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.F.B.)
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
- School of Engineering and Natural Sciences (D.F.G.)
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
- Faculty of Medicine, University of Iceland, Reykjavik (K.S.)
| | - Hilma Holm
- deCODE genetics/Amgen, Inc. (D.F.G., K.S., H.H.)
| | - Simon Winther
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Morten Bøttcher
- Department of Clinical Medicine (J.N.D., L.D.R., L.N., J.F.B., S.W., M.B.), Aarhus University
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark (J.N.D., L.D.R., L.N., S.W., M.B.)
| | - Mette Nyegaard
- Department of Biomedicine (P.L.M., M.N.), Aarhus University
- Department of Health Science and Technology, Aalborg University (P.L.M., P.D.R., S.E.S., M.N.)
| |
Collapse
|
10
|
Westergaard D, Steinthorsdottir V, Stefansdottir L, Rohde PD, Wu X, Geller F, Tyrmi J, Havulinna AS, Navais PS, Flatley C, Ostrowski SR, Pedersen OB, Erikstrup C, Sørensen E, Mikkelsen C, Brun MT, Jensen BA, Brodersen T, Ullum H, Magnus P, Andreassen OA, Njolstad PR, Kolte AM, Krebs L, Nyegaard M, Hansen TF, Fenstra B, Daly M, Lindgren CM, Thorleifsson G, Stefansson OA, Sveinbjornsson G, Gudbjartsson DF, Thorsteinsdottir U, Banasik K, Jacobsson B, Laisk T, Laivuori H, Stefansson K, Brunak S, Nielsen HS. Pregnancy-Associated Bleeding and Genetics: Five Sequence Variants in the Myometrium and Progesterone Signaling Pathway are associated with postpartum hemorrhage. medRxiv 2023:2023.08.10.23293932. [PMID: 37645979 PMCID: PMC10462219 DOI: 10.1101/2023.08.10.23293932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severity of these complications in maternal-fetal health. Here, we investigated the genetic variation underlying aspects of pregnancy-associated bleeding and identified five loci associated with PPH through a meta-analysis of 21,512 cases and 259,500 controls. Functional annotation analysis indicated candidate genes, HAND2, TBX3, and RAP2C/FRMD7, at three loci and showed that at each locus, associated variants were located within binding sites for progesterone receptors (PGR). Furthermore, there were strong genetic correlations with birth weight, gestational duration, and uterine fibroids. Early bleeding during pregnancy (28,898 cases and 302,894 controls) yielded no genome-wide association signals, but showed strong genetic correlation with a variety of human traits, indicative of polygenic and pleiotropic effects. Our results suggest that postpartum bleeding is related to myometrium dysregulation, whereas early bleeding is a complex trait related to underlying health and possibly socioeconomic status.
Collapse
Affiliation(s)
- David Westergaard
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | | | | | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Xiaoping Wu
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jaakko Tyrmi
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare - THL, Helsinki, Finland
| | - Pol Sole Navais
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Flatley
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Sisse Rye Ostrowski
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Pedersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christina Mikkelsen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mie Topholm Brun
- Clinical Immunological Research Unit, Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Thorsten Brodersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
| | - Henrik Ullum
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Per Magnus
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Pål R Njolstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Astrid Marie Kolte
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Lone Krebs
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Headache Center, Department of neurology, Copenhagen University Hospital, Glostrup, Denmark
| | - Bjarke Fenstra
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mark Daly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Big Data Institute Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Karina Banasik
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynaecology, Tampere University Hospital, Tampere, Finland
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
11
|
Winther S, Dupont Rasmussen L, Westra J, Abdulzahra SRK, Dahl JN, Gormsen LC, Christiansen EH, Brix GS, Mortensen J, Ejlersen JA, Søndergaard HM, Hansson NCL, Holm NR, Knudsen LL, Eftekhari A, Møller PL, Rohde PD, Nyegaard M, Böttcher M. Danish study of Non-Invasive Testing in Coronary Artery Disease 3 (Dan-NICAD 3): study design of a controlled study on optimal diagnostic strategy. Open Heart 2023; 10:e002328. [PMID: 37487656 PMCID: PMC10373750 DOI: 10.1136/openhrt-2023-002328] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
INTRODUCTION Current guideline recommend functional imaging for myocardial ischaemia if coronary CT angiography (CTA) has shown coronary artery disease (CAD) of uncertain functional significance. However, diagnostic accuracy of selective myocardial perfusion imaging after coronary CTA is currently unclear. The Danish study of Non-Invasive testing in Coronary Artery Disease 3 trial is designed to evaluate head to head the diagnostic accuracy of myocardial perfusion imaging with positron emission tomography (PET) using the tracers 82Rubidium (82Rb-PET) compared with oxygen-15 labelled water PET (15O-water-PET) in patients with symptoms of obstructive CAD and a coronary CT scan with suspected obstructive CAD. METHODS AND ANALYSIS This prospective, multicentre, cross-sectional study will include approximately 1000 symptomatic patients without previous CAD. Patients are included after referral to coronary CTA. All patients undergo a structured interview and blood is sampled for genetic and proteomic analysis and a coronary CTA. Patients with possible obstructive CAD at coronary CTA are examined with both 82Rb-PET, 15O-water-PET and invasive coronary angiography with three-vessel fractional flow reserve and thermodilution measurements of coronary flow reserve. After enrolment, patients are followed with Seattle Angina Questionnaires and follow-up PET scans in patients with an initially abnormal PET scan and for cardiovascular events in 10 years. ETHICS AND DISSEMINATION Ethical approval was obtained from Danish regional committee on health research ethics. Written informed consent will be provided by all study participants. Results of this study will be disseminated via articles in international peer-reviewed journal. TRIAL REGISTRATION NUMBER NCT04707859.
Collapse
Affiliation(s)
- Simon Winther
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
| | | | - Jelmer Westra
- Department of Cardiology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | - Jesper Mortensen
- Department of Nuclear Medicine, Gødstrup Hospital, Herning, Denmark
| | - June Anita Ejlersen
- Department of Nuclear Medicine, Regional Hospital Central Jutland, Viborg, Denmark
| | | | | | | | | | - Ashkan Eftekhari
- Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Peter L Møller
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Palle Duun Rohde
- Department of Health, Science and Technology, Aalborg University, Aalborg, Denmark
| | - Mette Nyegaard
- Health Science and Technology, Aalborg Universitet, Gistrup, Denmark
| | - Morten Böttcher
- Department of Cardiology, Gødstrup Hospital, Herning, Denmark
| |
Collapse
|
12
|
Baisgaard AE, Koldby KM, Kristensen TN, Nyegaard M, Rohde PD. Functionally Validating Evolutionary Conserved Risk Genes for Parkinson's Disease in Drosophila melanogaster. Insects 2023; 14:168. [PMID: 36835737 PMCID: PMC9958964 DOI: 10.3390/insects14020168] [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] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Parkinson's disease (PD) is a heterogeneous and complex neurodegenerative disorder and large-scale genetic studies have identified >130 genes associated with PD. Although genomic studies have been decisive for our understanding of the genetic contributions underlying PD, these associations remain as statistical associations. Lack of functional validation limits the biological interpretation; however, it is labour extensive, expensive, and time consuming. Therefore, the ideal biological system for functionally validating genetic findings must be simple. The study aim was to assess systematically evolutionary conserved PD-associated genes using Drosophila melanogaster. From a literature review, a total of 136 genes have found to be associated with PD in GWAS studies, of which 11 are strongly evolutionary conserved between Homo sapiens and D. melanogaster. By ubiquitous gene expression knockdown of the PD-genes in D. melanogaster, the flies' escape response was investigated by assessing their negative geotaxis response, a phenotype that has previously been used to investigate PD in D. melanogaster. Gene expression knockdown was successful in 9/11 lines, and phenotypic consequences were observed in 8/9 lines. The results provide evidence that genetically modifying expression levels of PD genes in D. melanogaster caused reduced climbing ability of the flies, potentially supporting their role in dysfunctional locomotion, a hallmark of PD.
Collapse
Affiliation(s)
- Amalie Elton Baisgaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | | | | | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| |
Collapse
|
13
|
Staehr C, Rohde PD, Krarup NT, Ringgaard S, Laustsen C, Johnsen J, Nielsen R, Beck HC, Morth JP, Lykke-Hartmann K, Jespersen NR, Abramochkin D, Nyegaard M, Bøtker HE, Aalkjaer C, Matchkov V. Migraine-Associated Mutation in the Na,K-ATPase Leads to Disturbances in Cardiac Metabolism and Reduced Cardiac Function. J Am Heart Assoc 2022; 11:e021814. [PMID: 35289188 PMCID: PMC9075430 DOI: 10.1161/jaha.121.021814] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Mutations in ATP1A2 gene encoding the Na,K‐ATPase α2 isoform are associated with familial hemiplegic migraine type 2. Migraine with aura is a known risk factor for heart disease. The Na,K‐ATPase is important for cardiac function, but its role for heart disease remains unknown. We hypothesized that ATP1A2 is a susceptibility gene for heart disease and aimed to assess the underlying disease mechanism. Methods and Results Mice heterozygous for the familial hemiplegic migraine type 2–associated G301R mutation in the Atp1a2 gene (α2+/G301R mice) and matching wild‐type controls were compared. Reduced expression of the Na,K‐ATPase α2 isoform and increased expression of the α1 isoform were observed in hearts from α2+/G301R mice (Western blot). Left ventricular dilation and reduced ejection fraction were shown in hearts from 8‐month‐old α2+/G301R mice (cardiac magnetic resonance imaging), and this was associated with reduced nocturnal blood pressure (radiotelemetry). Cardiac function and blood pressure of 3‐month‐old α2+/G301R mice were similar to wild‐type mice. Amplified Na,K‐ATPase–dependent Src kinase/Ras/Erk1/2 (p44/42 mitogen‐activated protein kinase) signaling was observed in hearts from 8‐month‐old α2+/G301R mice, and this was associated with mitochondrial uncoupling (respirometry), increased oxidative stress (malondialdehyde measurements), and a heart failure–associated metabolic shift (hyperpolarized magnetic resonance). Mitochondrial membrane potential (5,5´,6,6´‐tetrachloro‐1,1´,3,3´‐tetraethylbenzimidazolocarbocyanine iodide dye assay) and mitochondrial ultrastructure (transmission electron microscopy) were similar between the groups. Proteomics of heart tissue further suggested amplified Src/Ras/Erk1/2 signaling and increased oxidative stress and provided the molecular basis for systolic dysfunction in 8‐month‐old α2+/G301R mice. Conclusions Our findings suggest that ATP1A2 mutation leads to disturbed cardiac metabolism and reduced cardiac function mediated via Na,K‐ATPase–dependent reactive oxygen species signaling through the Src/Ras/Erk1/2 pathway.
Collapse
Affiliation(s)
- Christian Staehr
- Department of Biomedicine, Health Aarhus University Aarhus Denmark
| | - Palle Duun Rohde
- Department of Chemistry and Bioscience Aalborg University Aalborg Denmark
| | | | - Steffen Ringgaard
- MR Research Centre Department of Clinical Medicine Aarhus University Aarhus Denmark
| | - Christoffer Laustsen
- MR Research Centre Department of Clinical Medicine Aarhus University Aarhus Denmark
| | - Jacob Johnsen
- Department of Clinical Medicine Aarhus University Aarhus Denmark
| | - Rikke Nielsen
- Department of Biomedicine, Health Aarhus University Aarhus Denmark
| | - Hans Christian Beck
- Department for Clinical Biochemistry and Pharmacology Odense University Hospital Odense Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine Technical University of Denmark Kgs. Lyngby Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Health Aarhus University Aarhus Denmark.,Department of Clinical Medicine Aarhus University Aarhus Denmark.,Department of Clinical Genetics Aarhus University Hospital Aarhus Denmark
| | | | - Denis Abramochkin
- Department of Human and Animal Physiology Biological Faculty Lomonosov Moscow State University Moscow Russia
| | - Mette Nyegaard
- Department of Biomedicine, Health Aarhus University Aarhus Denmark.,Department of Health Science and Technology Aalborg University Aalborg Denmark
| | - Hans Erik Bøtker
- Department of Clinical Medicine Aarhus University Aarhus Denmark
| | - Christian Aalkjaer
- Department of Biomedicine, Health Aarhus University Aarhus Denmark.,Department of Biomedical Sciences Copenhagen University Copenhagen Denmark
| | | |
Collapse
|
14
|
Kloeve-Mogensen K, Rohde PD, Twisttmann S, Nygaard M, Koldby KM, Steffensen R, Dahl CM, Rytter D, Overgaard MT, Forman A, Christiansen L, Nyegaard M. Polygenic Risk Score Prediction for Endometriosis. Front Reprod Health 2021; 3:793226. [PMID: 36303976 PMCID: PMC9580817 DOI: 10.3389/frph.2021.793226] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Endometriosis is a major health care challenge because many young women with endometriosis go undetected for an extended period, which may lead to pain sensitization. Clinical tools to better identify candidates for laparoscopy-guided diagnosis are urgently needed. Since endometriosis has a strong genetic component, there is a growing interest in using genetics as part of the clinical risk assessment. The aim of this work was to investigate the discriminative ability of a polygenic risk score (PRS) for endometriosis using three different cohorts: surgically confirmed cases from the Western Danish endometriosis referral Center (249 cases, 348 controls), cases identified from the Danish Twin Registry (DTR) based on ICD-10 codes from the National Patient Registry (140 cases, 316 controls), and replication analysis in the UK Biobank (2,967 cases, 256,222 controls). Patients with adenomyosis from the DTR (25 cases) and from the UK Biobank (1,883 cases) were included for comparison. The PRS was derived from 14 genetic variants identified in a published genome-wide association study with more than 17,000 cases. The PRS was associated with endometriosis in surgically confirmed cases [odds ratio (OR) = 1.59, p = 2.57× 10−7] and in cases from the DTR biobank (OR = 1.50, p = 0.0001). Combining the two Danish cohorts, each standard deviation increase in PRS was associated with endometriosis (OR = 1.57, p = 2.5× 10−11), as well as the major subtypes of endometriosis; ovarian (OR = 1.72, p = 6.7× 10−5), infiltrating (OR = 1.66, p = 2.7× 10−9), and peritoneal (OR = 1.51, p = 2.6 × 10−3). These findings were replicated in the UK Biobank with a much larger sample size (OR = 1.28, p < 2.2× 10−16). The PRS was not associated with adenomyosis, suggesting that adenomyosis is not driven by the same genetic risk variants as endometriosis. Our results suggest that a PRS captures an increased risk of all types of endometriosis rather than an increased risk for endometriosis in specific locations. Although the discriminative accuracy is not yet sufficient as a stand-alone clinical utility, our data demonstrate that genetics risk variants in form of a simple PRS may add significant new discriminatory value. We suggest that an endometriosis PRS in combination with classical clinical risk factors and symptoms could be an important step in developing an urgently needed endometriosis risk stratification tool.
Collapse
Affiliation(s)
- Kirstine Kloeve-Mogensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Simone Twisttmann
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Marianne Nygaard
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Christian Møller Dahl
- Department of Business and Economics, University of Southern Denmark, Odense, Denmark
| | - Dorte Rytter
- Research Unit for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
| | | | - Axel Forman
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Skejby, Denmark
| | - Lene Christiansen
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Mette Nyegaard
| |
Collapse
|
15
|
Rohde PD, Nyegaard M, Kjolby M, Sørensen P. Multi-Trait Genomic Risk Stratification for Type 2 Diabetes. Front Med (Lausanne) 2021; 8:711208. [PMID: 34568370 PMCID: PMC8455930 DOI: 10.3389/fmed.2021.711208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/18/2021] [Accepted: 08/05/2021] [Indexed: 01/14/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is continuously rising with more disease cases every year. T2DM is a chronic disease with many severe comorbidities and therefore remains a burden for the patient and the society. Disease prevention, early diagnosis, and stratified treatment are important elements in slowing down the increase in diabetes prevalence. T2DM has a substantial genetic component with an estimated heritability of 40-70%, and more than 500 genetic loci have been associated with T2DM. Because of the intrinsic genetic basis of T2DM, one tool for risk assessment is genome-wide genetic risk scores (GRS). Current GRS only account for a small proportion of the T2DM risk; thus, better methods are warranted for more accurate risk assessment. T2DM is correlated with several other diseases and complex traits, and incorporating this information by adjusting effect size of the included markers could improve risk prediction. The aim of this study was to develop multi-trait (MT)-GRS leveraging correlated information. We used phenotype and genotype information from the UK Biobank, and summary statistics from two independent T2DM studies. Marker effects for T2DM and seven correlated traits, namely, height, body mass index, pulse rate, diastolic and systolic blood pressure, smoking status, and information on current medication use, were estimated (i.e., by logistic and linear regression) within the UK Biobank. These summary statistics, together with the two independent training summary statistics, were incorporated into the MT-GRS prediction in different combinations. The prediction accuracy of the MT-GRS was improved by 12.5% compared to the single-trait GRS. Testing the MT-GRS strategy in two independent T2DM studies resulted in an elevated accuracy by 50-94%. Finally, combining the seven information traits with the two independent T2DM studies further increased the prediction accuracy by 34%. Across comparisons, body mass index and current medication use were the two traits that displayed the largest weights in construction of the MT-GRS. These results explicitly demonstrate the added benefit of leveraging correlated information when constructing genetic scores. In conclusion, constructing GRS not only based on the disease itself but incorporating genomic information from other correlated traits as well is strongly advisable for obtaining improved individual risk stratification.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mads Kjolby
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Population Health and Genomics, University of Dundee, Dundee, United Kingdom.,Department of Clinical Pharmacology, Aarhus University Hospital, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Sørensen
- Centre for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| |
Collapse
|
16
|
Rohde PD, Kristensen TN, Sarup P, Muñoz J, Malmendal A. Prediction of complex phenotypes using the Drosophila melanogaster metabolome. Heredity (Edinb) 2021; 126:717-732. [PMID: 33510469 PMCID: PMC8102504 DOI: 10.1038/s41437-021-00404-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/18/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding the genotype-phenotype map and how variation at different levels of biological organization is associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at DNA level and on intermediate endophenotypes, such as RNA, proteins and metabolites. This can facilitate our understanding of the link between genotypes and molecular and functional organismal phenotypes. Here, we use the Drosophila melanogaster Genetic Reference Panel and nuclear magnetic resonance (NMR) metabolomics to investigate the ability of the metabolome to predict organismal phenotypes. We performed NMR metabolomics on four replicate pools of male flies from each of 170 different isogenic lines. Our results show that metabolite profiles are variable among the investigated lines and that this variation is highly heritable. Second, we identify genes associated with metabolome variation. Third, using the metabolome gave better prediction accuracies than genomic information for four of five quantitative traits analyzed. Our comprehensive characterization of population-scale diversity of metabolomes and its genetic basis illustrates that metabolites have large potential as predictors of organismal phenotypes. This finding is of great importance, e.g., in human medicine, evolutionary biology and animal and plant breeding.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Pernille Sarup
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Nordic Seed A/S, Odder, Denmark
| | - Joaquin Muñoz
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Malmendal
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
| |
Collapse
|
17
|
Rohde PD, Fourie Sørensen I, Sørensen P. qgg: an R package for large-scale quantitative genetic analyses. Bioinformatics 2019; 36:2614-2615. [DOI: 10.1093/bioinformatics/btz955] [Citation(s) in RCA: 25] [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] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 01/03/2023] Open
Abstract
Abstract
Summary
Here, we present the R package qgg, which provides an environment for large-scale genetic analyses of quantitative traits and diseases. The qgg package provides an infrastructure for efficient processing of large-scale genetic data and functions for estimating genetic parameters, and performing single and multiple marker association analyses and genomic-based predictions of phenotypes.
Availability and implementation
The qgg package is freely available. For the latest updates, user guides and example scripts, consult the main page http://psoerensen.github.io/qgg. The current release is available from CRAN (https://CRAN.R-project.org/package=qgg) for all major operating systems.
Supplementary information
Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Peter Sørensen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| |
Collapse
|
18
|
Affiliation(s)
- Palle Duun Rohde
- Department of Molecular Biology & Genetics, Aarhus University, Aarhus, Denmark
| | | |
Collapse
|
19
|
Rohde PD, Jensen IR, Sarup PM, Ørsted M, Demontis D, Sørensen P, Kristensen TN. Genetic Signatures of Drug Response Variability in Drosophila melanogaster. Genetics 2019; 213:633-650. [PMID: 31455722 PMCID: PMC6781897 DOI: 10.1534/genetics.119.302381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 05/31/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022] Open
Abstract
Knowledge of the genetic basis underlying variation in response to environmental exposures or treatments is important in many research areas. For example, knowing the set of causal genetic variants for drug responses could revolutionize personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying behavioral variability in response to methylphenidate (MPH), a drug used in the treatment of attention-deficit/hyperactivity disorder. We exposed a wild-type D. melanogaster population to MPH and a control treatment, and observed an increase in locomotor activity in MPH-exposed individuals. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations. To confirm these patterns in a different genetic background and to further advance knowledge on the genetic signature of drug response variability, we used a system of inbred lines, the Drosophila Genetic Reference Panel (DGRP). Based on the DGRP, we showed that the behavioral response to MPH was strongly genotype-dependent. Using an integrative genomic approach, we incorporated known gene interactions into the genomic analyses of the DGRP, and identified putative candidate genes for variability in drug response. We successfully validated 71% of the investigated candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross-generational behavioral and transcriptomic effects. Our findings establish a foundation for understanding the genetic mechanisms driving genotype-specific responses to medical treatment, and highlight the opportunities that integrative genomic approaches have in optimizing medical treatment of complex diseases.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
| | - Iben Ravnborg Jensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Pernille Merete Sarup
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Michael Ørsted
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
- Department of Biomedicine, Aarhus University, 8000, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Torsten Nygaard Kristensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
- Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University, 8000, Denmark
| |
Collapse
|
20
|
Ørsted M, Hoffmann AA, Rohde PD, Sørensen P, Kristensen TN. Strong impact of thermal environment on the quantitative genetic basis of a key stress tolerance trait. Heredity (Edinb) 2018; 122:315-325. [PMID: 30050062 DOI: 10.1038/s41437-018-0117-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/16/2022] Open
Abstract
Most organisms experience variable and sometimes suboptimal environments in their lifetime. While stressful environmental conditions are normally viewed as a strong selective force, they can also impact directly on the genetic basis of traits such as through environment-dependent gene action. Here, we used the Drosophila melanogaster Genetic Reference Panel to investigate the impact of developmental temperature on variance components and evolutionary potential of cold tolerance. We reared 166 lines at five temperatures and assessed cold tolerance of adult male flies from each line and environment. We show (1) that the expression of genetic variation for cold tolerance is highly dependent on developmental temperature, (2) that the genetic correlation of cold tolerance between environments decreases as developmental temperatures become more distinct, (3) that the correlation between cold tolerance at individual developmental temperatures and plasticity for cold tolerance differs across developmental temperatures, and even switches sign across the thermal developmental gradient, and (4) that evolvability decrease with increasing developmental temperatures. Our results show that the quantitative genetic basis of low temperature tolerance is environment specific. This conclusion is important for the understanding of evolution in variable thermal environments and for designing experiments aimed at pinpointing candidate genes and performing functional analyses of thermal resistance.
Collapse
Affiliation(s)
- Michael Ørsted
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Aalborg E, 9220, Denmark. .,Department of Bioscience, Section of Genetics, Ecology and Evolution, Aarhus University, Aarhus C, 8000, Denmark.
| | - Ary Anthony Hoffmann
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Aalborg E, 9220, Denmark.,School of Biosciences, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Palle Duun Rohde
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - Peter Sørensen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Aalborg E, 9220, Denmark.,Department of Bioscience, Section of Genetics, Ecology and Evolution, Aarhus University, Aarhus C, 8000, Denmark
| |
Collapse
|
21
|
Ørsted M, Rohde PD, Hoffmann AA, Sørensen P, Kristensen TN. Environmental variation partitioned into separate heritable components. Evolution 2017; 72:136-152. [DOI: 10.1111/evo.13391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Michael Ørsted
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Palle Duun Rohde
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
- i PSYCH; The Lundbeck Foundation Initiative for Integrative Psychiatric Research; 8000 Aarhus C Denmark
- i SEQ, Center for Integrative Sequencing; Aarhus University; Bartholins Allé 6 8000 Aarhus C Denmark
| | - Ary Anthony Hoffmann
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
| | - Torsten Nygaard Kristensen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- Section of Genetics, Ecology and Evolution, Department of Bioscience; Aarhus University; 8000 Aarhus C Denmark
| |
Collapse
|
22
|
Rohde PD, Gaertner B, Ward K, Sørensen P, Mackay TFC. Genomic Analysis of Genotype-by-Social Environment Interaction for Drosophila melanogaster Aggressive Behavior. Genetics 2017; 206:1969-1984. [PMID: 28550016 PMCID: PMC5560801 DOI: 10.1534/genetics.117.200642] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Human psychiatric disorders such as schizophrenia, bipolar disorder, and attention-deficit/hyperactivity disorder often include adverse behaviors including increased aggressiveness. Individuals with psychiatric disorders often exhibit social withdrawal, which can further increase the probability of conducting a violent act. Here, we used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to investigate the genetic basis of variation in male aggressive behavior for flies reared in a socialized and socially isolated environment. We identified genetic variation for aggressive behavior, as well as significant genotype-by-social environmental interaction (GSEI); i.e., variation among DGRP genotypes in the degree to which social isolation affected aggression. We performed genome-wide association (GWA) analyses to identify genetic variants associated with aggression within each environment. We used genomic prediction to partition genetic variants into gene ontology (GO) terms and constituent genes, and identified GO terms and genes with high prediction accuracies in both social environments and for GSEI. The top predictive GO terms significantly increased the proportion of variance explained, compared to prediction models based on all segregating variants. We performed genomic prediction across environments, and identified genes in common between the social environments that turned out to be enriched for genome-wide associated variants. A large proportion of the associated genes have previously been associated with aggressive behavior in Drosophila and mice. Further, many of these genes have human orthologs that have been associated with neurological disorders, indicating partially shared genetic mechanisms underlying aggression in animal models and human psychiatric disorders.
Collapse
Affiliation(s)
- Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus, Denmark
- ISEQ, Center for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Bryn Gaertner
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Kirsty Ward
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Trudy F C Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
23
|
Sørensen IF, Edwards SM, Rohde PD, Sørensen P. Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster. Sci Rep 2017; 7:2413. [PMID: 28546557 PMCID: PMC5445101 DOI: 10.1038/s41598-017-02281-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/10/2017] [Indexed: 12/29/2022] Open
Abstract
The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal genetic variants. We aimed at searching for patterns in GBLUP-derived single-marker statistics, by including them in genetic marker set tests, that could reveal associations between a set of genetic markers (genomic feature) and a complex trait. GBLUP-derived set tests proved to be powerful for detecting genomic features, here defined by gene ontology (GO) terms, enriched for causal variants affecting a quantitative trait in a population with low degree of relatedness. Different set test approaches were compared using simulated data illustrating the impact of trait- and genomic feature-specific factors on detection power. We extended the most powerful single trait set test, covariance association test (CVAT), to a multiple trait setting. The multiple trait CVAT (MT-CVAT) identified functionally relevant GO categories associated with the quantitative trait, chill coma recovery time, in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel.
Collapse
Affiliation(s)
- Izel Fourie Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
| | - Stefan M Edwards
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, 8000, Aarhus, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000, Aarhus, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| |
Collapse
|
24
|
Rohde PD, Madsen LS, Neumann Arvidson SM, Loeschcke V, Demontis D, Kristensen TN. Testing candidate genes for attention-deficit/hyperactivity disorder in fruit flies using a high throughput assay for complex behavior. Fly (Austin) 2016; 10:25-34. [PMID: 26954609 DOI: 10.1080/19336934.2016.1158365] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fruit flies are important model organisms for functional testing of candidate genes in multiple disciplines, including the study of human diseases. Here we use a high-throughput locomotor activity assay to test the response on activity behavior of gene disruption in Drosophila melanogaster. The aim was to investigate the impact of disruption of 14 candidate genes for human attention-deficit/hyperactivity disorder (ADHD) on fly behavior. By obtaining a range of correlated measures describing the space of variables for behavioral activity we show, that some mutants display similar phenotypic responses, and furthermore, that the genes disrupted in those mutants had common molecular functions; namely processes related to cGMP activity, cation channels and serotonin receptors. All but one of the candidate genes resulted in aberrant behavioral activity, suggesting involvement of these genes in behavioral activity in fruit flies. Results provide additional support for the investigated genes being risk candidate genes for ADHD in humans.
Collapse
Affiliation(s)
- Palle Duun Rohde
- a Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University , Tjele , Denmark.,b The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,c Center for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark
| | - Lisbeth Strøm Madsen
- d Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University , Aalborg , Denmark
| | - Sandra Marie Neumann Arvidson
- d Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University , Aalborg , Denmark
| | - Volker Loeschcke
- e Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University , Aarhus , Denmark
| | - Ditte Demontis
- b The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,c Center for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark.,f Department of Biomedicine , Aarhus University , Aarhus , Denmark
| | - Torsten Nygaard Kristensen
- d Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University , Aalborg , Denmark
| |
Collapse
|
25
|
|
26
|
Rohde PD, Rippingale S. Patients' preference on compulsory admissions. Lancet 1976; 2:1304. [PMID: 63779 DOI: 10.1016/s0140-6736(76)92069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
27
|
Shapiro DA, Caplan HL, Rohde PD, Watson JP. Personal questionnaire changes and their correlates in a psychotherapeutic group. Br J Med Psychol 1975; 48:207-15. [PMID: 1191580 DOI: 10.1111/j.2044-8341.1975.tb02324.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Personal questionnaires were constructed for seven members of a psychotherapy group. Self-reported changes during group sessions and over a period of up to 10 months' treatment were analysed. There was no general pattern of 'improvement' either during sessions or in the longer term. There was evidence suggestive of an inverse relationship between changes during sessions and over the period of the study. Some clinically meaningful relationships were discerned between the present data and repertory grid and verbal behaviour measures on the same group members reported in a previous paper. Theoretical and methodological implications are discussed.
Collapse
|
28
|
Caplan HL, Rohde PD, Shapiro DA, Watson JP. Some correlates of repertory grid measures used to study a psychotherapeutic group. Br J Med Psychol 1975; 48:217-26. [PMID: 1191581 DOI: 10.1111/j.2044-8341.1975.tb02325.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Repertory grid data provided monthly by the members of a psychotherapeutic group were related to measures of verbal behaviour during group sessions in ways which were both statistically significant and psychologically meaningful. There was evidence that the group members re-enacted earlier patterns of family relationship in their mutual interaction. For individual patient members of the group, speaking, being spoken to, and introducing several kinds of topic into the group discussion had significant associations with grid variables implicating self-esteem and patterns of identification with parents; but the correlation patterns varied between patients.
Collapse
|
29
|
Hirsch SR, Gaind R, Rohde PD, Stevens BC, Wing JK. Outpatient maintenance of chronic schizophrenic patients with long-acting fluphenazine: double-blind placebo trial. Report to the Medical Research Council Committee on Clinical Trials in Psychiatry. Br Med J 1973; 1:633-7. [PMID: 4571196 PMCID: PMC1588639 DOI: 10.1136/bmj.1.5854.633] [Citation(s) in RCA: 202] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A double-blind placebo trial of fluphenazine decanoate, a long-acting phenothiazine, was carried out to determine its value in maintenance therapy of chronic schizophrenic outpatients already established on the drug for a minimum period of eight weeks. In low doses it was significantly more effective than placebo in preventing relapse and admission to hospital. Relapse was accompanied by a resurgence of specifically schizophrenic symptoms and by an increase in abnormalities described by the relatives. There was no difference between the experimental and control groups in the treatment required for depression. The group on active medication required more treatment for Parkinsonism, but this difference did not reach statistical significance.In the context of a well-run special clinic for outpatient follow-up of chronic schizophrenic patients these results confirm the usefulness of long-acting fluphenazine. By inference, the benefit of this treatment highlights the need for adequate community services to deal with the residual chronic disabilities which are characteristic of these patients.
Collapse
|