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Zhou H, McPeek MS. Overcoming the "feast or famine" effect: improved interaction testing in genome-wide association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580168. [PMID: 38405994 PMCID: PMC10888770 DOI: 10.1101/2024.02.13.580168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In genetic association analysis of complex traits, detection of interaction (either GxG or GxE) can help to elucidate the genetic architecture and biological mechanisms underlying the trait. Detection of interaction in a genome-wide association study (GWAS) can be methodologically challenging for various reasons, including a high burden of multiple comparisons when testing for epistasis between all possible pairs of a set of genomewide variants, as well as heteroscedasticity effects occurring in the presence of GxG or GxE interaction. In this paper, we address the problem of an even more striking phenomenon that we call the "feast or famine" effect that occurs when testing interaction in a genomewide context. As we verify, even in a simplified setting in which there is no interaction at all (and so no heteroscedasticity), in a GWAS to detect GxG or GxE interaction with a fixed genetic variant or environmental factor, the distribution of the genome-wide p-values under the null hypothesis is not the i.i.d. uniform one that is commonly assumed. Using standard methods, even if all SNPs are independent, some GWASs will have systematically underinflated p-values ("feast"), and others will have systematically overinflated p-values ("famine"), which can lead to false detection of interaction, reduced power, inconsistent results across studies, and failure to replicate true signal. This startling phenomenon is specific to detection of interaction in a GWAS, and it may partly explain why such detection has so far proved challenging and difficult to replicate. We show theoretically that the key cause of this phenomenon is which variables are conditioned on in the analysis, and this suggests an approach to correct the problem by changing the way the conditioning is done. Using this insight, we have developed the TINGA method to adjust the interaction test statistics to make their p-values closer to uniform under the null hypothesis. In simulations we show that TINGA both controls type 1 error and improves power. TINGA allows for covariates and population structure through use of a linear mixed model and accounts for heteroscedasticity. We apply TINGA to detection of epistasis in a study of flowering time in Arabidopsis thaliana.
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Affiliation(s)
- Huanlin Zhou
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, U.S.A
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Pledger SL, Ahmadizar F. Gene-environment interactions and the effect on obesity risk in low and middle-income countries: a scoping review. Front Endocrinol (Lausanne) 2023; 14:1230445. [PMID: 37664850 PMCID: PMC10474324 DOI: 10.3389/fendo.2023.1230445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/18/2023] [Indexed: 09/05/2023] Open
Abstract
Background Obesity represents a major and preventable global health challenge as a complex disease and a modifiable risk factor for developing other non-communicable diseases. In recent years, obesity prevalence has risen more rapidly in low- and middle-income countries (LMICs) compared to high-income countries (HICs). Obesity traits are shown to be modulated by an interplay of genetic and environmental factors such as unhealthy diet and physical inactivity in studies from HICs focused on populations of European descent; however, genetic heterogeneity and environmental differences prevent the generalisation of study results to LMICs. Primary research investigating gene-environment interactions (GxE) on obesity in LMICs is limited but expanding. Synthesis of current research would provide an overview of the interactions between genetic variants and environmental factors that underlie the obesity epidemic and identify knowledge gaps for future studies. Methods Three databases were searched systematically using a combination of keywords such as "genes", "obesity", "LMIC", "diet", and "physical activity" to find all relevant observational studies published before November 2022. Results Eighteen of the 1,373 articles met the inclusion criteria, of which one was a genome-wide association study (GWAS), thirteen used a candidate gene approach, and five were assigned as genetic risk score studies. Statistically significant findings were reported for 12 individual SNPs; however, most studies were small-scale and without replication. Conclusion Although the results suggest significant GxE interactions on obesity in LMICs, updated robust statistical techniques with more precise and standardised exposure and outcome measurements are necessary for translatable results. Future research should focus on improved quality replication efforts, emphasising large-scale and long-term longitudinal study designs using multi-ethnic GWAS.
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Affiliation(s)
- Sophia L. Pledger
- Department of Epidemiology and Global Health, Julius Global Health, University Medical Center Utrecht, Utrecht, Netherlands
| | - Fariba Ahmadizar
- Department of Data Science and Biostatistics, Julius Global Health, University Medical Center Utrecht, Utrecht, Netherlands
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Huang M, Claussnitzer M, Saadat A, Coral DE, Kalamajski S, Franks PW. Engineered allele substitution at PPARGC1A rs8192678 alters human white adipocyte differentiation, lipogenesis, and PGC-1α content and turnover. Diabetologia 2023; 66:1289-1305. [PMID: 37171500 PMCID: PMC10244287 DOI: 10.1007/s00125-023-05915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/17/2023] [Indexed: 05/13/2023]
Abstract
AIMS/HYPOTHESIS PPARGC1A encodes peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α), a central regulator of energy metabolism and mitochondrial function. A common polymorphism in PPARGC1A (rs8192678, C/T, Gly482Ser) has been associated with obesity and related metabolic disorders, but no published functional studies have investigated direct allele-specific effects in adipocyte biology. We examined whether rs8192678 is a causal variant and reveal its biological function in human white adipose cells. METHODS We used CRISPR-Cas9 genome editing to perform an allelic switch (C-to-T or T-to-C) at rs8192678 in an isogenic human pre-adipocyte white adipose tissue (hWAs) cell line. Allele-edited single-cell clones were expanded and screened to obtain homozygous T/T (Ser482Ser), C/C (Gly482Gly) and heterozygous C/T (Gly482Ser) isogenic cell populations, followed by functional studies of the allele-dependent effects on white adipocyte differentiation and mitochondrial function. RESULTS After differentiation, the C/C adipocytes were visibly less BODIPY-positive than T/T and C/T adipocytes, and had significantly lower triacylglycerol content. The C allele presented a dose-dependent lowering effect on lipogenesis, as well as lower expression of genes critical for adipogenesis, lipid catabolism, lipogenesis and lipolysis. Moreover, C/C adipocytes had decreased oxygen consumption rate (OCR) at basal and maximal respiration, and lower ATP-linked OCR. We determined that these effects were a consequence of a C-allele-driven dysregulation of PGC-1α protein content, turnover rate and transcriptional coactivator activity. CONCLUSIONS/INTERPRETATION Our data show allele-specific causal effects of the rs8192678 variant on adipogenic differentiation. The C allele confers lower levels of PPARGC1A mRNA and PGC-1α protein, as well as disrupted dynamics of PGC-1α turnover and activity, with downstream effects on cellular differentiation and mitochondrial function. Our study provides the first experimentally deduced insights on the effects of rs8192678 on adipocyte phenotype.
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Affiliation(s)
- Mi Huang
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Melina Claussnitzer
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alham Saadat
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel E Coral
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Sebastian Kalamajski
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden.
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Wuni R, Ventura EF, Curi-Quinto K, Murray C, Nunes R, Lovegrove JA, Penny M, Favara M, Sanchez A, Vimaleswaran KS. Interactions between genetic and lifestyle factors on cardiometabolic disease-related outcomes in Latin American and Caribbean populations: A systematic review. Front Nutr 2023; 10:1067033. [PMID: 36776603 PMCID: PMC9909204 DOI: 10.3389/fnut.2023.1067033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The prevalence of cardiometabolic diseases has increased in Latin American and the Caribbean populations (LACP). To identify gene-lifestyle interactions that modify the risk of cardiometabolic diseases in LACP, a systematic search using 11 search engines was conducted up to May 2022. Methods Eligible studies were observational and interventional studies in either English, Spanish, or Portuguese. A total of 26,171 publications were screened for title and abstract; of these, 101 potential studies were evaluated for eligibility, and 74 articles were included in this study following full-text screening and risk of bias assessment. The Appraisal tool for Cross-Sectional Studies (AXIS) and the Risk Of Bias In Non-Randomized Studies-of Interventions (ROBINS-I) assessment tool were used to assess the methodological quality and risk of bias of the included studies. Results We identified 122 significant interactions between genetic and lifestyle factors on cardiometabolic traits and the vast majority of studies come from Brazil (29), Mexico (15) and Costa Rica (12) with FTO, APOE, and TCF7L2 being the most studied genes. The results of the gene-lifestyle interactions suggest effects which are population-, gender-, and ethnic-specific. Most of the gene-lifestyle interactions were conducted once, necessitating replication to reinforce these results. Discussion The findings of this review indicate that 27 out of 33 LACP have not conducted gene-lifestyle interaction studies and only five studies have been undertaken in low-socioeconomic settings. Most of the studies were cross-sectional, indicating a need for longitudinal/prospective studies. Future gene-lifestyle interaction studies will need to replicate primary research of already studied genetic variants to enable comparison, and to explore the interactions between genetic and other lifestyle factors such as those conditioned by socioeconomic factors and the built environment. The protocol has been registered on PROSPERO, number CRD42022308488. Systematic review registration https://clinicaltrials.gov, identifier CRD420223 08488.
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Affiliation(s)
- Ramatu Wuni
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Reading, United Kingdom
| | - Eduard F Ventura
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Reading, United Kingdom
| | | | - Claudia Murray
- Department of Real Estate and Planning, University of Reading, Reading, United Kingdom
| | - Richard Nunes
- Department of Real Estate and Planning, University of Reading, Reading, United Kingdom
| | - Julie A Lovegrove
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Reading, United Kingdom
| | - Mary Penny
- Instituto de Investigación Nutricional, Lima, Peru
| | - Marta Favara
- Oxford Department of International Development, University of Oxford, Oxford, United Kingdom
| | - Alan Sanchez
- Grupo de Análisis para el Desarrollo (GRADE), Lima, Peru
| | - Karani Santhanakrishnan Vimaleswaran
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences and Institute for Cardiovascular and Metabolic Research (ICMR), University of Reading, Reading, United Kingdom.,Institute for Food, Nutrition and Health (IFNH), University of Reading, Reading, United Kingdom
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McArdle CE, Bokhari H, Rodell CC, Buchanan V, Preudhomme LK, Isasi CR, Graff M, North K, Gallo LC, Pirzada A, Daviglus ML, Wojcik G, Cai J, Perreira K, Fernandez-Rhodes L. Findings from the Hispanic Community Health Study/Study of Latinos on the Importance of Sociocultural Environmental Interactors: Polygenic Risk Score-by-Immigration and Dietary Interactions. Front Genet 2021; 12:720750. [PMID: 34938310 PMCID: PMC8685455 DOI: 10.3389/fgene.2021.720750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/08/2021] [Indexed: 01/05/2023] Open
Abstract
Introduction: Hispanic/Latinos experience a disproportionate burden of obesity. Acculturation to US obesogenic diet and practices may lead to an exacerbation of innate genetic susceptibility. We examined the role of gene-environment interactions to better characterize the sociocultural environmental determinants and their genome-scale interactions, which may contribute to missing heritability of obesity. We utilized polygenic risk scores (PRSs) for body mass index (BMI) to perform analyses of PRS-by-acculturation and other environmental interactors among self-identified Hispanic/Latino adults from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Methods: PRSs were derived using genome-wide association study (GWAS) weights from a publicly available, large meta-analysis of European ancestry samples. Generalized linear models were run using a set of a priori acculturation-related and environmental factors measured at visit 1 (2008-2011) and visit 2 (2014-2016) in an analytic subsample of 8,109 unrelated individuals with genotypic, phenotypic, and complete case data at both visits. We evaluated continuous measures of BMI and waist-to-hip ratio. All models were weighted for complex sampling design, combined, and sex-stratified. Results: Overall, we observed a consistent increase of BMI with greater PRS across both visits. We found the best-fitting model adjusted for top five principal components of ancestry, sex, age, study site, Hispanic/Latino background genetic ancestry group, sociocultural factors and PRS interactions with age at immigration, years since first arrival to the United States (p < 0.0104), and healthy diet (p < 0.0036) and explained 16% of the variation in BMI. For every 1-SD increase in PRS, there was a corresponding 1.10 kg/m2 increase in BMI (p < 0.001). When these results were stratified by sex, we observed that this 1-SD effect of PRS on BMI was greater for women than men (1.45 vs. 0.79 kg/m2, p < 0.001). Discussion: We observe that age at immigration and the adoption of certain dietary patterns may play a significant role in modifying the effect of genetic risk on obesity. Careful consideration of sociocultural and immigration-related factors should be evaluated. The role of nongenetic factors, including the social environment, should not be overlooked when describing the performance of PRS or for promoting population health in understudied populations in genomics.
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Affiliation(s)
- Cristin E. McArdle
- Department of Biobehavioral Health, College of Health and Human Development, The Pennsylvania State University, University Park, PA, United States,*Correspondence: Cristin E. McArdle,
| | - Hassan Bokhari
- Department of Biobehavioral Health, College of Health and Human Development, The Pennsylvania State University, University Park, PA, United States
| | - Clinton C. Rodell
- Carey Business School, Johns Hopkins University, Baltimore, MD, United States
| | - Victoria Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Liana K. Preudhomme
- Department of Psychology, University of Miami, Coral Gables, FL, United States
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kari North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Carolina Center for Genome Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Linda C. Gallo
- Department of Psychology, San Diego State University, San Diego, CA, United States
| | - Amber Pirzada
- Institute for Minority Health Research, Carle Illinois College of Medicine, University of Illinois at Urbana–Champaign, Champaign, IL, United States
| | - Martha L. Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, United States
| | - Genevieve Wojcik
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, United States
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Krista Perreira
- Department of Social Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, The Pennsylvania State University, University Park, PA, United States,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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6
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McDaniel T, Wilson DK, Coulon MS, Sweeney AM, Van Horn ML. Interaction of Neighborhood and Genetic Risk on Waist Circumference in African-American Adults: A Longitudinal Study. Ann Behav Med 2021; 55:708-719. [PMID: 32914830 DOI: 10.1093/abm/kaaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Understanding determinants of metabolic risk has become a national priority given the increasingly high prevalence rate of this condition among U.S. adults. PURPOSE This study's aim was to assess the impact of gene-by-neighborhood social environment interactions on waist circumference (WC) as a primary marker of metabolic risk in underserved African-American adults. Based on a dual-risk model, it was hypothesized that those with the highest genetic risk and who experienced negative neighborhood environment conditions would demonstrate higher WC than those with fewer risk factors. METHODS This study utilized a subsample of participants from the Positive Action for Today's Health environmental intervention to improve access and safety for walking in higher-crime neighborhoods, who were willing to provide buccal swab samples for genotyping stress-related genetic pathways. Assessments were conducted with 228 African-American adults at baseline, 12, 18, and 24 months. RESULTS Analyses indicated three significant gene-by-environment interactions on WC outcomes within the sympathetic nervous system (SNS) genetic pathway. Two interactions supported the dual-risk hypotheses, including the SNS genetic risk-by-neighborhood social life interaction (b = -0.11, t(618) = -2.02, p = .04), and SNS genetic risk-by-informal social control interaction (b = -0.51, t(618) = -1.95, p = .05) on WC outcomes. These interactions indicated that higher genetic risk and lower social-environmental supports were associated with higher WC. There was also one significant SNS genetic risk-by-neighborhood satisfaction interaction (b = 1.48, t(618) = 2.23, p = .02) on WC that was inconsistent with the dual-risk pattern. CONCLUSIONS Findings indicate that neighborhood and genetic factors dually influence metabolic risk and that these relations may be complex and warrant further study. TRIAL REGISTRATION NCT01025726.
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Affiliation(s)
- Tyler McDaniel
- Department of Psychology, Barnwell College, University of South Carolina, Columbia, SC, USA
| | - Dawn K Wilson
- Department of Psychology, Barnwell College, University of South Carolina, Columbia, SC, USA
| | - M Sandra Coulon
- Department of Mental Health, Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - Allison M Sweeney
- Department of Psychology, Barnwell College, University of South Carolina, Columbia, SC, USA
| | - M Lee Van Horn
- Department of Educational Psychology, University of New Mexico, Albuquerque, NM, USA
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Schnurr TM, Stallknecht BM, Sørensen TIA, Kilpeläinen TO, Hansen T. Evidence for shared genetics between physical activity, sedentary behaviour and adiposity-related traits. Obes Rev 2021; 22:e13182. [PMID: 33354910 DOI: 10.1111/obr.13182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Observational, cross-sectional and longitudinal studies showed that physical activity and sedentary behaviour are associated with adiposity-related traits, apparently in a bidirectional manner. Physical activity is also suggested to suppress the genetic risk of adiposity. Since phenotypic associations with genetic variants are not subject to reverse causation or confounding, they may be used as tools to shed light on cause and effect in this complex interdependency. We review the evidence for shared genetics of physical activity and adiposity-related traits and for gene-by-physical activity interactions on adiposity-related traits in human studies. We outline limitations, challenges and opportunities in studying and understanding of these relationships. In summary, physical activity and sedentary behaviour are genetically correlated with body mass index and fat percentage but may not be correlated with lean body mass. Mendelian randomisation analyses show that physical activity and sedentary behaviour have bidirectional relationships with adiposity. Several studies suggest that physical activity suppresses genetic risk of adiposity. No studies have yet tested whether adiposity enhances genetic predisposition to sedentariness. The complexity of the comprehensive causal model makes the assessment of the single or combined components challenging. Substantial progress in this field may need long-term intervention studies.
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Affiliation(s)
- Theresia M Schnurr
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bente M Stallknecht
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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A statistical approach for high order epistasis interaction detection for prediction of diabetic macular edema. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ahmad S, Fatima SS, Rukh G, Smith CE. Gene Lifestyle Interactions With Relation to Obesity, Cardiometabolic, and Cardiovascular Traits Among South Asians. Front Endocrinol (Lausanne) 2019; 10:221. [PMID: 31024458 PMCID: PMC6465946 DOI: 10.3389/fendo.2019.00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/20/2019] [Indexed: 01/05/2023] Open
Abstract
The rapid rise of obesity, type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD) during the last few decades among South Asians has been largely attributed to a major shift in lifestyles including physical inactivity, unhealthy dietary patterns, and an overall pattern of sedentary lifestyle. Genetic predisposition to these cardiometabolic risk factors may have interacted with these obesogenic environments in determining the higher cardiometabolic disease prevalence. Based on the premise that gene-environment interactions cause obesity and cardiometabolic diseases, we systematically searched the literature and considered the knowledge gaps that future studies might fulfill. We identified only seven published studies that focused specifically on gene-environment interactions for cardiometabolic traits in South Asians, most of which were limited by relatively small sample and lack of replication. Some studies reported that the differences in metabolic response to higher physical activity and low caloric diet might be modified by genetic risk related to these cardiometabolic traits. Although studies on gene lifestyle interactions in cardiometabolic traits report significant interactions, future studies must focus on more precise assessment of lifestyle factors, investigation of a larger set of genetic variants and the application of powerful statistical methods to facilitate translatable approaches. Future studies should also be integrated with findings both using mechanistic studies through laboratory settings and randomized clinical trials for clinical outcomes.
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Affiliation(s)
- Shafqat Ahmad
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
- Preventive Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- *Correspondence: Shafqat Ahmad
| | - Syeda Sadia Fatima
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Gull Rukh
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Caren E. Smith
- Nutrition and Genomics Laboratory, Jean Mayer U. S. Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA, United States
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Ahmad S, Ahluwalia TS. Editorial: The Role of Genetic and Lifestyle Factors in Metabolic Diseases. Front Endocrinol (Lausanne) 2019; 10:475. [PMID: 31379743 PMCID: PMC6650930 DOI: 10.3389/fendo.2019.00475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/01/2019] [Indexed: 12/01/2022] Open
Affiliation(s)
- Shafqat Ahmad
- Molecular Epidemiology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Preventive Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- *Correspondence: Shafqat Ahmad
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Franks PW, Timpson NJ. Genotype-Based Recall Studies in Complex Cardiometabolic Traits. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001947. [PMID: 30354344 PMCID: PMC6813040 DOI: 10.1161/circgen.118.001947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In genotype-based recall (GBR) studies, people (or their biological samples) who carry genotypes of special interest for a given hypothesis test are recalled from a larger cohort (or biobank) for more detailed investigations. There are several GBR study designs that offer a range of powerful options to elucidate (1) genotype-phenotype associations (by increasing the efficiency of genetic association studies, thereby allowing bespoke phenotyping in relatively small cohorts), (2) the effects of environmental exposures (within the Mendelian randomization framework), and (3) gene-treatment interactions (within the setting of GBR interventional trials). In this review, we overview the literature on GBR studies as applied to cardiometabolic health outcomes. We also review the GBR approaches used to date and outline new methods and study designs that might enhance the utility of GBR-focused studies. Specifically, we highlight how GBR methods have the potential to augment randomized controlled trials, providing an alternative application for the now increasingly accepted Mendelian randomization methods usually applied to large-scale population-based data sets. Further to this, we consider how functional and basic science approaches alongside GBR designs offer intellectually intriguing and potentially powerful ways to explore the implications of alterations to specific (and potentially druggable) biological pathways.
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Affiliation(s)
- Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, SE-21741, Malmö, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, Avon Longitudinal Study of Parents and Children, Population Health Science, Bristol Medical School, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
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Coleman JRI, Krapohl E, Eley TC, Breen G. Individual and shared effects of social environment and polygenic risk scores on adolescent body mass index. Sci Rep 2018; 8:6344. [PMID: 29679049 PMCID: PMC5910407 DOI: 10.1038/s41598-018-24774-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/15/2018] [Indexed: 11/20/2022] Open
Abstract
Juvenile obesity is associated with adverse health outcomes. Understanding genetic and environmental influences on body mass index (BMI) during adolescence could inform interventions. We investigated independent and interactive effects of parenting, socioeconomic status (SES) and polygenic risk on BMI pre-adolescence, and on the rate of change in BMI across adolescence. Genome-wide genotype data, BMI and child perceptions of parental warmth and punitive discipline were available at 11 years old, and parental SES was available from birth on 3,414 unrelated participants. Linear models were used to test the effects of social environment and polygenic risk on pre-adolescent BMI. Change in BMI across adolescence was assessed in a subset (N = 1943). Sex-specific effects were assessed. Higher genetic risk was associated with increased BMI pre-adolescence and across adolescence (p < 0.00417, corrected for multiple tests). Negative parenting was not significantly associated with either phenotype, but lower SES was associated with increased BMI pre-adolescence. No interactions passed correction for multiple testing. Polygenic risk scores from adult GWAS meta-analyses are associated with BMI in juveniles, suggesting a stable genetic component. Pre-adolescent BMI was associated with social environment, but parental style has, at most, a small effect.
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Affiliation(s)
- Jonathan R I Coleman
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK.,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK
| | - Eva Krapohl
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK
| | - Thalia C Eley
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK. .,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK.
| | - Gerome Breen
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK. .,National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK.
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13
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Uppu S, Krishna A, Gopalan RP. A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:599-612. [PMID: 28060710 DOI: 10.1109/tcbb.2016.2635125] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature. These interaction studies are mathematically challenging and computationally complex. These challenges have been addressed by a number of data mining and machine learning approaches. This paper reviews the current methods and the related software packages to detect the SNP interactions that contribute to diseases. The issues that need to be considered when developing these models are addressed in this review. The paper also reviews the achievements in data simulation to evaluate the performance of these models. Further, it discusses the future of SNP interaction analysis.
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Guasch-Ferré M, Dashti HS, Merino J. Nutritional Genomics and Direct-to-Consumer Genetic Testing: An Overview. Adv Nutr 2018; 9:128-135. [PMID: 29659694 PMCID: PMC5916428 DOI: 10.1093/advances/nmy001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 12/26/2017] [Indexed: 01/04/2023] Open
Abstract
The increasing prevalence in polygenic diseases, such as obesity, cardiovascular disease, and type 2 diabetes, observed over the past few decades is more likely linked to a rapid transition in lifestyle rather than to changes in the sequence of the nuclear genome. In the new era of precision medicine, nutritional genomics holds the promise to be translated into tailored nutritional strategies to prevent and manage polygenic diseases more effectively. Nutritional genomics aims to prevent, treat, and manage polygenic diseases through targeted therapies formulated from individuals' genetic makeup and dietary intake. Direct-to-consumer genetic testing (DTC-GT) has become commercially available to equip individuals with information on their genetic vulnerability to different diseases. This information may potentially prompt behavioral changes against adverse factors. However, scientific evidence behind the clinical recommendations is a matter of continuous debate, and behavioral modifications after disclosing genetic information remain inconclusive. In this review, we provide an overview of nutritional genomics and related nutritional DTC-GT services and discuss whether available data are sufficient to be translated into clinical recommendations and public health initiatives. Overall, the scientific evidence supporting the dissemination of genomic information for nutrigenomic purposes remains sparse. Therefore, additional knowledge needs to be generated, particularly for polygenic traits.
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Affiliation(s)
- Marta Guasch-Ferré
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA
| | - Hassan S Dashti
- Center for Genomic Medicine Massachusetts General Hospital, Boston, MA,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jordi Merino
- Center for Genomic Medicine Massachusetts General Hospital, Boston, MA,Center for Diabetes Unit, Massachusetts General Hospital, Boston, MA,Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA,Address correspondence to JM (e-mail: )
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15
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Gene-lifestyle interplay in type 2 diabetes. Curr Opin Genet Dev 2018; 50:35-40. [PMID: 29459268 DOI: 10.1016/j.gde.2018.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Type 2 diabetes (T2D) is widespread, affecting the health of hundreds of millions worldwide. The disease results from the complex interplay of lifestyle factors acting on a backdrop of inherited DNA risk variants. Detecting and understanding biomarkers, whether genotypes or other downstream biological features that dictate a person's phenotypic response to different lifestyle exposures, may have tremendous utility in the prevention of T2D. Here, we explore (i) evidence of how human genetic adaptation to diverse local environments might interact with lifestyle factors in T2D, (ii) the key challenges facing the research area of gene×lifestyle interactions in T2D, and (iii) the solutions that might be pursued in future studies. Overall, many preliminary examples of such interactions exist, but none is sufficient to have a major impact on clinical decision making. Future studies, integrating genetics and other biological markers into regulatory networks, are likely to be necessary to facilitate the integration of genomics into lifestyle medicine in T2D.
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16
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Romieu I, Dossus L, Barquera S, Blottière HM, Franks PW, Gunter M, Hwalla N, Hursting SD, Leitzmann M, Margetts B, Nishida C, Potischman N, Seidell J, Stepien M, Wang Y, Westerterp K, Winichagoon P, Wiseman M, Willett WC. Energy balance and obesity: what are the main drivers? Cancer Causes Control 2017; 28:247-258. [PMID: 28210884 PMCID: PMC5325830 DOI: 10.1007/s10552-017-0869-z] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE The aim of this paper is to review the evidence of the association between energy balance and obesity. METHODS In December 2015, the International Agency for Research on Cancer (IARC), Lyon, France convened a Working Group of international experts to review the evidence regarding energy balance and obesity, with a focus on Low and Middle Income Countries (LMIC). RESULTS The global epidemic of obesity and the double burden, in LMICs, of malnutrition (coexistence of undernutrition and overnutrition) are both related to poor quality diet and unbalanced energy intake. Dietary patterns consistent with a traditional Mediterranean diet and other measures of diet quality can contribute to long-term weight control. Limiting consumption of sugar-sweetened beverages has a particularly important role in weight control. Genetic factors alone cannot explain the global epidemic of obesity. However, genetic, epigenetic factors and the microbiota could influence individual responses to diet and physical activity. CONCLUSION Energy intake that exceeds energy expenditure is the main driver of weight gain. The quality of the diet may exert its effect on energy balance through complex hormonal and neurological pathways that influence satiety and possibly through other mechanisms. The food environment, marketing of unhealthy foods and urbanization, and reduction in sedentary behaviors and physical activity play important roles. Most of the evidence comes from High Income Countries and more research is needed in LMICs.
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Affiliation(s)
- Isabelle Romieu
- Nutrition and Metabolism Section, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372, Lyon Cedex 08, France.
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - Simón Barquera
- Centro de Investigación en Nutrición y Salud, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Hervé M Blottière
- Micalis Institute, MGP MetagenoPolis, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, CRC, University hospital Malmö, Malmö, Sweden
| | - Marc Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - Nahla Hwalla
- Faculty of Agricultural and Food Science, American University of Beirut, Beirut, Lebanon
| | - Stephen D Hursting
- Department of Nutrition and the Nutrition Research Institute, The University of North Carolina, Chapel Hill, USA
| | - Michael Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Barrie Margetts
- Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Chizuru Nishida
- Nutrition Policy and Scientific Advice (NPU), Department of Nutrition for Health and Development (NHD), World Health Organization (WHO), Geneva, Switzerland
| | - Nancy Potischman
- Office of the Associate Director, Applied Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, USA
| | - Jacob Seidell
- Faculty of Earth and Life Sciences, Department of Health Sciences, University Amsterdam, Amsterdam, The Netherlands
| | - Magdalena Stepien
- Nutrition and Metabolism Section, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - Youfa Wang
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, Joint Appointments, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, USA
| | - Klaas Westerterp
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | | | | | - Walter C Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
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17
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Poveda A, Chen Y, Brändström A, Engberg E, Hallmans G, Johansson I, Renström F, Kurbasic A, Franks PW. The heritable basis of gene-environment interactions in cardiometabolic traits. Diabetologia 2017; 60:442-452. [PMID: 28004149 PMCID: PMC6518092 DOI: 10.1007/s00125-016-4184-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/24/2016] [Indexed: 11/17/2022]
Abstract
AIMS/HYPOTHESIS Little is known about the heritable basis of gene-environment interactions in humans. We therefore screened multiple cardiometabolic traits to assess the probability that they are influenced by genotype-environment interactions. METHODS Fourteen established environmental risk exposures and 11 cardiometabolic traits were analysed in the VIKING study, a cohort of 16,430 Swedish adults from 1682 extended pedigrees with available detailed genealogical, phenotypic and demographic information, using a maximum likelihood variance decomposition method in Sequential Oligogenic Linkage Analysis Routines software. RESULTS All cardiometabolic traits had statistically significant heritability estimates, with narrow-sense heritabilities (h 2) ranging from 24% to 47%. Genotype-environment interactions were detected for age and sex (for the majority of traits), physical activity (for triacylglycerols, 2 h glucose and diastolic BP), smoking (for weight), alcohol intake (for weight, BMI and 2 h glucose) and diet pattern (for weight, BMI, glycaemic traits and systolic BP). Genotype-age interactions for weight and systolic BP, genotype-sex interactions for BMI and triacylglycerols and genotype-alcohol intake interactions for weight remained significant after multiple test correction. CONCLUSIONS/INTERPRETATION Age, sex and alcohol intake are likely to be major modifiers of genetic effects for a range of cardiometabolic traits. This information may prove valuable for studies that seek to identify specific loci that modify the effects of lifestyle in cardiometabolic disease.
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Affiliation(s)
- Alaitz Poveda
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Jan Waldenströms gata 35, Building 91, Skåne University Hospital, SE-20502, Malmö, Sweden
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Yan Chen
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Jan Waldenströms gata 35, Building 91, Skåne University Hospital, SE-20502, Malmö, Sweden
| | - Anders Brändström
- Centre for Demographic and Ageing Research, Umeå University, Umeå, Sweden
| | - Elisabeth Engberg
- Centre for Demographic and Ageing Research, Umeå University, Umeå, Sweden
| | - Göran Hallmans
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Jan Waldenströms gata 35, Building 91, Skåne University Hospital, SE-20502, Malmö, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Azra Kurbasic
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Jan Waldenströms gata 35, Building 91, Skåne University Hospital, SE-20502, Malmö, Sweden
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund University, Jan Waldenströms gata 35, Building 91, Skåne University Hospital, SE-20502, Malmö, Sweden.
- Department of Public Health and Clinical Medicine, Section for Medicine, Umeå University, Umeå, Sweden.
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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18
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Proximate causes for diet-induced obesity in laboratory mice: a case study. Eur J Clin Nutr 2017; 71:306-317. [PMID: 28145422 DOI: 10.1038/ejcn.2016.243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND/OBJECTIVES Detailed protocols and recommendations for the assessment of energy balance have been provided to address the problems associated with different body mass and body composition as apparent for mouse models in obesity research. Here, we applied these guidelines to investigate energy balance in two inbred mouse strains with contrasting susceptibilities for diet-induced obesity (DIO). Mice of the AKR/J strain are highly susceptible, whereas the SWR/J mice are almost completely resistant. The proximate mechanisms responsible for this striking phenotypic difference are only partially understood. SUBJECTS/METHODS Body mass and body composition, metabolizable energy, energy expenditure (EE), body temperature and spontaneous physical activity behavior were first assessed in a cohort of male AKR/J (N=29) and SWR/J (N=30) mice fed on a low-fat control diet (CD) to identify metabolic adaptations determining resistance to DIO. Thereafter, the immediate metabolic responses to high-fat diet (HFD) feeding for 3 days were investigated. Groups of weight-matched AKR/J (N=8) and SWR/J (N=8) mice were selected from the initial cohort for this intervention. RESULTS Strain differences in body mass, fat mass and lean mass were adjusted by body mass as this was the only covariate significantly correlated with metabolizable energy and EE. On the CD, EE and fat oxidation was higher in SWR/J than in AKR/J mice, whereas no difference was found for metabolizable energy. In response to HFD feeding, both strains increased metabolizable energy intake, but also increased EE, body temperature, and fat oxidation. The catabolic adaptations to HFD feeding opposed the development of positive energy balance. Increased EE was not due to increased spontaneous physical activity. A significant strain difference was found when balancing metabolizable energy and daily energy expenditure (DEE). CONCLUSIONS The guidelines were applicable with some limitations related to the adjustment of differences in body composition. Metabolic phenotyping revealed that metabolizable energy, DEE and metabolic fuel selection all contribute to the development of DIO. Therefore, assessing both sides of the energy balance equation is essential to identify the proximate mechanisms.
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19
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Franks PW, McCarthy MI. Exposing the exposures responsible for type 2 diabetes and obesity. Science 2016; 354:69-73. [DOI: 10.1126/science.aaf5094] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Brunkwall L, Chen Y, Hindy G, Rukh G, Ericson U, Barroso I, Johansson I, Franks PW, Orho-Melander M, Renström F. Sugar-sweetened beverage consumption and genetic predisposition to obesity in 2 Swedish cohorts. Am J Clin Nutr 2016; 104:809-15. [PMID: 27465381 PMCID: PMC4997292 DOI: 10.3945/ajcn.115.126052] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The consumption of sugar-sweetened beverages (SSBs), which has increased substantially during the last decades, has been associated with obesity and weight gain. OBJECTIVE Common genetic susceptibility to obesity has been shown to modify the association between SSB intake and obesity risk in 3 prospective cohorts from the United States. We aimed to replicate these findings in 2 large Swedish cohorts. DESIGN Data were available for 21,824 healthy participants from the Malmö Diet and Cancer study and 4902 healthy participants from the Gene-Lifestyle Interactions and Complex Traits Involved in Elevated Disease Risk Study. Self-reported SSB intake was categorized into 4 levels (seldom, low, medium, and high). Unweighted and weighted genetic risk scores (GRSs) were constructed based on 30 body mass index [(BMI) in kg/m(2)]-associated loci, and effect modification was assessed in linear regression equations by modeling the product and marginal effects of the GRS and SSB intake adjusted for age-, sex-, and cohort-specific covariates, with BMI as the outcome. In a secondary analysis, models were additionally adjusted for putative confounders (total energy intake, alcohol consumption, smoking status, and physical activity). RESULTS In an inverse variance-weighted fixed-effects meta-analysis, each SSB intake category increment was associated with a 0.18 higher BMI (SE = 0.02; P = 1.7 × 10(-20); n = 26,726). In the fully adjusted model, a nominal significant interaction between SSB intake category and the unweighted GRS was observed (P-interaction = 0.03). Comparing the participants within the top and bottom quartiles of the GRS to each increment in SSB intake was associated with 0.24 (SE = 0.04; P = 2.9 × 10(-8); n = 6766) and 0.15 (SE = 0.04; P = 1.3 × 10(-4); n = 6835) higher BMIs, respectively. CONCLUSIONS The interaction observed in the Swedish cohorts is similar in magnitude to the previous analysis in US cohorts and indicates that the relation of SSB intake and BMI is stronger in people genetically predisposed to obesity.
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Affiliation(s)
| | - Yan Chen
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - George Hindy
- Diabetes and Cardiovascular Disease-Genetic Epidemiology and
| | - Gull Rukh
- Diabetes and Cardiovascular Disease-Genetic Epidemiology and
| | - Ulrika Ericson
- Diabetes and Cardiovascular Disease-Genetic Epidemiology and
| | - Inês Barroso
- National Institute for Health Research Cambridge Biomedical Research Centre and University of Cambridge, Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden; Public Health and Clinical Medicine, Section for Medicine, and Department of Nutrition, Harvard School of Public Health, Boston, MA
| | | | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden; Biobank Research, Umeå University, Umeå, Sweden; and
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Abstract
The genome is often the conduit through which environmental exposures convey their effects on health and disease. Whilst not all diseases act by directly perturbing the genome, the phenotypic responses are often genetically determined. Hence, whilst diseases are often defined has having differing degrees of genetic determination, genetic and environmental factors are, with few exceptions, inseparable features of most diseases, not least type 2 diabetes. It follows that to optimize diabetes, prevention and treatment will require that the etiological roles of genetic and environmental risk factors be jointly considered. As we discuss here, studies focused on quantifying gene-environment and gene-treatment interactions are gathering momentum and may eventually yield data that helps guide health-related choices and medical interventions for type 2 diabetes and other complex diseases.
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Affiliation(s)
- Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Clinical Research Center, Skåne University Hospital Malmö, Lund University, Building 91, Level 10, Jan Waldenströms gata 35, 205 02, Malmö, Sweden.
- Department of Public Health and Clinical Medicine, Umeå University, 90188, Umeå, Sweden.
- Department of Nutrition, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton General Hospital Campus, DB-CVSRI, 237 Barton Street East, Room C3103, Hamilton, ON, L8L 2X2, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Department of Clinical Epidemiology and Biostatistics, Population Genomics Program, McMaster University, Hamilton, ON, Canada
- Thrombosis and Atherosclerosis Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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22
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Differential expression of hypothalamic, metabolic and inflammatory genes in response to short-term calorie restriction in juvenile obese- and lean-prone JCR rats. Nutr Diabetes 2015; 5:e178. [PMID: 26302065 PMCID: PMC4558559 DOI: 10.1038/nutd.2015.28] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/08/2015] [Accepted: 07/21/2015] [Indexed: 01/02/2023] Open
Abstract
Background: Childhood obesity is an important early predictor of adult obesity and associated comorbidities. Common forms of obesity are underpinned by both environmental and genetic factors. However, the rising prevalence of obesity in genetically stable populations strongly suggests that contemporary lifestyle is a premier factor to the disease. In pediatric population, the current treatment/prevention options for obesity are lifestyle interventions such as caloric restriction (CR) and increase physical activity. In obese individuals, CR improves many metabolic parameters in peripheral tissues. Little is known about the effect of CR on the hypothalamus. This study aimed to assess the effect of CR on hypothalamic metabolic gene expression of young obese- and lean-prone animals. Methods: Male juvenile JCR:LA-cp obese-prone rats were freely fed (Obese-FF) or pair fed (Obese-FR) to lean-prone, free-feeding animals (Lean-FF). A group of lean-prone rats (Lean-FR) were matched for relative average degree of CR to Obese-FR rats. Results: In free-feeding conditions, obese-prone rats consumed more energy than lean-prone rats (P<0.001) and showed greater increases in body weight, fat mass, plasma glucose, insulin and lipids (P<0.01). These metabolic differences were associated with alterations of feeding-related neuropeptides expression in the hypothalamus, as well as pro-inflammatory cytokines and oxidative stress markers. When submitted to the same degree of CR, the two genotypes responded differently; hypothalamic inflammatory and oxidative stress gene expression was improved in Obese-FR, while it was worsened in Lean-FR rats. Conclusions: We demonstrate in JCR rats that the metabolic and inflammatory response of the brain to CR is genotype dependent.
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Yazdi FT, Clee SM, Meyre D. Obesity genetics in mouse and human: back and forth, and back again. PeerJ 2015; 3:e856. [PMID: 25825681 PMCID: PMC4375971 DOI: 10.7717/peerj.856] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Obesity is a major public health concern. This condition results from a constant and complex interplay between predisposing genes and environmental stimuli. Current attempts to manage obesity have been moderately effective and a better understanding of the etiology of obesity is required for the development of more successful and personalized prevention and treatment options. To that effect, mouse models have been an essential tool in expanding our understanding of obesity, due to the availability of their complete genome sequence, genetically identified and defined strains, various tools for genetic manipulation and the accessibility of target tissues for obesity that are not easily attainable from humans. Our knowledge of monogenic obesity in humans greatly benefited from the mouse obesity genetics field. Genes underlying highly penetrant forms of monogenic obesity are part of the leptin-melanocortin pathway in the hypothalamus. Recently, hypothesis-generating genome-wide association studies for polygenic obesity traits in humans have led to the identification of 119 common gene variants with modest effect, most of them having an unknown function. These discoveries have led to novel animal models and have illuminated new biologic pathways. Integrated mouse-human genetic approaches have firmly established new obesity candidate genes. Innovative strategies recently developed by scientists are described in this review to accelerate the identification of causal genes and deepen our understanding of obesity etiology. An exhaustive dissection of the molecular roots of obesity may ultimately help to tackle the growing obesity epidemic worldwide.
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Affiliation(s)
- Fereshteh T. Yazdi
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Susanne M. Clee
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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Huang T, Hu FB. Gene-environment interactions and obesity: recent developments and future directions. BMC Med Genomics 2015; 8 Suppl 1:S2. [PMID: 25951849 PMCID: PMC4315311 DOI: 10.1186/1755-8794-8-s1-s2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Obesity, a major public health concern, is a multifactorial disease caused by both environmental and genetic factors. Although recent genome-wide association studies have identified many loci related to obesity or body mass index, the identified variants explain only a small proportion of the heritability of obesity. Better understanding of the interplay between genetic and environmental factors is the basis for developing effective personalized obesity prevention and management strategies. This article reviews recent advances in identifying gene-environment interactions related to obesity and describes epidemiological designs and newly developed statistical approaches to characterizing and discovering gene-environment interactions on obesity risk.
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Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies. Curr Nutr Rep 2014; 3:400-411. [PMID: 25396097 DOI: 10.1007/s13668-014-0100-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Most complex diseases have well-established genetic and non-genetic risk factors. In some instances, these risk factors are likely to interact, whereby their joint effects convey a level of risk that is either significantly more or less than the sum of these risks. Characterizing these gene-environment interactions may help elucidate the biology of complex diseases, as well as to guide strategies for their targeted prevention. In most cases, the detection of gene-environment interactions will require sample sizes in excess of those needed to detect the marginal effects of the genetic and environmental risk factors. Although many consortia have been formed, comprising multiple diverse cohorts to detect gene-environment interactions, few robust examples of such interactions have been discovered. This may be because combining data across studies, usually through meta-analysis of summary data from the contributing cohorts, is often a statistically inefficient approach for the detection of gene-environment interactions. Ideally, single, very large and well-genotyped prospective cohorts, with validated measures of environmental risk factor and disease outcomes should be used to study interactions. The presence of strong founder effects within those cohorts might further strengthen the capacity to detect novel genetic effects and gene-environment interactions. Access to accurate genealogical data would also aid in studying the diploid nature of the human genome, such as genomic imprinting (parent-of-origin effects). Here we describe two studies from northern Sweden (the GLACIER and VIKING studies) that fulfill these characteristics.
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Estampador AC, Franks PW. Genetic and epigenetic catalysts in early-life programming of adult cardiometabolic disorders. Diabetes Metab Syndr Obes 2014; 7:575-86. [PMID: 25489250 PMCID: PMC4257022 DOI: 10.2147/dmso.s51433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Evidence has emerged across the past few decades that the lifetime risk of developing morbidities like type 2 diabetes, obesity, and cardiovascular disease may be influenced by exposures that occur in utero and in childhood. Developmental abnormalities are known to occur at various stages in fetal growth. Epidemiological and mechanistic studies have sought to delineate developmental processes and plausible risk factors influencing pregnancy outcomes and later health. Whether these observations reflect causal processes or are confounded by genetic and social factors remains unclear, although animal (and some human) studies suggest that epigenetic programming events may be involved. Regardless of the causal basis to observations of early-life risk factors and later disease risk, the fact that such associations exist and that they are of a fairly large magnitude justifies further research around this topic. Furthermore, additional information is needed to substantiate public health guidelines on lifestyle behaviors during pregnancy to improve infant health outcomes. Indeed, lifestyle intervention clinical trials in pregnancy are now coming online, where materials and data are being collected that should facilitate understanding of the causal nature of intrauterine exposures related with gestational weight gain, such as elevated maternal blood glucose concentrations. In this review, we provide an overview of these concepts.
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Affiliation(s)
- Angela C Estampador
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Endocrinology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Correspondence: Paul W Franks, Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, CRC, Building 91, Level 10, Jan Waldenströms Gata 35, Skåne University Hospital Malmö, SE-205 02, Malmö, Sweden, Tel +46 40 391 149, Fax +46 40 391 222, Email
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