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Gwynne K, Jiang S, Venema R, Christie V, Boughtwood T, Ritha M, Skinner J, Ali N, Rambaldini B, Calma T. Genomics and inclusion of Indigenous peoples in high income countries. Hum Genet 2023; 142:1407-1416. [PMID: 37479894 PMCID: PMC10449672 DOI: 10.1007/s00439-023-02587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
Genomics research related to Indigenous people has been at worst exploitative and at best, retrospectively on a journey to improve effective engagement of Indigenous individuals and communities. Genomics can positively impact all stages of clinical management, and to improve genomic effectiveness researchers aggregate genomic data from diverse global sub-populations, such as shared ancestry groupings, as people within these groupings will have a greater proportion of shared DNA traits. While genomics is already being used worldwide to improve lives, its utility and effectiveness has not been maximized for individuals with Indigenous ancestry. Several large datasets of human genetic variation have been made publicly available, of which the most widely used is the Genome Aggregation Database (gnomAD), but none of these databases currently contain any population-specific data for Indigenous populations. There are many reasons why Indigenous people have been largely left out of genomics research and, because of this, miss out on the benefits offered. It is also clear that if research is to be effective, it needs to be done 'with' and not 'on' Indigenous communities. This systematic review of the literature regarding Indigenous peoples (in high income countries) and genomics aims to review the existing literature and identify areas of strength and weakness in study design and conduct, focusing on the effectiveness of Indigenous community engagement.
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Affiliation(s)
- Kylie Gwynne
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Shirley Jiang
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Robertson Venema
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Vita Christie
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, 50 Flemington Rd, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Marida Ritha
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - John Skinner
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Nyesa Ali
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Boe Rambaldini
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Tom Calma
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
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Boyer BB, Hopkins SE, Wiener HW, Purnell JQ, O'Brien DM, Zhang CX, Aslan JE, Aliwarga T, Pomeroy JJ, Thummel KE, Tiwari HK. Habitual Intake of Marine-Derived n-3 PUFAs is Inversely Associated with a Cardiometabolic Inflammatory Profile in Yup'ik Alaska Native People. J Nutr 2022; 152:844-855. [PMID: 34871429 PMCID: PMC8891177 DOI: 10.1093/jn/nxab412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The relationship between dietary n-3 PUFAs and the prevention of cardiometabolic diseases, including type 2 diabetes, is unresolved. Examination of the association between n-3 PUFAs and chronic low-grade inflammation in a population where many individuals have had an extremely high intake of marine mammals and fish throughout their lifespan may provide important clues regarding the impact of n-3 PUFAs on health. OBJECTIVES The aim of this study was to explore associations between concentrations of n-3 PUFAs resulting from habitual intake of natural food sources high in fish and marine mammals with immune biomarkers of metabolic inflammation and parameters of glucose regulation. METHODS A total of 569 Yup'ik Alaska Native adults (18-87 years old) were enrolled in this cross-sectional study between December 2016 and November 2019. The RBC nitrogen isotope ratio (NIR; 15N/14N) was used as a validated measure of n-3 PUFA intake to select 165 participant samples from the first and fourth quartiles of n-3 PUFA intakes. Outcomes included 38 pro- and anti-inflammatory cytokines and 8 measures of glucose homeostasis associated with type 2 diabetes risks. These outcomes were evaluated for their associations with direct measurements of EPA, DHA, and arachidonic acid in RBCs. ANALYSIS Linear regression was used to detect significant relationships with cytokines and n-3 PUFAs, adiposity, and glucose-related variables. RESULTS The DHA concentration in RBC membranes was inversely associated with IL-6 (β = -0.0066; P < 0.001); EPA was inversely associated with TNFα (β = -0.4925; P < 0.001); and the NIR was inversely associated with Monocyte chemoattractant protein-1 (MCP-1) (β = -0.8345; P < 0.001) and IL-10 (β = -1.2868; P < 0.001). CONCLUSIONS Habitual intake of marine mammals and fish rich in n-3 PUFAs in this study population of Yup'ik Alaska Native adults is associated with reduced systemic inflammation, which may contribute to the low prevalence of diseases in which inflammation plays an important role.
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Affiliation(s)
- Bert B Boyer
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Scarlett E Hopkins
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Howard W Wiener
- Department of Statistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jonathan Q Purnell
- Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Diane M O'Brien
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Cindy X Zhang
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Joseph E Aslan
- Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Theresa Aliwarga
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Jeremy J Pomeroy
- Clinical Research Center, Marshfield Clinic, Marshfield, WI, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Hemant K Tiwari
- Department of Statistics, University of Alabama at Birmingham, Birmingham, AL, USA
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The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders. PLoS Genet 2020; 16:e1008544. [PMID: 31978080 PMCID: PMC7001991 DOI: 10.1371/journal.pgen.1008544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 02/05/2020] [Accepted: 11/27/2019] [Indexed: 11/19/2022] Open
Abstract
The genetic architecture of the small and isolated Greenlandic population is advantageous for identification of novel genetic variants associated with cardio-metabolic traits. We aimed to identify genetic loci associated with body mass index (BMI), to expand the knowledge of the genetic and biological mechanisms underlying obesity. Stage 1 BMI-association analyses were performed in 4,626 Greenlanders. Stage 2 replication and meta-analysis were performed in additional cohorts comprising 1,058 Yup'ik Alaska Native people, and 1,529 Greenlanders. Obesity-related traits were assessed in the stage 1 study population. We identified a common variant on chromosome 11, rs4936356, where the derived G-allele had a frequency of 24% in the stage 1 study population. The derived allele was genome-wide significantly associated with lower BMI (beta (SE), -0.14 SD (0.03), p = 3.2x10-8), corresponding to 0.64 kg/m2 lower BMI per G allele in the stage 1 study population. We observed a similar effect in the Yup'ik cohort (-0.09 SD, p = 0.038), and a non-significant effect in the same direction in the independent Greenlandic stage 2 cohort (-0.03 SD, p = 0.514). The association remained genome-wide significant in meta-analysis of the Arctic cohorts (-0.10 SD (0.02), p = 4.7x10-8). Moreover, the variant was associated with a leaner body type (weight, -1.68 (0.37) kg; waist circumference, -1.52 (0.33) cm; hip circumference, -0.85 (0.24) cm; lean mass, -0.84 (0.19) kg; fat mass and percent, -1.66 (0.33) kg and -1.39 (0.27) %; visceral adipose tissue, -0.30 (0.07) cm; subcutaneous adipose tissue, -0.16 (0.05) cm, all p<0.0002), lower insulin resistance (HOMA-IR, -0.12 (0.04), p = 0.00021), and favorable lipid levels (triglyceride, -0.05 (0.02) mmol/l, p = 0.025; HDL-cholesterol, 0.04 (0.01) mmol/l, p = 0.0015). In conclusion, we identified a novel variant, where the derived G-allele possibly associated with lower BMI in Arctic populations, and as a consequence also leaner body type, lower insulin resistance, and a favorable lipid profile.
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Grarup N, Moltke I, Andersen MK, Bjerregaard P, Larsen CVL, Dahl-Petersen IK, Jørsboe E, Tiwari HK, Hopkins SE, Wiener HW, Boyer BB, Linneberg A, Pedersen O, Jørgensen ME, Albrechtsen A, Hansen T. Identification of novel high-impact recessively inherited type 2 diabetes risk variants in the Greenlandic population. Diabetologia 2018; 61:2005-2015. [PMID: 29926116 PMCID: PMC6096637 DOI: 10.1007/s00125-018-4659-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/03/2018] [Indexed: 12/21/2022]
Abstract
AIMS/HYPOTHESIS In a recent study using a standard additive genetic model, we identified a TBC1D4 loss-of-function variant with a large recessive impact on risk of type 2 diabetes in Greenlanders. The aim of the current study was to identify additional genetic variation underlying type 2 diabetes using a recessive genetic model, thereby increasing the power to detect variants with recessive effects. METHODS We investigated three cohorts of Greenlanders (B99, n = 1401; IHIT, n = 3115; and BBH, n = 547), which were genotyped using Illumina MetaboChip. Of the 4674 genotyped individuals passing quality control, 4648 had phenotype data available, and type 2 diabetes association analyses were performed for 317 individuals with type 2 diabetes and 2631 participants with normal glucose tolerance. Statistical association analyses were performed using a linear mixed model. RESULTS Using a recessive genetic model, we identified two novel loci associated with type 2 diabetes in Greenlanders, namely rs870992 in ITGA1 on chromosome 5 (OR 2.79, p = 1.8 × 10-8), and rs16993330 upstream of LARGE1 on chromosome 22 (OR 3.52, p = 1.3 × 10-7). The LARGE1 variant did not reach the conventional threshold for genome-wide significance (p < 5 × 10-8) but did withstand a study-wide Bonferroni-corrected significance threshold. Both variants were common in Greenlanders, with minor allele frequencies of 23% and 16%, respectively, and were estimated to have large recessive effects on risk of type 2 diabetes in Greenlanders, compared with additively inherited variants previously observed in European populations. CONCLUSIONS/INTERPRETATION We demonstrate the value of using a recessive genetic model in a historically small and isolated population to identify genetic risk variants. Our findings give new insights into the genetic architecture of type 2 diabetes, and further support the existence of high-effect genetic risk factors of potential clinical relevance, particularly in isolated populations. DATA AVAILABILITY The Greenlandic MetaboChip-genotype data are available at European Genome-Phenome Archive (EGA; https://ega-archive.org/ ) under the accession EGAS00001002641.
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Affiliation(s)
- Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Peter Bjerregaard
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Christina V L Larsen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
| | - Inger K Dahl-Petersen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Scarlett E Hopkins
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Howard W Wiener
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bert B Boyer
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Marit E Jørgensen
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
- Greenland Centre for Health Research, University of Greenland, Nuuk, Greenland
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
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Aslibekyan S, Vaughan LK, Wiener HW, Hidalgo BA, Lemas DJ, O’Brien DM, Hopkins SE, Stanhope KL, Havel PJ, Thummel KE, Boyer BB, Tiwari HK. Linkage and association analysis of circulating vitamin D and parathyroid hormone identifies novel loci in Alaska Native Yup'ik people. GENES & NUTRITION 2016; 11:23. [PMID: 27579147 PMCID: PMC4971612 DOI: 10.1186/s12263-016-0538-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/18/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Vitamin D deficiency is a well-documented public health issue with both genetic and environmental determinants. Populations living at far northern latitudes are vulnerable to vitamin D deficiency and its health sequelae, although consumption of traditional native dietary pattern rich in fish and marine mammals may buffer the effects of reduced sunlight exposure. To date, few studies have investigated the genetics of vitamin D metabolism in circumpolar populations or considered genediet interactions with fish and n-3 fatty acid intake. METHODS We searched for genomic regions exhibiting linkage and association with circulating levels of vitamin D and parathyroid hormone (PTH) in 982 Yup'ik individuals from the Center for Alaska Native Health Research Study. We also investigated potential interactions between genetic variants and a biomarker of traditional dietary intake, the δ15N value. RESULTS We identified several novel regions linked with circulating vitamin D and PTH as well as replicated a previous linkage finding on 2p16.2 for vitamin D. Bioinformatic analysis revealed multiple candidate genes for both PTH and vitamin D, including CUBN, MGAT3, and NFKBIA. Targeted association analysis identified NEBL as a candidate gene for vitamin D and FNDC3B for PTH. We observed significant associations between a variant in MXD1 and vitamin D only when an interaction with the δ15N value was included. Finally, we integrated pathway level information to illustrate the biological validity of the proposed candidate genes. CONCLUSION We provide evidence of linkage between several biologically plausible genomic regions and vitamin D metabolism in a circumpolar population. Additionally, these findings suggest that a traditional dietary pattern may modulate genetic effects on circulating vitamin D.
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Affiliation(s)
- Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Laura K. Vaughan
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL USA
- Department of Biology, King University, Bristol, TN USA
| | - Howard W. Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Bertha A. Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Dominick J. Lemas
- Department of Health Outcomes and Policy, College of Medicine, University of Florida, Gainesville, FL USA
| | - Diane M. O’Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK USA
| | - Scarlett E. Hopkins
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK USA
| | - Kimber L. Stanhope
- Departments of Molecular Biosciences and Nutrition, University of California at Davis, Davis, CA USA
| | - Peter J. Havel
- Departments of Molecular Biosciences and Nutrition, University of California at Davis, Davis, CA USA
| | | | - Bert B. Boyer
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL USA
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Vaughan LK, Wiener HW, Aslibekyan S, Allison DB, Havel PJ, Stanhope KL, O'Brien DM, Hopkins SE, Lemas DJ, Boyer BB, Tiwari HK. Linkage and association analysis of obesity traits reveals novel loci and interactions with dietary n-3 fatty acids in an Alaska Native (Yup'ik) population. Metabolism 2015; 64:689-97. [PMID: 25772781 PMCID: PMC4408244 DOI: 10.1016/j.metabol.2015.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 01/30/2015] [Accepted: 02/28/2015] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To identify novel genetic markers of obesity-related traits and to identify gene-diet interactions with n-3 polyunsaturated fatty acid (n-3 PUFA) intake in Yup'ik people. MATERIAL AND METHODS We measured body composition, plasma adipokines and ghrelin in 982 participants enrolled in the Center for Alaska Native Health Research (CANHR) Study. We conducted a genome-wide SNP linkage scan and targeted association analysis, fitting additional models to investigate putative gene-diet interactions. Finally, we performed bioinformatic analysis to uncover likely candidate genes within the identified linkage peaks. RESULTS We observed evidence of linkage for all obesity-related traits, replicating previous results and identifying novel regions of interest for adiponectin (10q26.13-2) and thigh circumference (8q21.11-13). Bioinformatic analysis revealed DOCK1, PTPRE (10q26.13-2) and FABP4 (8q21.11-13) as putative candidate genes in the newly identified regions. Targeted SNP analysis under the linkage peaks identified associations between three SNPs and obesity-related traits: rs1007750 on chromosome 8 and thigh circumference (P=0.0005), rs878953 on chromosome 5 and thigh skinfold (P=0.0004), and rs1596854 on chromosome 11 for waist circumference (P=0.0003). Finally, we showed that n-3 PUFA modified the association between obesity related traits and two additional variants (rs2048417 on chromosome 3 for adiponectin, P for interaction=0.0006 and rs730414 on chromosome 11 for percentage body fat, P for interaction=0.0004). CONCLUSIONS This study presents evidence of novel genomic regions and gene-diet interactions that may contribute to the pathophysiology of obesity-related traits among Yup'ik people.
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Affiliation(s)
- Laura Kelly Vaughan
- Department of Biology, King University, 1350 King College Rd, Bristol, TN 37620, USA.
| | - Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - David B Allison
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
| | - Peter J Havel
- Departments of Nutrition and Molecular Biosciences, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Kimber L Stanhope
- Departments of Nutrition and Molecular Biosciences, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Diane M O'Brien
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Scarlett E Hopkins
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Dominick J Lemas
- Department of Pediatrics, Section of Neonatology, University of Colorado Anschutz Medical Campus, 13123 East 16th Ave, Aurora, CO 80045, USA.
| | - Bert B Boyer
- USACenter for Alaska Native Health Research, Institute of Arctic Biology, 311 Irving I Building, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35294, USA.
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Abstract
Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently, there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short- and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general US population. Approaches to improve specificity for specific foods are needed; for example, by modeling intake using multiple stable isotope ratios or by isolating and measuring specific molecules linked to foods of interest.
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Affiliation(s)
- Diane M O'Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska, Fairbanks, Alaska 99775-7000;
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O’Brien DM, Kristal AR, Nash SH, Hopkins SE, Luick BR, Stanhope KL, Havel PJ, Boyer BB. A stable isotope biomarker of marine food intake captures associations between n-3 fatty acid intake and chronic disease risk in a Yup'ik study population, and detects new associations with blood pressure and adiponectin. J Nutr 2014; 144:706-13. [PMID: 24598880 PMCID: PMC3985827 DOI: 10.3945/jn.113.189381] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nitrogen isotope ratio (δ(15)N) of RBCs has been proposed as a biomarker of marine food intake in Yup'ik people based on strong associations with RBC eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). However, EPA and DHA derive from marine fats, whereas elevated δ(15)N derives from marine protein, and these dietary components may have different biologic effects. Whether δ(15)N is similarly associated with chronic disease risk factors compared with RBC EPA and DHA is not known. We used covariate-adjusted linear models to describe biomarker associations with chronic disease risk factors in Yup'ik people, first in a smaller (n = 363) cross-sectional study population using RBC EPA, DHA, and δ(15)N, and then in a larger (n = 772) cross-sectional study population using δ(15)N only. In the smaller sample, associations of RBC EPA, DHA, and δ(15)N with obesity and chronic disease risk factors were similar in direction and significance: δ(15)N was positively associated with total, HDL, and LDL cholesterol, apolipoprotein A-I, and insulin-like growth factor binding protein-3 (IGFBP-3), and inversely associated with triglycerides. Based on comparisons between covariate-adjusted β-coefficients, EPA was more strongly associated with circulating lipids and lipoproteins, whereas δ(15)N was more strongly associated with adipokines, the inflammatory marker interleukin-6, and IGFBP-3. In the larger sample there were new findings for this population: δ(15)N was inversely associated with blood pressure and there was a significant association (with inverse linear and positive quadratic terms) with adiponectin. In conclusion, δ(15)N is a valid measure for evaluating associations between EPA and DHA intake and chronic disease risk in Yup'ik people and may be used in larger studies. By measuring δ(15)N, we report beneficial associations of marine food intake with blood pressure and adiponectin, which may contribute to a lower incidence of some chronic diseases in Yup'ik people.
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Affiliation(s)
- Diane M. O’Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology, and,Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK,To whom correspondence should be addressed: E-mail:
| | - Alan R. Kristal
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA; and
| | - Sarah H. Nash
- Center for Alaska Native Health Research, Institute of Arctic Biology, and,Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK
| | | | - Bret R. Luick
- Center for Alaska Native Health Research, Institute of Arctic Biology, and
| | - Kimber L. Stanhope
- Department of Molecular Biosciences, School of Veterinary Medicine, and,Department of Nutrition, University of California, Davis, Davis, CA
| | - Peter J. Havel
- Department of Molecular Biosciences, School of Veterinary Medicine, and,Department of Nutrition, University of California, Davis, Davis, CA
| | - Bert B. Boyer
- Center for Alaska Native Health Research, Institute of Arctic Biology, and
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KLIMENTIDIS YC, LEMAS DJ, WIENER HH, O’BRIEN DM, HAVEL PJ, STANHOPE KL, HOPKINS SE, TIWARI HK, BOYER BB. CDKAL1 and HHEX are associated with type 2 diabetes-related traits among Yup'ik people. J Diabetes 2014; 6:251-9. [PMID: 24112421 PMCID: PMC3964139 DOI: 10.1111/1753-0407.12093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), mainly among individuals of European ancestry. In the present study, we examined the frequency of these SNPs and their association with T2D-related traits in an Alaska Native study population with a historically low prevalence of T2D. We also investigated whether dietary characteristics that may protect against T2D, such as n-3 polyunsaturated fatty acid (PUFA) intake, modify these associations. METHODS In 1144 Yup'ik people, we examined 17 SNPs repeatedly identified in GWAS for individual and cumulative associations with T2D-related traits. Cumulative associations were evaluated using a genetic risk score (GRS) calculated by summing risk alleles. Associations were tested for interactions with sex, body mass index (BMI), and n-3 PUFA intake. RESULTS The rs7754840 SNP in CDKAL1 is significantly associated with HbA1c (P = 0.00091). The rs5015480 SNP near HHEX is significantly associated (in opposite direction to that in Europeans) with a combined fasting glucose (FG) and HbA1c measure (P = 0.00046) and with homeostatic model assessment of β-cell function (HOMA-B; P = 0.0014). The GRS is significantly associated with FG and combined FG and HbA1c only when the HHEX SNP is dropped from the GRS. Associations are not modified by BMI or n-3 PUFA intake. CONCLUSION Our results highlight the potential importance of CDKAL1 and HHEX in glucose homeostasis in this Alaska Native population with a low prevalence of T2D, and suggest that these loci should be examined in greater detail in this population.
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Affiliation(s)
- Yann C. KLIMENTIDIS
- Mel and Enid Zuckerman College of Public Health, Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, 85724
| | - Dominick J. LEMAS
- Department of Pediatrics, Section of Neonatology, University of Colorado Denver, Aurora, CO 80045
| | - Howard H. WIENER
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Diane M. O’BRIEN
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Peter J. HAVEL
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
- Department of Nutrition, University of California, Davis, Davis, CA 95616
| | - Kimber L. STANHOPE
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
- Department of Nutrition, University of California, Davis, Davis, CA 95616
| | - Scarlett E. HOPKINS
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Hemant K. TIWARI
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Bert B. BOYER
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
- Corresponding author: Yann C. Klimentidis, PhD, Mel and Enid Zuckerman College of Public Health, Division of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, 85724. Phone: 520-621-1047,
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Aslibekyan S, Wiener HW, Havel PJ, Stanhope KL, O’Brien DM, Hopkins SE, Absher DM, Tiwari HK, Boyer BB. DNA methylation patterns are associated with n-3 fatty acid intake in Yup'ik people. J Nutr 2014; 144:425-30. [PMID: 24477300 PMCID: PMC3952620 DOI: 10.3945/jn.113.187203] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A large body of evidence links a high dietary intake of n-3 (ω-3) polyunsaturated fatty acids (PUFAs) with improved cardiometabolic outcomes. Recent studies suggested that the biologic processes underlying the observed associations may involve epigenetic changes, specifically DNA methylation. To evaluate changes in methylation associated with n-3 PUFA intake, we conducted an epigenome-wide methylation association study of long-chain n-3 PUFA intake and tested associations between the diabetes- and cardiovascular disease-related traits. We assessed DNA methylation at ∼470,000 cytosine-phosphate-guanine (CpG) sites in a cross-sectional study of 185 Yup'ik Alaska Native individuals representing the top and bottom deciles of PUFA intake. Linear regression models were used to test for the associations of interest, adjusting for age, sex, and community group. We identified 27 differentially methylated CpG sites at biologically relevant regions that reached epigenome-wide significance (P < 1 × 10⁻⁷). Specifically, regions on chromosomes 3 (helicase-like transcription factor), 10 (actin α 2 smooth muscle/Fas cell surface death receptor), and 16 (protease serine 36/C16 open reading frame 67) each harbored 2 significant correlates of n-3 PUFA intake. In conclusion, we present promising evidence of association between several biologically relevant epigenetic markers and long-term intake of marine-derived n-3 PUFAs.
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Affiliation(s)
| | | | - Peter J. Havel
- Departments of Nutrition and,Molecular Biosciences, University of California, Davis, Davis, CA
| | - Kimber L. Stanhope
- Departments of Nutrition and,Molecular Biosciences, University of California, Davis, Davis, CA
| | - Diane M. O’Brien
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska, Fairbanks, AK; and
| | - Scarlett E. Hopkins
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska, Fairbanks, AK; and
| | | | | | - Bert B. Boyer
- Center for Alaska Native Health Research, Institute of Arctic Biology, University of Alaska, Fairbanks, AK; and,To whom correspondence should be addressed. E-mail:
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