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Çokoğlu SS, Koptekin D, Fidan FR, Somel M. Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise. Evol Appl 2024; 17:e13743. [PMID: 38957308 PMCID: PMC11217591 DOI: 10.1111/eva.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024] Open
Abstract
The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.
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Affiliation(s)
| | - Dilek Koptekin
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
| | | | - Mehmet Somel
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
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2
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Pavlova NI, Krylov AV, Bochurov AA, Alekseev VA, Kurtanov KA. High Frequency of Ancestral Haplotype A of Fatty Acid Desaturase Genes in the Yakut Population. Genet Test Mol Biomarkers 2024. [PMID: 38860387 DOI: 10.1089/gtmb.2024.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Aims: The purpose of this study was to study the correlation of the body weight of Yakuts with the variability of polymorphisms rs174537, rs174546 and rs3834458 of the FADS1 - FADS2 region to identify the connection of certain genotypes with obesity. Materials and Methods: For genotyping, classical methods of PCR-RFLP analysis were used. A sample of 446 DNA samples from Yakut volunteers without chronic diseases (143 women and 303 men) was studied. Results: The predominance of the ancestral alleles of SNPs rs174537, rs174546 and rs3834458 was established in all of our studied groups. Analysis of the odds ratio of allele and genotype frequencies in patients with normal BMI, high BMI and obesity did not show statistically significant values. We did not find an association between rs174537, rs174546 and rs3834458 with obesity, but we did not take into account the diet of the subjects, which may have had a stronger effect on BMI. Analysis of pairwise linkage disequilibrium and assessment of haplotypes for 3 SNPs in the FADS1 and FADS2 genes showed strong linkage of all three SNPs to each other (r2 = 0.93-0.96). Conclusions: According to the result of genotyping of SNP rs174537, the frequency of haplotype A in the Yakut population was 0.76 and, in comparison with other world data, is quite high. Which in turn is associated with lower conversion of short-chain polyunsaturated fatty acid to long-chain polyunsaturated fatty acid. Accordingly, a shift in nutrition towards more plant foods can negatively impact the health of the Yakuts. At the moment, the exact dosage of polyunsaturated fatty acids (PUFAs) for humans has not yet been established, but judging by the fact that all recommendations are mainly made on the basis of European populations, in connection with the results of the study, the Yakuts have a particularly high need for PUFAs.
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Affiliation(s)
- Nadezhda I Pavlova
- Federal State Budgetary Scientific Institution, Yakut Scientific Center for Medical Problems, Yakutsk, Russian Federation
| | - Alexey V Krylov
- Federal State Budgetary Scientific Institution, Yakut Scientific Center for Medical Problems, Yakutsk, Russian Federation
| | - Alexey A Bochurov
- Federal State Budgetary Scientific Institution, Yakut Scientific Center for Medical Problems, Yakutsk, Russian Federation
| | - Vladislav A Alekseev
- Federal State Budgetary Scientific Institution, Yakut Scientific Center for Medical Problems, Yakutsk, Russian Federation
| | - Khariton A Kurtanov
- Federal State Autonomous Educational Institution of Higher Education, M K Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
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3
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Yazdanpanah M, Yazdanpanah N, Gamache I, Ong K, Perry JRB, Manousaki D. Metabolome-wide Mendelian randomization for age at menarche and age at natural menopause. Genome Med 2024; 16:69. [PMID: 38802955 PMCID: PMC11131236 DOI: 10.1186/s13073-024-01322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/22/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND The role of metabolism in the variation of age at menarche (AAM) and age at natural menopause (ANM) in the female population is not entirely known. We aimed to investigate the causal role of circulating metabolites in AAM and ANM using Mendelian randomization (MR). METHODS We combined MR with genetic colocalization to investigate potential causal associations between 658 metabolites and AAM and between 684 metabolites and ANM. We extracted genetic instruments for our exposures from four genome-wide association studies (GWAS) on circulating metabolites and queried the effects of these variants on the outcomes in two large GWAS from the ReproGen consortium. Additionally, we assessed the mediating role of the body mass index (BMI) in these associations, identified metabolic pathways implicated in AAM and ANM, and sought validation for selected metabolites in the Avon Longitudinal Study of Parents and Children (ALSPAC). RESULTS Our analysis identified 10 candidate metabolites for AAM, but none of them colocalized with AAM. For ANM, 76 metabolites were prioritized (FDR-adjusted MR P-value ≤ 0.05), with 17 colocalizing, primarily in the glycerophosphocholines class, including the omega-3 fatty acid and phosphatidylcholine (PC) categories. Pathway analyses and validation in ALSPAC mothers also highlighted the role of omega and polyunsaturated fatty acids levels in delaying age at menopause. CONCLUSIONS Our study suggests that metabolites from the glycerophosphocholine and fatty acid families play a causal role in the timing of both menarche and menopause. This underscores the significance of specific metabolic pathways in the biology of female reproductive longevity.
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Affiliation(s)
- Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, Université de Montréal, 3175 Côte-Sainte-Catherine, Montréal, Québec, H3T 1C5, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, Université de Montréal, 3175 Côte-Sainte-Catherine, Montréal, Québec, H3T 1C5, Canada
| | - Isabel Gamache
- Research Center of the Sainte-Justine University Hospital, Université de Montréal, 3175 Côte-Sainte-Catherine, Montréal, Québec, H3T 1C5, Canada
| | - Ken Ong
- MRC Epidemiology Unit, School of Clinical Medicine, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Metabolic Research Laboratory, School of Clinical Medicine, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, Université de Montréal, 3175 Côte-Sainte-Catherine, Montréal, Québec, H3T 1C5, Canada.
- Departments of Pediatrics, Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada.
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4
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He W, Liu X, Feng Y, Ding H, Sun H, Li Z, Shi B. Dietary fat supplementation relieves cold temperature-induced energy stress through AMPK-mediated mitochondrial homeostasis in pigs. J Anim Sci Biotechnol 2024; 15:56. [PMID: 38584279 PMCID: PMC11000307 DOI: 10.1186/s40104-024-01014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Cold stress has negative effects on the growth and health of mammals, and has become a factor restricting livestock development at high latitudes and on plateaus. The gut-liver axis is central to energy metabolism, and the mechanisms by which it regulates host energy metabolism at cold temperatures have rarely been illustrated. In this study, we evaluated the status of glycolipid metabolism and oxidative stress in pigs based on the gut-liver axis and propose that AMP-activated protein kinase (AMPK) is a key target for alleviating energy stress at cold temperatures by dietary fat supplementation. RESULTS Dietary fat supplementation alleviated the negative effects of cold temperatures on growth performance and digestive enzymes, while hormonal homeostasis was also restored. Moreover, cold temperature exposure increased glucose transport in the jejunum. In contrast, we observed abnormalities in lipid metabolism, which was characterized by the accumulation of bile acids in the ileum and plasma. In addition, the results of the ileal metabolomic analysis were consistent with the energy metabolism measurements in the jejunum, and dietary fat supplementation increased the activity of the mitochondrial respiratory chain and lipid metabolism. As the central nexus of energy metabolism, the state of glycolipid metabolism and oxidative stress in the liver are inconsistent with that in the small intestine. Specifically, we found that cold temperature exposure increased glucose transport in the liver, which fully validates the idea that hormones can act on the liver to regulate glucose output. Additionally, dietary fat supplementation inhibited glucose transport and glycolysis, but increased gluconeogenesis, bile acid cycling, and lipid metabolism. Sustained activation of AMPK, which an energy receptor and regulator, leads to oxidative stress and apoptosis in the liver; dietary fat supplementation alleviates energy stress by reducing AMPK phosphorylation. CONCLUSIONS Cold stress reduced the growth performance and aggravated glycolipid metabolism disorders and oxidative stress damage in pigs. Dietary fat supplementation improved growth performance and alleviated cold temperature-induced energy stress through AMPK-mediated mitochondrial homeostasis. In this study, we highlight the importance of AMPK in dietary fat supplementation-mediated alleviation of host energy stress in response to environmental changes.
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Affiliation(s)
- Wei He
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Xinyu Liu
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Ye Feng
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Hongwei Ding
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Haoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Zhongyu Li
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China
| | - Baoming Shi
- College of Animal Science and Technology, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, PR China.
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5
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Poyraz L, Colbran LL, Mathieson I. Predicting Functional Consequences of Recent Natural Selection in Britain. Mol Biol Evol 2024; 41:msae053. [PMID: 38466119 PMCID: PMC10962637 DOI: 10.1093/molbev/msae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/02/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024] Open
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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6
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Jelenkovic A, Ibáñez-Zamacona ME, Rebato E. Human adaptations to diet: Biological and cultural coevolution. ADVANCES IN GENETICS 2024; 111:117-147. [PMID: 38908898 DOI: 10.1016/bs.adgen.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Modern humans evolved in Africa some 200,000 years ago, and since then, human populations have expanded and diversified to occupy a broad range of habitats and use different subsistence modes. This has resulted in different adaptations, such as differential responses to diseases and different abilities to digest or tolerate certain foods. The shift from a subsistence strategy based on hunting and gathering during the Palaeolithic to a lifestyle based on the consumption of domesticated animals and plants in the Neolithic can be considered one of the most important dietary transitions of Homo sapiens. In this text, we review four examples of gene-culture coevolution: (i) the persistence of the enzyme lactase after weaning, which allows the digestion of milk in adulthood, related to the emergence of dairy farming during the Neolithic; (ii) the population differences in alcohol susceptibility, in particular the ethanol intolerance of Asian populations due to the increased accumulation of the toxic acetaldehyde, related to the spread of rice domestication; (iii) the maintenance of gluten intolerance (celiac disease) with the subsequent reduced fitness of its sufferers, related to the emergence of agriculture and (iv) the considerable variation in the biosynthetic pathway of long-chain polyunsaturated fatty acids in native populations with extreme diets.
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Affiliation(s)
- Aline Jelenkovic
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - María Eugenia Ibáñez-Zamacona
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Esther Rebato
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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7
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He W, Ding H, Feng Y, Liu X, Fang X, Gao F, Shi B. Dietary-fat supplementation alleviates cold temperature-induced metabolic dysbiosis and barrier impairment by remodeling gut microbiota. Food Funct 2024; 15:1443-1459. [PMID: 38226701 DOI: 10.1039/d3fo04916g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
As important components of the mammalian diet and tissues, fats are involved in a variety of biological processes in addition to providing energy. In general, the increase in basal metabolism and health risks under cold temperature conditions causes the host to need more energy to maintain body temperature and normal biological processes. The intestine and its microbiota are key components in orchestrating host metabolic homeostasis and immunity, and respond rapidly to changing environmental conditions. However, the role of dietary-fat supplementation in regulating host homeostasis of metabolism and barrier functions through gut microbiota at cold temperatures is incompletely understood. Our results showed that dietary-fat supplementation alleviated the negative effects of cold temperatures on the alpha-diversity of both ileal and colonic microbiota. Cold temperatures altered the ileal and colonic microbiota of pigs, and the extent of changes was more pronounced in the colonic microbiota. Translocation of the gut microbiota was restored after supplementation with a high-fat diet. In addition, cold temperatures exacerbated ileal mucosal damage and inflammation, and disrupted barrier function, which may be associated with decreased concentrations of butyrate and isobutyrate. Cold temperature-induced metabolic dysbiosis was manifested by altered hormone levels and upregulation of expression of multiple metabolites involved in metabolism (lipids, amino acids and minerals) and the immune response. Supplementation with a high-fat diet restored metabolic homeostasis and barrier function by improving gut-microbiota composition and increasing SCFAs concentrations in pigs. In conclusion, cold temperatures induced severe translocation of microbiota and barrier damage. These actions increased the risk of metabolic imbalance. Dietary-fat supplementation alleviated the adverse effects of cold temperatures on host metabolism by remodeling the gut microbiota.
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Affiliation(s)
- Wei He
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Hongwei Ding
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Ye Feng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Xinyu Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Xiuyu Fang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Feng Gao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Baoming Shi
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
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8
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Gao Z. Unveiling recent and ongoing adaptive selection in human populations. PLoS Biol 2024; 22:e3002469. [PMID: 38236800 PMCID: PMC10796035 DOI: 10.1371/journal.pbio.3002469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
Genome-wide scans for signals of selection have become a routine part of the analysis of population genomic variation datasets and have resulted in compelling evidence of selection during recent human evolution. This Essay spotlights methodological innovations that have enabled the detection of selection over very recent timescales, even in contemporary human populations. By harnessing large-scale genomic and phenotypic datasets, these new methods use different strategies to uncover connections between genotype, phenotype, and fitness. This Essay outlines the rationale and key findings of each strategy, discusses challenges in interpretation, and describes opportunities to improve detection and understanding of ongoing selection in human populations.
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Affiliation(s)
- Ziyue Gao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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9
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Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
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Affiliation(s)
- Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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10
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Kawai Y, Watanabe Y, Omae Y, Miyahara R, Khor SS, Noiri E, Kitajima K, Shimanuki H, Gatanaga H, Hata K, Hattori K, Iida A, Ishibashi-Ueda H, Kaname T, Kanto T, Matsumura R, Miyo K, Noguchi M, Ozaki K, Sugiyama M, Takahashi A, Tokuda H, Tomita T, Umezawa A, Watanabe H, Yoshida S, Goto YI, Maruoka Y, Matsubara Y, Niida S, Mizokami M, Tokunaga K. Exploring the genetic diversity of the Japanese population: Insights from a large-scale whole genome sequencing analysis. PLoS Genet 2023; 19:e1010625. [PMID: 38060463 PMCID: PMC10703243 DOI: 10.1371/journal.pgen.1010625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. We analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective from the genomic data of 9,287 samples obtained by high-coverage whole-genome sequencing (WGS) by the National Center Biobank Network. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Haplotype analysis suggested increased allele frequencies for genes related to alcohol and fatty acid metabolism, which were reported as loci that had experienced positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to increase in the allele frequency; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production.
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Affiliation(s)
- Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Watanabe
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Reiko Miyahara
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Eisei Noiri
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
| | - Koji Kitajima
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
- Department of Data Science Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hideyuki Shimanuki
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
- Department of Data Science Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Kotaro Hattori
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Aritoshi Iida
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Tatsuya Kanto
- Department of Liver Disease, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Ryo Matsumura
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Kengo Miyo
- Center for Medical Informatics Intelligence, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Michio Noguchi
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Masaya Sugiyama
- Department of Viral Pathogenesis and Controls, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Ayako Takahashi
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Haruhiko Tokuda
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Department of Metabolic Research, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Department of Clinical Laboratory, Hospital, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Tsutomu Tomita
- NCVC Biobank, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, Research Institute, National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Hiroshi Watanabe
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
- Innovation Center for Translational Research, Hospital, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Sumiko Yoshida
- Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yu-ichi Goto
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yutaka Maruoka
- Department of Oral and Maxillofacial Surgery, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yoichi Matsubara
- National Center for Child Health and Development, Setagaya-ku, Tokyo, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Masashi Mizokami
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- Central Biobank, National Center Biobank Network, Shinjuku-ku, Tokyo, Japan
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11
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Poyraz L, Colbran LL, Mathieson I. Predicting functional consequences of recent natural selection in Britain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562549. [PMID: 37904954 PMCID: PMC10614889 DOI: 10.1101/2023.10.16.562549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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12
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Yang C, Veenstra J, Bartz TM, Pahl MC, Hallmark B, Chen YDI, Westra J, Steffen LM, Brown CD, Siscovick D, Tsai MY, Wood AC, Rich SS, Smith CE, O'Connor TD, Mozaffarian D, Grant SFA, Chilton FH, Tintle NL, Lemaitre RN, Manichaikul A. Genome-wide association studies and fine-mapping identify genomic loci for n-3 and n-6 polyunsaturated fatty acids in Hispanic American and African American cohorts. Commun Biol 2023; 6:852. [PMID: 37587153 PMCID: PMC10432561 DOI: 10.1038/s42003-023-05219-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) play critical roles in human health. Prior genome-wide association studies (GWAS) of n-3 and n-6 PUFAs in European Americans from the CHARGE Consortium have documented strong genetic signals in/near the FADS locus on chromosome 11. We performed a GWAS of four n-3 and four n-6 PUFAs in Hispanic American (n = 1454) and African American (n = 2278) participants from three CHARGE cohorts. Applying a genome-wide significance threshold of P < 5 × 10-8, we confirmed association of the FADS signal and found evidence of two additional signals (in DAGLA and BEST1) within 200 kb of the originally reported FADS signal. Outside of the FADS region, we identified novel signals for arachidonic acid (AA) in Hispanic Americans located in/near genes including TMX2, SLC29A2, ANKRD13D and POLD4, and spanning a > 9 Mb region on chromosome 11 (57.5 Mb ~ 67.1 Mb). Among these novel signals, we found associations unique to Hispanic Americans, including rs28364240, a POLD4 missense variant for AA that is common in CHARGE Hispanic Americans but absent in other race/ancestry groups. Our study sheds light on the genetics of PUFAs and the value of investigating complex trait genetics across diverse ancestry populations.
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Affiliation(s)
- Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jenna Veenstra
- Departments of Biology and Statistics, Dordt University, Sioux Center, IA, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brian Hallmark
- Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jason Westra
- Fatty Acid Research Institute, Sioux Falls, SD, USA
| | - Lyn M Steffen
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Caren E Smith
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences; Program in Personalized and Genomic Medicine; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dariush Mozaffarian
- Friedman School of Nutrition Science & Policy, Tufts University, Tufts School of Medicine and Division of Cardiology, Tufts Medical Center, Boston, MA, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Floyd H Chilton
- School of Nutritional Sciences and Wellness and the BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Nathan L Tintle
- Fatty Acid Research Institute, Sioux Falls, SD, USA
- University of Illinois, Chicago, Chicago, IL, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
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13
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Konner M, Eaton SB. Hunter-gatherer diets and activity as a model for health promotion: Challenges, responses, and confirmations. Evol Anthropol 2023; 32:206-222. [PMID: 37417918 DOI: 10.1002/evan.21987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 07/27/2022] [Accepted: 04/17/2023] [Indexed: 07/08/2023]
Abstract
Beginning in 1985, we and others presented estimates of hunter-gatherer (and ultimately ancestral) diet and physical activity, hoping to provide a model for health promotion. The Hunter-Gatherer Model was designed to offset the apparent mismatch between our genes and the current Western-type lifestyle, a mismatch that arguably affects prevalence of many chronic degenerative diseases. The effort has always been controversial and subject to both scientific and popular critiques. The present article (1) addresses eight such challenges, presenting for each how the model has been modified in response, or how the criticism can be rebutted; (2) reviews new epidemiological and experimental evidence (including especially randomized controlled clinical trials); and (3) shows how official recommendations put forth by governments and health authorities have converged toward the model. Such convergence suggests that evolutionary anthropology can make significant contributions to human health.
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Affiliation(s)
- Melvin Konner
- Department of Anthropology, Program in Anthropology and Human Biology, Emory University, Atlanta, Georgia, USA
| | - S Boyd Eaton
- Department of Radiology, Emory University School of Medicine (Emeritus), Adjunct Lecturer, Department of Anthropology, Emory University, Atlanta, Georgia, USA
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14
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Tian J, Zhang L, La X, Fan X, Li A, Wu C, An Y, Yan S, Dong X, Wu H, Li Z. Tumor-secreted GRP78 induces M2 polarization of macrophages by promoting lipid catabolism. Cell Signal 2023; 108:110719. [PMID: 37207940 DOI: 10.1016/j.cellsig.2023.110719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Macrophages in hypoxic regions of advanced colorectal tumors often exhibit M2-type features, but prefer oxygen-consuming lipid catabolism, which is contradictory in oxygen demand and supply. In this study, the results from bioinformatics analysis and intestinal lesions immunohistochemistry of 40 colorectal cancer patients illustrated that glucose-regulatory protein 78 (GRP78) was positively correlated with M2 macrophages. Furthermore, tumor-secreted GRP78 could enter macrophages and polarize them to M2-type. Mechanistically, entered GRP78 located in lipid droplets of macrophages, and elevated protein stabilization of adipose triglyceride lipase ATGL by interacting with it to inhibit its ubiquitination. Increased ATGL promoted the hydrolysis of triglycerides and the production of arachidonic acid (ARA) and docosahexaenoic acid (DHA). Excessive ARA and DHA interacted with PPARγ to encourage its activation, which mediated the M2 polarization of macrophages. In summary, our study showed that secreted GRP78 in the tumor hypoxic microenvironment mediated the domestication of tumor cells to macrophages and maintained tumor immunosuppressive microenvironment by promoting lipolysis, and the lipid catabolism not only provides energy for macrophages but also plays an important role in maintenance of immunosuppressive properties.
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Affiliation(s)
- Jinmiao Tian
- Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Lichao Zhang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China.
| | - Xiaoqin La
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Xiaxia Fan
- Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Aiping Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Yuxuan An
- Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Shuning Yan
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Xiushan Dong
- General Surgery Department, Shanxi Bethune Hospital, Taiyuan 030032, China
| | - Haitao Wu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China
| | - Zhuoyu Li
- Institute of Biotechnology, Shanxi University, Taiyuan 030006, China.
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15
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Rundblad A, Sandoval V, Holven KB, Ordovás JM, Ulven SM. Omega-3 fatty acids and individual variability in plasma triglyceride response: A mini-review. Redox Biol 2023; 63:102730. [PMID: 37150150 PMCID: PMC10184047 DOI: 10.1016/j.redox.2023.102730] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/09/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of death worldwide. Supplementation with the marine omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) is associated with lower CVD risk. However, results from randomized controlled trials that examine the effect of omega-3 supplementation on CVD risk are inconsistent. This risk-reducing effect may be mediated by reducing inflammation, oxidative stress and serum triglyceride (TG) levels. However, not all individuals respond by reducing TG levels after omega-3 supplementation. This inter-individual variability in TG response to omega-3 supplementation is not fully understood. Hence, we aim to review the evidence for how interactions between omega-3 fatty acid supplementation and genetic variants, epigenetic and gene expression profiling, gut microbiota and habitual intake of omega-3 fatty acids can explain why the TG response differs between individuals. This may contribute to understanding the current controversies and play a role in defining future personalized guidelines to prevent CVD.
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Affiliation(s)
- Amanda Rundblad
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, P.O Box 1046 Blindern, 0317, Oslo, Norway
| | - Viviana Sandoval
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, P.O Box 1046 Blindern, 0317, Oslo, Norway; Escuela de Nutrición y Dietética, Facultad de Ciencias para el Cuidado de la Salud, Universidad San Sebastián, Gral. Lagos 1025, 5110693, Valdivia, Chile
| | - Kirsten B Holven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, P.O Box 1046 Blindern, 0317, Oslo, Norway; Norwegian National Advisory Unit on Familial Hypercholesterolemia, Oslo University Hospital, Norway
| | - José M Ordovás
- Nutrition and Genomics Laboratory, USDA ARS, JM-USDA Human Research Center on Aging at Tufts University, Boston, MA, USA; Nutritional Genomics and Epigenomics Group, Precision Nutrition and Obesity Program, IMDEA Food, CEI UAM + CSIC, Madrid, Spain; Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Institute of Health Carlos III, Madrid, Spain
| | - Stine M Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, P.O Box 1046 Blindern, 0317, Oslo, Norway.
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16
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Mathieson I, Day FR, Barban N, Tropf FC, Brazel DM, Vaez A, van Zuydam N, Bitarello BD, Gardner EJ, Akimova ET, Azad A, Bergmann S, Bielak LF, Boomsma DI, Bosak K, Brumat M, Buring JE, Cesarini D, Chasman DI, Chavarro JE, Cocca M, Concas MP, Davey Smith G, Davies G, Deary IJ, Esko T, Faul JD, Franco O, Ganna A, Gaskins AJ, Gelemanovic A, de Geus EJC, Gieger C, Girotto G, Gopinath B, Grabe HJ, Gunderson EP, Hayward C, He C, van Heemst D, Hill WD, Hoffmann ER, Homuth G, Hottenga JJ, Huang H, Hyppӧnen E, Ikram MA, Jansen R, Johannesson M, Kamali Z, Kardia SLR, Kavousi M, Kifley A, Kiiskinen T, Kraft P, Kühnel B, Langenberg C, Liew G, Lind PA, Luan J, Mägi R, Magnusson PKE, Mahajan A, Martin NG, Mbarek H, McCarthy MI, McMahon G, Medland SE, Meitinger T, Metspalu A, Mihailov E, Milani L, Missmer SA, Mitchell P, Møllegaard S, Mook-Kanamori DO, Morgan A, van der Most PJ, de Mutsert R, Nauck M, Nolte IM, Noordam R, Penninx BWJH, Peters A, Peyser PA, Polašek O, Power C, Pribisalic A, Redmond P, Rich-Edwards JW, Ridker PM, Rietveld CA, Ring SM, Rose LM, Rueedi R, Shukla V, Smith JA, Stankovic S, Stefánsson K, Stöckl D, Strauch K, Swertz MA, Teumer A, Thorleifsson G, Thorsteinsdottir U, Thurik AR, Timpson NJ, Turman C, Uitterlinden AG, Waldenberger M, Wareham NJ, Weir DR, Willemsen G, Zhao JH, Zhao W, Zhao Y, Snieder H, den Hoed M, Ong KK, Mills MC, Perry JRB. Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus. Nat Hum Behav 2023; 7:790-801. [PMID: 36864135 DOI: 10.1038/s41562-023-01528-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/12/2023] [Indexed: 03/04/2023]
Abstract
Identifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identified 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology, including puberty timing, age at first birth, sex hormone regulation, endometriosis and age at menopause. Missense variants in ARHGAP27 were associated with higher NEB but shorter reproductive lifespan, suggesting a trade-off at this locus between reproductive ageing and intensity. Other genes implicated by coding variants include PIK3IP1, ZFP82 and LRP4, and our results suggest a new role for the melanocortin 1 receptor (MC1R) in reproductive biology. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Integration with data from historical selection scans highlighted an allele in the FADS1/2 gene locus that has been under selection for thousands of years and remains so today. Collectively, our findings demonstrate that a broad range of biological mechanisms contribute to reproductive success.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicola Barban
- Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Felix C Tropf
- Nuffield College, University of Oxford, Oxford, UK
- École Nationale de la Statistique et de L'administration Économique (ENSAE), Paris, France
- Center for Research in Economics and Statistics (CREST), Paris, France
| | - David M Brazel
- Nuffield College, University of Oxford, Oxford, UK
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Natalie van Zuydam
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Bárbara D Bitarello
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Evelina T Akimova
- Nuffield College, University of Oxford, Oxford, UK
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK
| | - Ajuna Azad
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, the Netherlands
| | | | - Marco Brumat
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Julie E Buring
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - David Cesarini
- Department of Economics, New York University, New York, NY, USA
- Research Institute for Industrial Economics, Stockholm, Sweden
- National Bureau of Economic Research, Cambridge, MA, USA
| | - Daniel I Chasman
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jorge E Chavarro
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | | | - Gail Davies
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Oscar Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Audrey J Gaskins
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Giorgia Girotto
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Bamini Gopinath
- Centre for Vision Research, Westmead Institute for Medical Research and Department of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Erica P Gunderson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chunyan He
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Internal Medicine, Division of Medical Oncology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - W David Hill
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hongyang Huang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elina Hyppӧnen
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Rick Jansen
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm, Sweden
| | - Zoha Kamali
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Annette Kifley
- Centre for Vision Research, Westmead Institute for Medical Research and Department of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Gerald Liew
- Centre for Vision Research, Westmead Institute for Medical Research and Department of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Penelope A Lind
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Qatar Genome Programme, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - George McMahon
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Stacey A Missmer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Paul Mitchell
- Centre for Vision Research, Westmead Institute for Medical Research and Department of Ophthalmology, University of Sydney, Sydney, New South Wales, Australia
| | - Stine Møllegaard
- Department of Sociology, University of Copenhagen, Copenhagen, Denmark
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Anna Morgan
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, EMGO Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University Medical Center/GGZ inGeest, Amsterdam, the Netherlands
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Chris Power
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Janet W Rich-Edwards
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Women's Health, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Cornelius A Rietveld
- Erasmus University Rotterdam Institute for Behavior and Biology, Rotterdam, the Netherlands
- Department of Applied Economics, Erasmus School of Economics, Rotterdam, the Netherlands
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vallari Shukla
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Stasa Stankovic
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Doris Stöckl
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | | | | | - A Roy Thurik
- Erasmus University Rotterdam Institute for Behavior and Biology, Rotterdam, the Netherlands
- Department of Applied Economics, Erasmus School of Economics, Rotterdam, the Netherlands
- Montpellier Business School, Montpellier, France
| | | | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - André G Uitterlinden
- Erasmus University Rotterdam Institute for Behavior and Biology, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jing Hau Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marcel den Hoed
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Melinda C Mills
- Nuffield College, University of Oxford, Oxford, UK.
- Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Department of Economics, Econometrics and Finance, University of Groningen, Groningen, the Netherlands.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Yang C, Veenstra J, Bartz T, Pahl M, Hallmark B, Chen YDI, Westra J, Steffen L, Brown C, Siscovick D, Tsai M, Wood A, Rich S, Smith C, O'Connor T, Mozaffarian D, Grant S, Chilton F, Tintle N, Lemaitre R, Manichaikul A. Genome-Wide Association Studies and fine-mapping of genomic loci for n-3 and n-6 Polyunsaturated Fatty Acids in Hispanic American and African American Cohorts. RESEARCH SQUARE 2023:rs.3.rs-2073736. [PMID: 36865120 PMCID: PMC9980229 DOI: 10.21203/rs.3.rs-2073736/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) play critical roles in human health. Prior genome-wide association studies (GWAS) of n-3 and n-6 PUFAs in European Americans from the CHARGE Consortium have documented strong genetic signals in/near the FADS locus on chromosome 11. We performed a GWAS of four n-3 and four n-6 PUFAs in Hispanic American (n = 1454) and African American (n = 2278) participants from three CHARGE cohorts. Applying a genome-wide significance threshold of P < 5 x 10 - 8 , we confirmed association of the FADS signal and found evidence of two additional signals (in DAGLA and BEST1 ) within 200 kb of the originally reported FADS signal. Outside of the FADS region, we identified novel signals for arachidonic acid (AA) in Hispanic Americans located in/near genes including TMX2 , SLC29A2 , ANKRD13D and POLD4, and spanning a > 9 Mb region on chromosome 11 (57.5Mb ~ 67.1Mb). Among these novel signals, we found associations unique to Hispanic Americans, including rs28364240, a POLD4 missense variant for AA that is common in CHARGE Hispanic Americans but absent in other race/ancestry groups. Our study sheds light on the genetics of PUFAs and the value of investigating complex trait genetics across diverse ancestry populations.
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Affiliation(s)
| | | | | | | | | | - Yii-Der Ida Chen
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | | | | | | | | | | | | | | | | | | | | | - Struan Grant
- Children's Hospital of Philadelphia Research Institute
| | | | | | - Rozenn Lemaitre
- Cardiovascular Health Research Unit, University of Washington
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Lundberg M, Mackintosh A, Petri A, Bensch S. Inversions maintain differences between migratory phenotypes of a songbird. Nat Commun 2023; 14:452. [PMID: 36707538 PMCID: PMC9883250 DOI: 10.1038/s41467-023-36167-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.
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Affiliation(s)
- Max Lundberg
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Anna Petri
- Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
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Sinkala M, Elsheikh SSM, Mbiyavanga M, Cullinan J, Mulder NJ. A genome-wide association study identifies distinct variants associated with pulmonary function among European and African ancestries from the UK Biobank. Commun Biol 2023; 6:49. [PMID: 36641522 PMCID: PMC9840173 DOI: 10.1038/s42003-023-04443-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 01/09/2023] [Indexed: 01/16/2023] Open
Abstract
Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause of death worldwide. We analysed the UK Biobank genome-wide association summary statistics of pulmonary function for Europeans and individuals of recent African descent to identify variants associated with the trait in the two ancestries. Here, we show 627 variants in Europeans and 3 in Africans associated with three pulmonary function parameters. In addition to the 110 variants in Europeans previously reported to be associated with phenotypes related to pulmonary function, we identify 279 novel loci, including an ISX intergenic variant rs369476290 on chromosome 22 in Africans. Remarkably, we find no shared variants among Africans and Europeans. Furthermore, enrichment analyses of variants separately for each ancestry background reveal significant enrichment for terms related to pulmonary phenotypes in Europeans but not Africans. Further analysis of studies of pulmonary phenotypes reveals that individuals of European background are disproportionally overrepresented in datasets compared to Africans, with the gap widening over the past five years. Our findings extend our understanding of the different variants that modify the pulmonary function in Africans and Europeans, a promising finding for future GWASs and medical studies.
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Affiliation(s)
- Musalula Sinkala
- Computational Biology Division, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Cape Town, South Africa.
| | - Samar S M Elsheikh
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Mamana Mbiyavanga
- Computational Biology Division, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Cape Town, South Africa
| | - Joshua Cullinan
- Computational Biology Division, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Cape Town, South Africa
| | - Nicola J Mulder
- Computational Biology Division, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925, Cape Town, South Africa
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20
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Mezzavilla M, Cocca M, Maisano Delser P, Badii R, Abbaszadeh F, Hadi KA, Giorgia G, Gasparini P. Ancestry-related distribution of Runs of homozygosity and functional variants in Qatari population. BMC Genom Data 2022; 23:73. [PMID: 36131251 PMCID: PMC9490902 DOI: 10.1186/s12863-022-01087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background Describing how genetic history shapes the pattern of medically relevant variants could improve the understanding of how specific loci interact with each other and affect diseases and traits prevalence. The Qatari population is characterized by a complex history of admixture and substructure, and the study of its population genomic features would provide valuable insights into the genetic landscape of functional variants. Here, we analyzed the genomic variation of 186 newly-genotyped healthy individuals from the Qatari peninsula. Results We discovered an intricate genetic structure using ancestry related analyses. In particular, the presence of three different clusters, Cluster 1, Cluster 2 and Cluster 3 (with Near Eastern, South Asian and African ancestry, respectively), was detected with an additional fourth one (Cluster 4) with East Asian ancestry. These subpopulations show differences in the distribution of runs of homozygosity (ROH) and admixture events in the past, ranging from 40 to 5 generations ago. This complex genetic history led to a peculiar pattern of functional markers under positive selection, differentiated in shared signals and private signals. Interestingly we found several signatures of shared selection on SNPs in the FADS2 gene, hinting at a possible common evolutionary link to dietary intake. Among the private signals, we found enrichment for markers associated with HDL and LDL for Cluster 1(Near Eastern ancestry) and Cluster 3 (South Asian ancestry) and height and blood traits for Cluster 2 (African ancestry). The differences in genetic history among these populations also resulted in the different frequency distribution of putative loss of function variants. For example, homozygous carriers for rs2884737, a variant linked to an anticoagulant drug (warfarin) response, are mainly represented by individuals with predominant Bedouin ancestry (risk allele frequency G at 0.48). Conclusions We provided a detailed catalogue of the different ancestral pattern in the Qatari population highlighting differences and similarities in the distribution of selected variants and putative loss of functions. Finally, these results would provide useful guidance for assessing genetic risk factors linked to consanguinity and genetic ancestry.
Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01087-1.
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Al-Garadi MA, Al-Baadani HH, Alqhtani AH. Growth Performance, Histological Changes and Functional Tests of Broiler Chickens Fed Diets Supplemented with Tribulus Terrestris Powder. Animals (Basel) 2022; 12:ani12151930. [PMID: 35953919 PMCID: PMC9367280 DOI: 10.3390/ani12151930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
The current experiment aimed to investigate the effects of TT powder on performance parameters and functional tests, as well as on morphological and histological changes in the liver, kidney and ileum in broiler chickens. Commercial broilers (total = 168 females) were used, equally divided into three dietary treatments (C = 0.0, T1 = 0.75, and T2 = 1.5 g/kg diet). The growth performance (1−35 days of age), absolute and relative weight, liver and kidney functional tests, intestinal morphology (14 and 35 days of age), and histomorphology of the ileum (35 days of age) were evaluated. At 35 days of age, histopathological changes in the ileum, liver, and kidney were also examined. The results showed that the growth performance and absolute and relative weights of the liver and kidney had no negative effects when dietary supplementation with TT powder was given at 0.75 g/kg diet (T1), whereas a decrease was observed at T2 (p < 0.05). Liver and kidney functional tests showed no significant effects in all feed treatments (14 days), while T1 showed lower (p < 0.05) ALT and AST levels (35 days). T1 exhibited higher weights, lengths, and weight-to-length ratios of the small intestine, and relative lengths of the duodenum (p < 0.05). Histomorphometric measurements of the ileum were higher (p < 0.05) in chickens fed the 0.75 g TT/kg diet, and except for in the goblet cell count and epithelial thickness, there were no differences between treatments (p > 0.05). In T1, hepatocytes were more normal but hepatic sinusoids were dilated, whereas in T2, lymphocytes had infiltrated around the central vein and lining endothelial cells had been lost. The kidney was improved in T1 and T2 compared with the control group. Ileal villi were shorter in T2, and some villi fused with enterocyte necrosis and inflammatory cells accumulated in the lumen. We concluded that TT powder (0.75 g/kg feed) has a safe effect and is healthy for broilers.
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Microalgae: Bioactive Composition, Health Benefits, Safety and Prospects as Potential High-Value Ingredients for the Functional Food Industry. Foods 2022; 11:foods11121744. [PMID: 35741941 PMCID: PMC9222421 DOI: 10.3390/foods11121744] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/27/2023] Open
Abstract
Global population is estimated to reach about 9.22 billion by 2075. The increasing knowledge on the relationship between food biochemistry and positive health gives an indication of the urgency to exploit food resources that are not only sustainable but also impact human health beyond basic nutrition. A typical example of such novel food is microalgae, an aquatic microorganism with a plethora of diverse bioactive compounds including phenolics, carotenoids, vitamin B12 and peptides. Microalgal bioactive compounds have been shown to possess positive health effects such as antihypertensive, anti-obesity, antioxidative, anticancer and cardiovascular protection. Although, the utilization of microalgal biomass by the functional food industry has faced lots of challenges because of species diversity and variations in biomass and cultivation factors. Other documented challenges were ascribed to changes in functional structures during extraction and purification due to inefficient bio-processing techniques, inconclusive literature information on the bioavailability and safety of the microalgal bioactive compounds and the fishy odor and taste when applied in food formulations. In spite of these challenges, great opportunities exist to exploit their utilization for the development of functional foods. Microalgae are a renewable resource and have fast growth rate. Therefore, detailed research is needed to bridge these challenges to pave way for large-scale commercialization of microalgal-based healthy foods. The focus of this review is to discuss the potential of microalgae as natural ingredients for functional food development, factors limiting their acceptance and utilization in the food industry as well as their safety concerns with respect to human consumption.
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Duan H, Pan J, Guo M, Li J, Yu L, Fan L. Dietary strategies with anti-aging potential: dietary patterns and supplements. Food Res Int 2022; 158:111501. [DOI: 10.1016/j.foodres.2022.111501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/04/2022]
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24
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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25
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Chilton FH, Manichaikul A, Yang C, O'Connor TD, Johnstone LM, Blomquist S, Schembre SM, Sergeant S, Zec M, Tsai MY, Rich SS, Bridgewater SJ, Mathias RA, Hallmark B. Interpreting Clinical Trials With Omega-3 Supplements in the Context of Ancestry and FADS Genetic Variation. Front Nutr 2022; 8:808054. [PMID: 35211495 PMCID: PMC8861490 DOI: 10.3389/fnut.2021.808054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
Human diets in developed countries such as the US have changed dramatically over the past 75 years, leading to increased obesity, inflammation, and cardiometabolic dysfunction. Evidence over the past decade indicates that the interaction of genetic variation with changes in the intake of 18-carbon essential dietary omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFA), linoleic acid (LA) and α-linolenic acid (ALA), respectively, has impacted numerous molecular and clinical phenotypes. Interactions are particularly relevant with the FADS1 and FADS2 genes, which encode key fatty acid desaturases in the pathway that converts LA and ALA to their long chain (≥20 carbons), highly unsaturated fatty acid (HUFA) counterparts. These gene by nutrient interactions affect the levels and balance of n-6 and n-3 HUFA that in turn are converted to a wide array of lipids with signaling roles, including eicosanoids, docosanoids, other oxylipins and endocannabinoids. With few exceptions, n-6 HUFA are precursors of pro-inflammatory/pro-thrombotic signaling lipids, and n-3 HUFA are generally anti-inflammatory/anti-thrombotic. We and others have demonstrated that African ancestry populations have much higher frequencies (vs. European-, Asian- or indigenous Americas-ancestry populations) of a FADS “derived” haplotype that is associated with the efficient conversion of high levels of dietary n-6 PUFA to pro-inflammatory n-6 HUFA. By contrast, an “ancestral” haplotype, carrying alleles associated with a limited capacity to synthesize HUFA, which can lead to n-3 HUFA deficiency, is found at high frequency in certain Hispanic populations and is nearly fixed in several indigenous populations from the Americas. Based on these observations, a focused secondary subgroup analysis of the VITAL n-3 HUFA supplementation trial stratifying the data based on self-reported ancestry revealed that African Americans may benefit from n-3 HUFA supplementation, and both ancestry and FADS variability should be factored into future clinical trials design.
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Affiliation(s)
- Floyd H. Chilton
- School of Nutritional Sciences and Wellness, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
- *Correspondence: Floyd H. Chilton
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Timothy D. O'Connor
- Program in Personalized and Genomic Medicine, Department of Medicine, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Laurel M. Johnstone
- University of Arizona Genetics Core, University of Arizona, Tucson, AZ, United States
| | - Sarah Blomquist
- School of Nutritional Sciences and Wellness, University of Arizona, Tucson, AZ, United States
| | - Susan M. Schembre
- Department of Family and Community Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ, United States
| | - Susan Sergeant
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Manja Zec
- School of Nutritional Sciences and Wellness, University of Arizona, Tucson, AZ, United States
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | | | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Brian Hallmark
- Center for Biomedical Informatics and Biostatistics, BIO5 Institute, University of Arizona, Tucson, AZ, United States
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Marnetto D, Pankratov V, Mondal M, Montinaro F, Pärna K, Vallini L, Molinaro L, Saag L, Loog L, Montagnese S, Costa R, Metspalu M, Eriksson A, Pagani L. Ancestral genomic contributions to complex traits in contemporary Europeans. Curr Biol 2022; 32:1412-1419.e3. [DOI: 10.1016/j.cub.2022.01.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
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Hatton SL, Pandey MK. Fat and Protein Combat Triggers Immunological Weapons of Innate and Adaptive Immune Systems to Launch Neuroinflammation in Parkinson's Disease. Int J Mol Sci 2022; 23:1089. [PMID: 35163013 PMCID: PMC8835271 DOI: 10.3390/ijms23031089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
Parkinson's disease (PD) is the second-most common neurodegenerative disease in the world, affecting up to 10 million people. This disease mainly happens due to the loss of dopaminergic neurons accountable for memory and motor function. Partial glucocerebrosidase enzyme deficiency and the resultant excess accumulation of glycosphingolipids and alpha-synuclein (α-syn) aggregation have been linked to predominant risk factors that lead to neurodegeneration and memory and motor defects in PD, with known and unknown causes. An increasing body of evidence uncovers the role of several other lipids and their association with α-syn aggregation, which activates the innate and adaptive immune system and sparks brain inflammation in PD. Here, we review the emerging role of a number of lipids, i.e., triglyceride (TG), diglycerides (DG), glycerophosphoethanolamines (GPE), polyunsaturated fatty acids (PUFA), sphingolipids, gangliosides, glycerophospholipids (GPL), and cholesterols, and their connection with α-syn aggregation as well as the induction of innate and adaptive immune reactions that trigger neuroinflammation in PD.
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Affiliation(s)
- Shelby Loraine Hatton
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Cincinnati, OH 45229, USA;
| | - Manoj Kumar Pandey
- Cincinnati Children’s Hospital Medical Center, Division of Human Genetics, 3333 Burnet Avenue, Cincinnati, OH 45229, USA;
- Department of Pediatrics, Division of Human Genetics, College of Medicine, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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28
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Pathak AK, Sukhavasi K, Marnetto D, Chaubey G, Pandey AK. Human population genomics approach in food metabolism. FUTURE FOODS 2022. [DOI: 10.1016/b978-0-323-91001-9.00033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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29
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Colbran LL, Johnson MR, Mathieson I, Capra JA. Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. Genome Biol Evol 2021; 13:evab237. [PMID: 34718543 PMCID: PMC8576593 DOI: 10.1093/gbe/evab237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2021] [Indexed: 12/16/2022] Open
Abstract
As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.
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Affiliation(s)
- Laura L Colbran
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA
| | - Maya R Johnson
- School for Science and Math at Vanderbilt, Vanderbilt University, USA
- Department of Computer Science, Bryn Mawr College, Pennsylvania, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA
- Department of Biological Sciences, Vanderbilt University, USA
- Department of Biomedical Informatics, Vanderbilt University, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
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Prado-Cabrero A, Nolan JM. Omega-3 nutraceuticals, climate change and threats to the environment: The cases of Antarctic krill and Calanus finmarchicus. AMBIO 2021; 50:1184-1199. [PMID: 33502683 PMCID: PMC8068752 DOI: 10.1007/s13280-020-01472-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/20/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
The nutraceutical market for EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) is promoting fishing for Euphasia superba (Antarctic krill) in the Southern Ocean and Calanus finmarchicus in Norwegian waters. This industry argues that these species are underexploited, but they are essential in their ecosystems, and climate change is altering their geographical distribution. In this perspective, we advocate the cessation of fishing for these species to produce nutraceuticals with EPA and DHA. We argue that this is possible because, contrary to what this industry promotes, the benefits of these fatty acids only seem significant to specific population groups, and not for the general population. Next, we explain that this is desirable because there is evidence that these fisheries may interact with the impact of climate change. Greener sources of EPA and DHA are already available on the market, and their reasonable use would ease pressure on the Arctic and Antarctic ecosystems.
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Affiliation(s)
- Alfonso Prado-Cabrero
- Nutrition Research Centre Ireland, School of Health Science, Carriganore House, Waterford Institute of Technology, West Campus, Carriganore, Waterford, Ireland
| | - John M. Nolan
- Nutrition Research Centre Ireland, School of Health Science, Carriganore House, Waterford Institute of Technology, West Campus, Carriganore, Waterford, Ireland
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Harris AM, DeGiorgio M. A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data. Mol Biol Evol 2021; 37:3023-3046. [PMID: 32392293 PMCID: PMC7530616 DOI: 10.1093/molbev/msaa115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, PA.,Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
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32
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Abstract
The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection—postdating the split from Native Americans—in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Abstract
Evolutionary processes, including mutation, migration and natural selection, have influenced the prevalence and distribution of various disorders in humans. However, despite a few well-known examples, such as the APOL1 variants - which have undergone positive genetic selection for their ability to confer resistance to Trypanosoma brucei infection but confer a higher risk of chronic kidney disease - little is known about the effects of evolutionary processes that have shaped genetic variation on kidney disease. An understanding of basic concepts in evolutionary genetics provides an opportunity to consider how findings from ancient and archaic genomes could inform our knowledge of evolution and provide insights into how population migration and genetic admixture have shaped the current distribution and landscape of human kidney-associated diseases. Differences in exposures to infectious agents, environmental toxins, dietary components and climate also have the potential to influence the evolutionary genetics of kidneys. Of note, selective pressure on loci associated with kidney disease is often from non-kidney diseases, and thus it is important to understand how the link between genome-wide selected loci and kidney disease occurs in relation to secondary nephropathies.
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Changes in human milk fatty acid composition and maternal lifestyle-related factors over a decade: a comparison between the two Ulm Birth Cohort Studies. Br J Nutr 2020; 126:228-235. [DOI: 10.1017/s0007114520004006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AbstractHuman milk fatty acid composition varies during lactation and is influenced by maternal diet, maternal lifestyle-related factors and genetic background. This is one of the first studies to investigate a period effect, that is, the impact of lifestyle-related changes on human milk fatty acid composition, in two different cohorts. Lactating women were recruited from the general population a decade apart in Ulm, Germany, using similar methodology. Human milk samples collected 6 weeks postpartum were analysed (Ulm Birth Cohort Study (UBCS (2000)), n 567; Ulm SPATZ Health Study (SPATZ (2012)), n 458). Centred log ratio transformation was applied to fatty acid data. Principal component analysis was used to determine study-dependent fatty acid profiles. A general linear model was used to determine the study (or period) effect on fatty acid profiles adjusting for duration of gestation, age, education, delivery mode, smoking and pre-pregnancy BMI. Two principal components were retained (PC1 and PC2). PC1 was associated with UBCS, while PC2 was associated with SPATZ. PC1 comprised high SFA, and low MUFA, n-6 and n-3 long-chain PUFA (LCPUFA). The inverse was true for PC2. Although human milk remains a source of essential fatty acids, infants could be at risk of inadequate n-3 and n-6 LCPUFA intake through human milk. The differences in the human milk fatty acid profiles also reflect changes in maternal dietary habits in the more recent cohort, which may comprise lower intakes of dietary trans-fatty acids and SFA and higher intakes of vegetable oils.
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Mathieson I. Human adaptation over the past 40,000 years. Curr Opin Genet Dev 2020; 62:97-104. [PMID: 32745952 PMCID: PMC7484260 DOI: 10.1016/j.gde.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States.
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36
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Omega-3 PUFA Responders and Non-Responders and the Prevention of Lipid Dysmetabolism and Related Diseases. Nutrients 2020; 12:nu12051363. [PMID: 32397619 PMCID: PMC7284582 DOI: 10.3390/nu12051363] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023] Open
Abstract
The long-chain omega-3 polyunsaturated fatty acids (LC-omega-3 PUFAs) eicosapentaenoic acid and docosahexaenoic acid are the most popular dietary supplements recommended for the prevention/management of lipid dysmetabolisms and related diseases. However, remarkable inconsistencies exist among the outcomes of the human intervention studies in this field, which contrast with the impressive homogeneity of positive results of most of the preclinical studies. In the present review, we will firstly examine a series of factors-such as background diet composition, gut microbiota and genetic/epigenetic variants, which may lie beneath these inconsistencies. Moreover, we will discuss the recent advance in the knowledge of possible specific biomarkers (genetic-, epigenetic- and microbiota-related) that are being investigated with the goal to apply them in a personalized supplementation with omega-3 PUFAs. We will also consider the possibility of using already available parameters (Omega-3 index, Omega-6 PUFA/Omega-3 PUFA ratio) able to predict the individual responsiveness to these fatty acids and will discuss the optimal timing for their use. Finally, we will critically examine the results of those human studies that have already adopted the distinction of the subjects into omega-3 PUFA responders and non-responders and will discuss the advantage of using such an approach.
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Dehasque M, Ávila‐Arcos MC, Díez‐del‐Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas A, Marques‐Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020; 4:94-108. [PMID: 32313686 PMCID: PMC7156104 DOI: 10.1002/evl3.165] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 01/01/2023] Open
Abstract
Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.
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Affiliation(s)
- Marianne Dehasque
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - María C. Ávila‐Arcos
- International Laboratory for Human Genome Research (LIIGH)UNAM JuriquillaQueretaro76230Mexico
| | - David Díez‐del‐Molino
- Centre for Palaeogenetics10691StockholmSweden
- Department of ZoologyStockholm University10691StockholmSweden
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park CampusImperial College LondonAscotSL5 7PYUnited Kingdom
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Science for Life LaboratoryUppsala University75236UppsalaSweden
| | | | - Anna‐Sapfo Malaspinas
- Department of Computational BiologyUniversity of Lausanne1015LausanneSwitzerland
- SIB Swiss Institute of Bioinformatics1015LausanneSwitzerland
| | - Tomas Marques‐Bonet
- Institut de Biologia Evolutiva(CSIC‐Universitat Pompeu Fabra), Parc de Recerca Biomèdica de BarcelonaBarcelonaSpain
- National Centre for Genomic Analysis—Centre for Genomic RegulationBarcelona Institute of Science and Technology08028BarcelonaSpain
- Institucio Catalana de Recerca i Estudis Avançats08010BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaCerdanyola del VallèsSpain
| | - Michael D. Martin
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Gemma G. R. Murray
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB2 1TNUnited Kingdom
| | - Alexander S. T. Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
| | | | - Daniel Wegmann
- Department of BiologyUniversité de Fribourg1700FribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Love Dalén
- Centre for Palaeogenetics10691StockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural History10405StockholmSweden
| | - Andrew D. Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological SciencesBangor UniversityBangorLL57 2UWUnited Kingdom
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Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet 2020; 21:355-366. [DOI: 10.1038/s41576-020-0218-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 01/01/2023]
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Coltell O, Sorlí JV, Asensio EM, Barragán R, González JI, Giménez-Alba IM, Zanón-Moreno V, Estruch R, Ramírez-Sabio JB, Pascual EC, Ortega-Azorín C, Ordovas JM, Corella D. Genome-Wide Association Study for Serum Omega-3 and Omega-6 Polyunsaturated Fatty Acids: Exploratory Analysis of the Sex-Specific Effects and Dietary Modulation in Mediterranean Subjects with Metabolic Syndrome. Nutrients 2020; 12:E310. [PMID: 31991592 PMCID: PMC7071282 DOI: 10.3390/nu12020310] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Many early studies presented beneficial effects of polyunsaturated fatty acids (PUFA) on cardiovascular risk factors and disease. However, results from recent meta-analyses indicate that this effect would be very low or nil. One of the factors that may contribute to the inconsistency of the results is that, in most studies, genetic factors have not been taken into consideration. It is known that fatty acid desaturase (FADS) gene cluster in chromosome 11 is a very important determinant of plasma PUFA, and that the prevalence of the single nucleotide polymorphisms (SNPs) varies greatly between populations and may constitute a bias in meta-analyses. Previous genome-wide association studies (GWAS) have been carried out in other populations and none of them have investigated sex and Mediterranean dietary pattern interactions at the genome-wide level. Our aims were to undertake a GWAS to discover the genes most associated with serum PUFA concentrations (omega-3, omega-6, and some fatty acids) in a scarcely studied Mediterranean population with metabolic syndrome, and to explore sex and adherence to Mediterranean diet (MedDiet) interactions at the genome-wide level. Serum PUFA were determined by NMR spectroscopy. We found strong robust associations between various SNPs in the FADS cluster and omega-3 concentrations (top-ranked in the adjusted model: FADS1-rs174547, p = 3.34 × 10-14; FADS1-rs174550, p = 5.35 × 10-14; FADS2-rs1535, p = 5.85 × 10-14; FADS1-rs174546, p = 6.72 × 10-14; FADS2-rs174546, p = 9.75 × 10-14; FADS2- rs174576, p = 1.17 × 10-13; FADS2-rs174577, p = 1.12 × 10-12, among others). We also detected a genome-wide significant association with other genes in chromosome 11: MYRF (myelin regulatory factor)-rs174535, p = 1.49 × 10-12; TMEM258 (transmembrane protein 258)-rs102275, p = 2.43 × 10-12; FEN1 (flap structure-specific endonuclease 1)-rs174538, p = 1.96 × 10-11). Similar genome-wide statistically significant results were found for docosahexaenoic fatty acid (DHA). However, no such associations were detected for omega-6 PUFAs or linoleic acid (LA). For total PUFA, we observed a consistent gene*sex interaction with the DNTTIP2 (deoxynucleotidyl transferase terminal interacting protein 2)-rs3747965 p = 1.36 × 10-8. For adherence to MedDiet, we obtained a relevant interaction with the ME1 (malic enzyme 1) gene (a gene strongly regulated by fat) in determining serum omega-3. The top-ranked SNP for this interaction was ME1-rs3798890 (p = 2.15 × 10-7). In the regional-wide association study, specifically focused on the FADS1/FASD2/FADS3 and ELOVL (fatty acid elongase) 2/ELOVL 5 regions, we detected several statistically significant associations at p < 0.05. In conclusion, our results confirm a robust role of the FADS cluster on serum PUFA in this population, but the associations vary depending on the PUFA. Moreover, the detection of some sex and diet interactions underlines the need for these associations/interactions to be studied in all specific populations so as to better understand the complex metabolism of PUFA.
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Affiliation(s)
- Oscar Coltell
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain;
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
| | - Jose V. Sorlí
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Eva M. Asensio
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Rocío Barragán
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - José I. González
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Ignacio M. Giménez-Alba
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Vicente Zanón-Moreno
- Area of Health Sciences, Valencian International University, 46002 Valencia, Spain;
- Red Temática de Investigación Cooperativa en Patología Ocular (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Ophthalmology Research Unit “Santiago Grisolia”, Dr. Peset University Hospital, 46017 Valencia, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Internal Medicine, Hospital Clinic, Institut d’Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | | | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
- Assisted Reproduction Unit of the University Hospital of Valencia, 46010 Valencia, Spain
| | - Carolina Ortega-Azorín
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
| | - Jose M. Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111 USA;
- Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- IMDEA Alimentación, 28049 Madrid, Spain
| | - Dolores Corella
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.V.S.); (E.M.A.); (R.B.); (J.I.G.); (I.M.G.-A.); (R.E.); (C.O.-A.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain;
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40
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Gladyshev MI, Sushchik NN. Long-chain Omega-3 Polyunsaturated Fatty Acids in Natural Ecosystems and the Human Diet: Assumptions and Challenges. Biomolecules 2019; 9:biom9090485. [PMID: 31547473 PMCID: PMC6770104 DOI: 10.3390/biom9090485] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/28/2019] [Accepted: 09/07/2019] [Indexed: 01/05/2023] Open
Abstract
Over the past three decades, studies of essential biomolecules, long-chain polyunsaturated fatty acids of the omega-3 family (LC-PUFAs), namely eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA), have made considerable progress, resulting in several important assumptions. However, new data, which continue to appear, challenge these assumptions. Based on the current literature, an attempt is made to reconsider the following assumptions: 1. There are algal classes of high and low nutritive quality. 2. EPA and DHA decrease with increasing eutrophication in aquatic ecosystems. 3. Animals need EPA and DHA. 4. Fish are the main food source of EPA and DHA for humans. 5. Culinary treatment decreases EPA and DHA in products. As demonstrated, some of the above assumptions need to be substantially specified and changed.
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Affiliation(s)
- Michail I Gladyshev
- Institute of Biophysics of Siberian Branch of Russian Academy of Sciences, Akademgorodok, 50/50, Krasnoyarsk 660036, Russia.
- Siberian Federal University, Svobodny av. 79, Krasnoyarsk 660041, Russia.
| | - Nadezhda N Sushchik
- Institute of Biophysics of Siberian Branch of Russian Academy of Sciences, Akademgorodok, 50/50, Krasnoyarsk 660036, Russia.
- Siberian Federal University, Svobodny av. 79, Krasnoyarsk 660041, Russia.
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41
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Harris DN, Ruczinski I, Yanek LR, Becker LC, Becker DM, Guio H, Cui T, Chilton FH, Mathias RA, O'Connor TD. Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World. Genome Biol Evol 2019; 11:1417-1430. [PMID: 30942856 PMCID: PMC6514828 DOI: 10.1093/gbe/evz071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.
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Affiliation(s)
- Daniel N Harris
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Lisa R Yanek
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lewis C Becker
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Diane M Becker
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Heinner Guio
- Laboratorio de Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Tao Cui
- Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Floyd H Chilton
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona
| | - Rasika A Mathias
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland
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42
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Koletzko B, Reischl E, Tanjung C, Gonzalez-Casanova I, Ramakrishnan U, Meldrum S, Simmer K, Heinrich J, Demmelmair H. FADS1 and FADS2 Polymorphisms Modulate Fatty Acid Metabolism and Dietary Impact on Health. Annu Rev Nutr 2019; 39:21-44. [PMID: 31433740 DOI: 10.1146/annurev-nutr-082018-124250] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Variants in the FADS gene cluster modify the activity of polyunsaturated fatty acid (PUFA) desaturation and the lipid composition in human blood and tissue. FADS variants have been associated with plasma lipid concentrations, risk of cardiovascular diseases, overweight, eczema, pregnancy outcomes, and cognitive function. Studies on variations in the FADS genecluster provided some of the first examples for marked gene-diet interactions in modulating complex phenotypes, such as eczema, asthma, and cognition. Genotype distribution differs markedly among ethnicities, apparently reflecting an evolutionary advantage of genotypes enabling active long-chain PUFA synthesis when the introduction of agriculture provided diets rich in linoleic acid but with little arachidonic and eicosapentaenoic acids. Discovering differential effects of PUFA supply that depend on variation of FADS genotypes could open new opportunities for developing precision nutrition strategies based either on an individual's genotype or on genotype distributions in specific populations.
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Affiliation(s)
- Berthold Koletzko
- Dr. von Hauner Children's Hospital, University of Munich Medical Center, Ludwig-Maximilians-Universität München, 80337 Munich, Germany;
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München (German Research Center for Environmental Health), 85764 Neuherberg, Germany
| | - Conny Tanjung
- Jakarta and Indonesian Medical Education and Research Institute, Hubert Pantai Indah Kapuk Hospital, Jakarta 14460, Indonesia
| | - Ines Gonzalez-Casanova
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
| | - Usha Ramakrishnan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
| | - Suzanne Meldrum
- Centre for Neonatal Research and Education, School of Medicine, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Karen Simmer
- Centre for Neonatal Research and Education, School of Medicine, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine, Comprehensive Pneumology Center (CPC) Munich, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
- Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hans Demmelmair
- Dr. von Hauner Children's Hospital, University of Munich Medical Center, Ludwig-Maximilians-Universität München, 80337 Munich, Germany;
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43
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Çalışkan M, Manduchi E, Rao HS, Segert JA, Beltrame MH, Trizzino M, Park Y, Baker SW, Chesi A, Johnson ME, Hodge KM, Leonard ME, Loza B, Xin D, Berrido AM, Hand NJ, Bauer RC, Wells AD, Olthoff KM, Shaked A, Rader DJ, Grant SFA, Brown CD. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver. Am J Hum Genet 2019; 105:89-107. [PMID: 31204013 PMCID: PMC6612522 DOI: 10.1016/j.ajhg.2019.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 05/13/2019] [Indexed: 12/14/2022] Open
Abstract
Deciphering the impact of genetic variation on gene regulation is fundamental to understanding common, complex human diseases. Although histone modifications are important markers of gene regulatory elements of the genome, any specific histone modification has not been assayed in more than a few individuals in the human liver. As a result, the effects of genetic variation on histone modification states in the liver are poorly understood. Here, we generate the most comprehensive genome-wide dataset of two epigenetic marks, H3K4me3 and H3K27ac, and annotate thousands of putative regulatory elements in the human liver. We integrate these findings with genome-wide gene expression data collected from the same human liver tissues and high-resolution promoter-focused chromatin interaction maps collected from human liver-derived HepG2 cells. We demonstrate widespread functional consequences of natural genetic variation on putative regulatory element activity and gene expression levels. Leveraging these extensive datasets, we fine-map a total of 74 GWAS loci that have been associated with at least one complex phenotype. Our results reveal a repertoire of genes and regulatory mechanisms governing complex disease development and further the basic understanding of genetic and epigenetic regulation of gene expression in the human liver tissue.
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Affiliation(s)
- Minal Çalışkan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Elisabetta Manduchi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - H Shanker Rao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julian A Segert
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcia Holsbach Beltrame
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Trizzino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - YoSon Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel W Baker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew E Johnson
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kenyaita M Hodge
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michelle E Leonard
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Baoli Loza
- Division of Transplant Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dong Xin
- Division of Transplant Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea M Berrido
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas J Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert C Bauer
- Division of Cardiology, Columbia University, New York, NY 10032, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kim M Olthoff
- Division of Transplant Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abraham Shaked
- Division of Transplant Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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44
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James WPT, Johnson RJ, Speakman JR, Wallace DC, Frühbeck G, Iversen PO, Stover PJ. Nutrition and its role in human evolution. J Intern Med 2019; 285:533-549. [PMID: 30772945 DOI: 10.1111/joim.12878] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.
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Affiliation(s)
- W P T James
- London School of Hygiene and Tropical Medicine, London, UK
| | - R J Johnson
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, CO, USA
| | - J R Speakman
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D C Wallace
- Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - G Frühbeck
- Endocrinology and Nutrition, Clinica Universidad de Navarra, Pamplona, Spain
| | - P O Iversen
- Department of Nutrition, University of Oslo, Oslo, Norway
| | - P J Stover
- Vice Chancellor and Dean for Agriculture and Life Sciences, Texas A&M AgriLife, College Station, TX, USA
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45
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Barroso I, McCarthy MI. The Genetic Basis of Metabolic Disease. Cell 2019; 177:146-161. [PMID: 30901536 PMCID: PMC6432945 DOI: 10.1016/j.cell.2019.02.024] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 02/06/2023]
Abstract
Recent developments in genetics and genomics are providing a detailed and systematic characterization of the genetic underpinnings of common metabolic diseases and traits, highlighting the inherent complexity within systems for homeostatic control and the many ways in which that control can fail. The genetic architecture underlying these common metabolic phenotypes is complex, with each trait influenced by hundreds of loci spanning a range of allele frequencies and effect sizes. Here, we review the growing appreciation of this complexity and how this has fostered the implementation of genome-scale approaches that deliver robust mechanistic inference and unveil new strategies for translational exploitation.
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Affiliation(s)
- Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford OX3 7LJ, UK; Oxford NIHR Biomedical Research Centre, Churchill Hospital, Old Road, Headington, Oxford OX3 7LJ, UK
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46
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The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity. Genes (Basel) 2019; 10:genes10030222. [PMID: 30884759 PMCID: PMC6471373 DOI: 10.3390/genes10030222] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.
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47
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Prohaska A, Racimo F, Schork AJ, Sikora M, Stern AJ, Ilardo M, Allentoft ME, Folkersen L, Buil A, Moreno-Mayar JV, Korneliussen T, Geschwind D, Ingason A, Werge T, Nielsen R, Willerslev E. Human Disease Variation in the Light of Population Genomics. Cell 2019; 177:115-131. [DOI: 10.1016/j.cell.2019.01.052] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 01/25/2023]
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48
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Abstract
Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size.
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Affiliation(s)
- Sara Mathieson
- Department of Computer Science, Swarthmore College, Swarthmore, PA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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49
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Tanjung C, Rzehak P, Sudoyo H, Mansyur M, Munasir Z, Immanuel S, Irawan R, Reischl E, Demmelmair H, Hadinegoro SR, Sjarif DR, Koletzko B. The association of fatty acid desaturase gene polymorphisms on long-chain polyunsaturated fatty acid composition in Indonesian infants. Am J Clin Nutr 2018; 108:1135-1144. [PMID: 30475958 PMCID: PMC6250987 DOI: 10.1093/ajcn/nqy166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/28/2018] [Indexed: 11/14/2022] Open
Abstract
Background Adequate availability of long-chain polyunsaturated fatty acids (LC-PUFAs) is important for human health from pregnancy to adulthood. Previous studies on fatty acid desaturase (FADS) gene single-nucleotide polymorphisms (SNPs) have been performed predominantly in Western populations and showed that FADS SNPs had a marked impact on LC-PUFA composition in blood and tissues. Objectives We aimed to investigate the influence of fetal FADS genotypes on LC-PUFA composition in umbilical artery plasma lipids in Indonesian infants. Design We performed a cross-sectional study to assess for these associations. Results A total of 12 cord plasma n-6 (ω-6) and n-3 (ω-3) fatty acids were analyzed for associations with 18 FADS gene cluster SNPs from 390 women with single parturition from the Indonesian Prospective Study of Atopic Dermatitis in Infants (ISADI). Fetal FADS genotypes influenced cord plasma LC-PUFA composition, but, in contrast to previous studies from Western populations, the quantitatively predominant SNPs were associated with lower LC-PUFA content. Conclusion To our knowledge, this study was the first in South East Asia on FADS genotypes and arterial cord blood fatty acids to show an association between fetal LC-PUFA composition and fetal FADS SNPs. The FADS genotype distribution differs markedly between different geographical populations. This trial was registered at clinicaltrials.gov as NCT02401178.
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Affiliation(s)
- Conny Tanjung
- Pantai Indah Kapuk Hospital, Jakarta, Indonesia
- Human Genetic, Indonesian Medical Education and Research Institute, Jakarta, Indonesia
| | - Peter Rzehak
- LMU - Ludwig-Maximilians-Universität München, Dr von Hauner Children's Hospital, Division of Metabolic and Nutritional Medicine, University of Munich Medical Centre, Munich, Germany
| | - Herawati Sudoyo
- Faculty of Medicine, Sydney University, Sydney, Australia
- Department of Medical Biology, Faculty of Medicine
| | | | | | - Suzanna Immanuel
- Clinical Pathology, Faculty of Medicine, Universitas Indonesia, Dr Ciptomangunkusumo National Referral Hospital, Jakarta, Indonesia
| | - Roedi Irawan
- Department of Pediatrics, Faculty of Medicine, Universitas Airlangga, Dr Sutomo General Hospital, Surabaya, Indonesia
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Muenchen, Munich, Germany
| | - Hans Demmelmair
- LMU - Ludwig-Maximilians-Universität München, Dr von Hauner Children's Hospital, Division of Metabolic and Nutritional Medicine, University of Munich Medical Centre, Munich, Germany
| | | | - Damayanti Rusli Sjarif
- Human Genetic, Indonesian Medical Education and Research Institute, Jakarta, Indonesia
- Departments of Pediatrics
- Address correspondence to DRS (e-mail: )
| | - Berthold Koletzko
- LMU - Ludwig-Maximilians-Universität München, Dr von Hauner Children's Hospital, Division of Metabolic and Nutritional Medicine, University of Munich Medical Centre, Munich, Germany
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Andersen MK, Hansen T. Genetics of metabolic traits in Greenlanders: lessons from an isolated population. J Intern Med 2018; 284:464-477. [PMID: 30101502 DOI: 10.1111/joim.12814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, we describe the extraordinary population of Greenland, which differs from large outbred populations of Europe and Asia, both in terms of population history and living conditions. Many years in isolation, small population size and an extreme environment have shaped the genetic composition of the Greenlandic population. The unique genetic background combined with the transition from a traditional Inuit lifestyle and diet, to a more Westernized lifestyle, has led to an increase in the prevalence of metabolic conditions like obesity, where the prevalence from 1993 to 2010 has increased from 16.4% to 19.4% among men, and from 13.0% to 25.4% among women, type 2 diabetes and cardiovascular diseases. The genetic susceptibility to metabolic conditions has been explored in Greenlanders, as well as other isolated populations, taking advantage of population-genetic properties of these populations. During the last 10 years, these studies have provided examples of loci showing evidence of positive selection, due to adaption to Arctic climate and Inuit diet, including TBC1D4 and FADS/CPT1A, and have facilitated the discovery of several loci associated with metabolic phenotypes. Most recently, the c.2433-1G>A loss-of-function variant in ADCY3 associated with obesity and type 2 diabetes was described. This locus has provided novel biological insights, as it has been shown that reduced ADCY3 function causes obesity through disrupted function in primary cilia. Future studies of isolated populations will likely provide further genetic as well as biological insights.
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Affiliation(s)
- M K Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - T Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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