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Karageorgiou C, Gokcumen O, Dennis MY. Deciphering the role of structural variation in human evolution: a functional perspective. Curr Opin Genet Dev 2024; 88:102240. [PMID: 39121701 DOI: 10.1016/j.gde.2024.102240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]
Abstract
Advances in sequencing technologies have enabled the comparison of high-quality genomes of diverse primate species, revealing vast amounts of divergence due to structural variation. Given their large size, structural variants (SVs) can simultaneously alter the function and regulation of multiple genes. Studies estimate that collectively more than 3.5% of the genome is divergent in humans versus other great apes, impacting thousands of genes. Functional genomics and gene-editing tools in various model systems recently emerged as an exciting frontier - investigating the wide-ranging impacts of SVs on molecular, cellular, and systems-level phenotypes. This review examines existing research and identifies future directions to broaden our understanding of the functional roles of SVs on phenotypic innovations and diversity impacting uniquely human features, ranging from cognition to metabolic adaptations.
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Affiliation(s)
- Charikleia Karageorgiou
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, USA. https://twitter.com/@evobioclio
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, USA
| | - Megan Y Dennis
- Department of Biochemistry & Molecular Medicine, Genome Center, and MIND Institute, University of California, Davis, CA 95616, USA.
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2
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Otto M, Zheng Y, Grablowitz P, Wiehe T. Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion. Hum Genome Var 2024; 11:37. [PMID: 39313504 PMCID: PMC11420239 DOI: 10.1038/s41439-024-00293-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/05/2024] [Accepted: 07/22/2024] [Indexed: 09/25/2024] Open
Abstract
Genes with multiple copies are likely to be maintained by stabilizing selection, which puts a bound to unlimited expansion of copy number. We designed a model in which copy number variation is generated by unequal recombination, which fits well with several genes surveyed in three human populations. Based on this theoretical model and computer simulations, we were interested in determining whether the gene copy number distribution in the derived European and Asian populations can be explained by a purely demographic scenario or whether shifts in the distribution are signatures of adaptation. Although the copy number distribution in most of the analyzed gene clusters can be explained by a bottleneck, such as in the out-of-Africa expansion of Homo sapiens 60-10 kyrs ago, we identified several candidate genes, such as AMY1A and PGA3, whose copy numbers are likely to differ among African, Asian, and European populations.
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Affiliation(s)
- Moritz Otto
- Institue for Genetics, University of Cologne, Cologne, Germany
| | - Yichen Zheng
- Institue for Genetics, University of Cologne, Cologne, Germany
| | - Paul Grablowitz
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Thomas Wiehe
- Institue for Genetics, University of Cologne, Cologne, Germany.
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3
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Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin CS, Garrison E, Sudmant PH. Recurrent evolution and selection shape structural diversity at the amylase locus. Nature 2024:10.1038/s41586-024-07911-1. [PMID: 39232174 DOI: 10.1038/s41586-024-07911-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/06/2024] [Indexed: 09/06/2024]
Abstract
The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations1. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake2, although evidence of recent selection is lacking3,4. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately 5,600 contemporary and ancient humans, we resolve the diversity and evolutionary history of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in agricultural populations than in fishing, hunting and pastoral populations. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events with mutation rates up to more than 10,000-fold the single-nucleotide polymorphism mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome-based approach, we infer structural haplotypes across thousands of humans identifying extensively duplicated haplotypes at higher frequency in modern agricultural populations. Leveraging 533 ancient human genomes, we find that duplication-containing haplotypes (with more gene copies than the ancestral haplotype) have rapidly increased in frequency over the past 12,000 years in West Eurasians, suggestive of positive selection. Together, our study highlights the potential effects of the agricultural revolution on human genomes and the importance of structural variation in human adaptation.
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Affiliation(s)
| | - Alma Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Runyang Nicolas Lou
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Joana L Rocha
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nicole Soranzo
- Human Technopole, Milan, Italy
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge Biomedical Campus, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Chen-Shan Chin
- Foundation for Biological Data Science, Belmont, CA, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA.
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4
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Bragazzi NL, Del Rio D, Mayer EA, Mena P. We Are What, When, And How We Eat: The Evolutionary Impact of Dietary Shifts on Physical and Cognitive Development, Health, and Disease. Adv Nutr 2024; 15:100280. [PMID: 39067763 PMCID: PMC11367649 DOI: 10.1016/j.advnut.2024.100280] [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: 05/24/2024] [Revised: 07/07/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
"We are what, when, and how we eat": the evolution of human dietary habits mirrors the evolution of humans themselves. Key developments in human history, such as the advent of stone tool technology, the shift to a meat-based diet, control of fire, advancements in cooking and fermentation techniques, and the domestication of plants and animals, have significantly influenced human anatomical, physiological, social, cognitive, and behavioral changes. Advancements in scientific methods, such as the analysis of microfossils like starch granules, plant-derived phytoliths, and coprolites, have yielded unprecedented insights into past diets. Nonetheless, the isolation of ancient food matrices remains analytically challenging. Future technological breakthroughs and a more comprehensive integration of paleogenomics, paleoproteomics, paleoglycomics, and paleometabolomics will enable a more nuanced understanding of early human ancestors' diets, which holds the potential to guide contemporary dietary recommendations and tackle modern health challenges, with far-reaching implications for human well-being, and ecological impact on the planet.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy
| | - Daniele Del Rio
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy.
| | - Emeran A Mayer
- Goodman-Luskin Microbiome Center, David Geffen School of Medicine, University of California, Los Angeles, CA, United States; G. Oppenheimer Center for Neurobiology of Stress and Resilience, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | - Pedro Mena
- Human Nutrition Unit (HNU), Department of Food and Drugs, University of Parma, Parma, Italy
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M JN, Bharadwaj D. The complex web of obesity: from genetics to precision medicine. Expert Rev Endocrinol Metab 2024:1-16. [PMID: 38869356 DOI: 10.1080/17446651.2024.2365785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
INTRODUCTION Obesity is a growing public health concern affecting both children and adults. Since it involves both genetic and environmental components, the management of obesity requires both, an understanding of the underlying genetics and changes in lifestyle. The knowledge of obesity genetics will enable the possibility of precision medicine in anti-obesity medications. AREAS COVERED Here, we explore health complications and the prevalence of obesity. We discuss disruptions in energy balance as a symptom of obesity, examining evolutionary theories, its multi-factorial origins, and heritability. Additionally, we discuss monogenic and polygenic obesity, the converging biological pathways, potential pharmacogenomics applications, and existing anti-obesity medications - specifically focussing on the leptin-melanocortin and incretin pathways. Comparisons between childhood and adult obesity genetics are made, along with insights into structural variants, epigenetic changes, and environmental influences on epigenetic signatures. EXPERT OPINION With recent advancements in anti-obesity drugs, genetic studies pinpoint new targets and allow for repurposing existing drugs. This creates opportunities for genotype-informed treatment options. Also, lifestyle interventions can help in the prevention and treatment of obesity by altering the epigenetic signatures. The comparison of genetic architecture in adults and children revealed a significant overlap. However, more robust studies with diverse ethnic representation is required in childhood obesity.
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Affiliation(s)
- Janaki Nair M
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin J, Garrison E, Sudmant PH. Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579378. [PMID: 38370750 PMCID: PMC10871346 DOI: 10.1101/2024.02.07.579378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The adoption of agriculture, first documented ~12,000 years ago in the Fertile Crescent, triggered a rapid shift toward starch-rich diets in human populations. Amylase genes facilitate starch digestion and increased salivary amylase copy number has been observed in some modern human populations with high starch intake, though evidence of recent selection is lacking. Here, using 52 long-read diploid assemblies and short read data from ~5,600 contemporary and ancient humans, we resolve the diversity, evolutionary history, and selective impact of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in populations with agricultural subsistence compared to fishing, hunting, and pastoral groups. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each exhibit multiple duplications/deletions with mutation rates >10,000-fold the SNP mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome graph-based approach to infer structural haplotypes across thousands of humans, we identify extensively duplicated haplotypes present at higher frequencies in modern day populations with traditionally agricultural diets. Leveraging 533 ancient human genomes we find that duplication-containing haplotypes (i.e. haplotypes with more amylase gene copies than the ancestral haplotype) have increased in frequency more than seven-fold over the last 12,000 years providing evidence for recent selection in West Eurasians. Together, our study highlights the potential impacts of the agricultural revolution on human genomes and the importance of long-read sequencing in identifying signatures of selection at structurally complex loci.
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Affiliation(s)
| | - Alma Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | - Runyang Nicolas Lou
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | | | - Joana L Rocha
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | | | - Jason Chin
- Foundation for Biological Data Science, Belmont, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
- Center for Computational Biology, University of California Berkeley, Berkeley, USA
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Yilmaz F, Karageorgiou C, Kim K, Pajic P, Scheer K, Beck CR, Torregrossa AM, Lee C, Gokcumen O. Paleolithic Gene Duplications Primed Adaptive Evolution of Human Amylase Locus Upon Agriculture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.27.568916. [PMID: 38077078 PMCID: PMC10705236 DOI: 10.1101/2023.11.27.568916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Starch digestion is a cornerstone of human nutrition. The amylase genes code for the starch-digesting amylase enzyme. Previous studies suggested that the salivary amylase (AMY1) gene copy number increased in response to agricultural diets. However, the lack of nucleotide resolution of the amylase locus hindered detailed evolutionary analyses. Here, we have resolved this locus at nucleotide resolution in 98 present-day humans and identified 30 distinct haplotypes, revealing that the coding sequences of all amylase gene copies are evolving under negative selection. The phylogenetic reconstruction suggested that haplotypes with three AMY1 gene copies, prevalent across all continents and constituting about 70% of observed haplotypes, originated before the out-of-Africa migrations of ancestral modern humans. Using thousands of unique 25 base pair sequences across the amylase locus, we showed that additional AMY1 gene copies existed in the genomes of four archaic hominin genomes, indicating that the initial duplication of this locus may have occurred as far back 800,000 years ago. We similarly analyzed 73 ancient human genomes dating from 300 - 45,000 years ago and found that the AMY1 copy number variation observed today existed long before the advent of agriculture (~10,000 years ago), predisposing this locus to adaptive increase in the frequency of higher amylase copy number with the spread of agriculture. Mechanistically, the common three-copy haplotypes seeded non-allelic homologous recombination events that appear to be occurring at one of the fastest rates seen for tandem repeats in the human genome. Our study provides a comprehensive population-level understanding of the genomic structure of the amylase locus, identifying the mechanisms and evolutionary history underlying its duplication and copy number variability in relation to the onset of agriculture.
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Al Akl NS, Khalifa O, Habibullah M, Arredouani A. Salivary α-amylase activity is associated with cardiometabolic and inflammatory biomarkers in overweight/obese, non-diabetic Qatari women. Front Endocrinol (Lausanne) 2024; 15:1348853. [PMID: 38562410 PMCID: PMC10982335 DOI: 10.3389/fendo.2024.1348853] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Obesity, prevalent in approximately 80% of Qatar's adult population, increases the risk of complications like type 2 diabetes and cardiovascular diseases. Predictive biomarkers are crucial for preventive strategies. Salivary α-amylase activity (sAAa) inversely correlates with obesity and insulin resistance in adults and children. However, the connection between sAAa and cardiometabolic risk factors or chronic low-grade inflammation markers remains unclear. This study explores the association between serum sAAa and adiposity markers related to cardiovascular diseases, as well as markers indicative of chronic low-grade inflammation. Methods Serum samples and clinical data of 1500 adult, non-diabetic, Overweight/Obese participants were obtained from Qatar Biobank (QBB). We quantified sAAa and C reactive protein (CRP) levels with an autoanalyzer. Cytokines, adipokines, and adiponectin of a subset of 228 samples were quantified using a bead-based multiplex assay. The associations between the sAAa and the adiposity indices and low-grade inflammatory protein CRP and multiple cytokines were assessed using Pearson's correlation and adjusted linear regression. Results The mean age of the participants was 36 ± 10 years for both sexes of which 76.6% are women. Our analysis revealed a significant linear association between sAAa and adiposity-associated biomarkers, including body mass index β -0.032 [95% CI -0.049 to -0.05], waist circumference β -0.05 [95% CI -0.09 to -0.02], hip circumference β -0.052 [95% CI -0.087 to -0.017], and HDL β 0.002 [95% CI 0.001 to 0.004], albeit only in women. Additionally, sAAa demonstrated a significant positive association with adiponectin β 0.007 [95% CI 0.001 to 0.01]while concurrently displaying significant negative associations with CRP β -0.02 [95% CI -0.044 to -0.0001], TNF-α β -0.105 [95% CI -0.207 to -0.004], IL-6 β [95% CI -0.39 -0.75 to -0.04], and ghrelin β -5.95 [95% CI -11.71 to -0.20], specifically within the female population. Conclusion Our findings delineate significant associations between sAAa and markers indicative of cardiovascular disease risk and inflammation among overweight/obese adult Qatari females. Subsequent investigations are warranted to elucidate the nuances of these gender-specific associations comprehensively.
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Affiliation(s)
- Neyla S. Al Akl
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Olfa Khalifa
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | | | - Abdelilah Arredouani
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
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9
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Jalal M, Gbadegesin SA, Tehami N, Nakajima K. What is the clinical significance of low serum amylase? Systematic review of the conditions associated with low serum amylase. Frontline Gastroenterol 2024; 15:154-161. [PMID: 38779473 PMCID: PMC11106763 DOI: 10.1136/flgastro-2023-102405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/15/2023] [Indexed: 05/25/2024] Open
Abstract
Objective Most studies have assessed the impact of elevated serum amylase levels in clinical practice, but only a few have investigated the significance of low serum amylase. We therefore, aimed to review the literature to understand the conditions associated with low serum amylase and its clinical relevance. Method This systematic review was performed in accordance with the criteria established in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The search was conducted on Medline and Embase databases until November 2022. After identifying relevant titles, abstracts were read and data of eligible articles retrieved. The conditions associated with low serum amylase were evaluated. The quality of the studies was assessed using the Newcastle-Ottawa Score. Results Our search strategy identified 19 studies including a total of 15 097 patients for systematic review. All the studies were observational including two studies which used secretin-induced test. The main conditions associated with low serum amylase were diabetes mellitus (n=9), metabolic syndrome (n=3), chronic pancreatitis (CP) (n=3), non-alcoholic fatty liver disease (n=2) and obesity (n=1). Low serum amylase showed a high specificity (94%) with low sensitivity (38.7%-59%) in diagnosing chronic pancreatitis. Conclusion This systematic review revealed a unique insight into the relevance of low serum amylase in clinical practice. Low serum amylase can be a useful adjunct test in the assessment of patients with CP, pancreatic exocrine insufficiency, diabetes mellitus and metabolic syndrome.
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Affiliation(s)
- Mustafa Jalal
- Department of Gastroenterology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Nadeem Tehami
- Hepatology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Kei Nakajima
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Japan
- Department of Endocrinology and Diabetes, Saitama Medical University, Iruma-gun, Japan
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10
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Gkouskou KK, Grammatikopoulou MG, Lazou E, Vasilogiannakopoulou T, Sanoudou D, Eliopoulos AG. A genomics perspective of personalized prevention and management of obesity. Hum Genomics 2024; 18:4. [PMID: 38281958 PMCID: PMC10823690 DOI: 10.1186/s40246-024-00570-3] [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: 11/18/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024] Open
Abstract
This review discusses the landscape of personalized prevention and management of obesity from a nutrigenetics perspective. Focusing on macronutrient tailoring, we discuss the impact of genetic variation on responses to carbohydrate, lipid, protein, and fiber consumption. Our bioinformatic analysis of genomic variants guiding macronutrient intake revealed enrichment of pathways associated with circadian rhythm, melatonin metabolism, cholesterol and lipoprotein remodeling and PPAR signaling as potential targets of macronutrients for the management of obesity in relevant genetic backgrounds. Notably, our data-based in silico predictions suggest the potential of repurposing the SYK inhibitor fostamatinib for obesity treatment in relevant genetic profiles. In addition to dietary considerations, we address genetic variations guiding lifestyle changes in weight management, including exercise and chrononutrition. Finally, we emphasize the need for a refined understanding and expanded research into the complex genetic landscape underlying obesity and its management.
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Affiliation(s)
- Kalliopi K Gkouskou
- Department of Biology, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 11527, Athens, Greece.
- GENOSOPHY P.C., Athens, Greece.
| | - Maria G Grammatikopoulou
- Unit of Immunonutrition and Clinical Nutrition, Department of Rheumatology and Clinical Immunology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | | | - Theodora Vasilogiannakopoulou
- Department of Biology, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 11527, Athens, Greece
| | - Despina Sanoudou
- Clinical Genomics and Pharmacogenomics Unit, 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Aristides G Eliopoulos
- Department of Biology, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 11527, Athens, Greece.
- GENOSOPHY P.C., Athens, Greece.
- Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Devarakonda SLS, Superdock DK, Ren J, Johnson LM, Loinard-González A(AP, Poole AC. Gut microbial features and dietary fiber intake predict gut microbiota response to resistant starch supplementation. Gut Microbes 2024; 16:2367301. [PMID: 38913541 PMCID: PMC11197919 DOI: 10.1080/19490976.2024.2367301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/07/2024] [Indexed: 06/26/2024] Open
Abstract
Resistant starch (RS) consumption can have beneficial effects on metabolic health, but the response, in terms of effects on the gut microbiota and host physiology, varies between individuals. Factors predicting the response to RS are not yet established and would be useful for developing precision nutrition approaches that maximize the benefits of dietary fiber intake. We sought to identify predictors of gut microbiota response to RS supplementation. We enrolled 76 healthy adults into a 7-week crossover study with 59 individuals completing the study. Participants consumed RS type 2 (RS2), RS type 4 (RS4), and digestible starch, for 10 d each with 5-d washout periods in between. We collected fecal and saliva samples and food records during each treatment period. We performed 16S rRNA gene sequencing and measured fecal short-chain fatty acids (SCFAs), salivary amylase (AMY1) gene copy number, and salivary amylase activity (SAA). Dietary fiber intake was predictive of the relative abundance of several amplicon sequence variants (ASVs) at the end of both RS treatments. AMY1-related metrics were not predictive of response to RS. SAA was only predictive of the relative abundance of one ASV after digestible starch supplementation. Interestingly, SCFA concentrations increased the most during digestible starch supplementation. Treatment order (the order of consumption of RS2 and RS4), alpha diversity, and a subset of ASVs were predictive of SCFA changes after RS supplementation. Based on our findings, dietary fiber intake and gut microbiome composition would be informative if assessed prior to recommending RS supplementation because these data can be used to predict changes in specific ASVs and fecal SCFA concentrations. These findings lay a foundation to support the premise that using a precision nutrition approach to optimize the benefits of dietary fibers such as RS could be an effective strategy to compensate for the low consumption of dietary fiber nationwide.
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Affiliation(s)
| | | | - Jennifer Ren
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Lynn M. Johnson
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY, USA
| | | | - Angela C. Poole
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
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12
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Huang Q, Wang J, Wang J, Yu D, Zhan Y, Liu Z. Emerging Health Risks of Crumb Rubber: Inhalation of Environmentally Persistent Free Radicals via Saliva During Artificial Turf Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21005-21015. [PMID: 38048287 DOI: 10.1021/acs.est.3c03278] [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: 12/06/2023]
Abstract
Crumb rubber (CR) is a commonly used infill material in artificial turf worldwide. However, the potential health risk associated with exposure to CR containing environmentally persistent free radicals (EPFRs) remains under investigation. Herein, we observed the widespread presence of CR particles in the range of 2.8-51.4 μg/m3 and EPFRs exceeding 6 × 1015 spins/g in the ambient air surrounding artificial turf fields. Notably, the abundance of these particles tended to increase with the number of operating years of the playing fields. Furthermore, by analyzing saliva samples from 200 participants, we established for the first time that EPFR-carrying CR could be found in saliva specimens, suggesting the potential for inhaling them through the oral cavity and their exposure to the human body. After 40 min of exercise on the turf, we detected a substantial presence of EPFRs, reaching as high as (1.15 ± 1.00) × 1016 spins of EPFR per 10 mL of saliva. Moreover, the presence of EPFRs considerably increased the oxidative potential of CR, leading to the inactivation of Ca2+, redox reactions, and changes in spatial binding of the α-1,4-chain of salivary amylase to Ca2+, all of which could influence human saliva health. Our study provides insights into a new pathway of human exposure to CR with EPFRs in artificial turf infill, indicating an increased human health risk of CR exposure.
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Affiliation(s)
- Qian'en Huang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Xining, Qinghai 810008, China
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqun Wang
- Department of Stomatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jianping Wang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Xining, Qinghai 810008, China
| | - Dongmei Yu
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Xining, Qinghai 810008, China
| | - Yuanbo Zhan
- Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Ze Liu
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Xining, Qinghai 810008, China
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13
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Pierzynowska K, Wychowański P, Zaworski K, Woliński J, Donaldson J, Pierzynowski S. Anti-Incretin Gut Features Induced by Feed Supplementation with Alpha-Amylase: Studies on EPI Pigs. Int J Mol Sci 2023; 24:16177. [PMID: 38003366 PMCID: PMC10671445 DOI: 10.3390/ijms242216177] [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: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The acini-islet-acinar (AIA) axis concept justifies the anatomical placement of the Langerhans islets within the exocrine pancreatic parenchyma and explains the existence of the pancreas as a single organ. Amylase has been suggested to play a key role as an anti-incretin factor. Oral glucose tolerance tests (OGTT) were performed on 18 piglets in both a healthy (prior to pancreatic duct ligation (PDL) surgery, study Day 10) and an exocrine pancreatic insufficient (EPI) state (30 days after PDL, study Day 48)). Amylase (4000 units/feeding) or Creon® (100,000 units/feeding) was administered to pigs with the morning and evening meals, according to study design randomization, for 37 days following the first OGTT. Blood glucose levels, as well as plasma levels of insulin, GLP-1, and GIP, were measured, and the HOMA-IR index was calculated. EPI status did not affect the area under the curve (AUC) of insulin release, fasting insulin levels, or the HOMA-IR index, while amylase supplementation led to a significant (p < 0.05) decrease in the above-mentioned parameters. At the same time, EPI led to a significant (p < 0.05) increase in GLP-1 levels, and neither amylase nor Creon® supplementation had any effects on this EPI-related increase. Fasting plasma levels of GIP were not affected by EPI; however, the GIP response in EPI and Amylase-treated EPI animals was significantly lower (p < 0.05) when compared to that of the intact, healthy pigs. Orally administered amylase induces gut anti-incretin action, normalizing glucose homeostasis and reducing HOMA-IR as a long-term outcome, thus lowering the risk of diabetes type II development. Amylase has long-lasting anti-incretin effects, and one could consider the existence of a long-lasting gut memory for amylase, which decreases hyperinsulinemia and hyperglycemia for up to 16 h after the last exposure of the gut to amylase.
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Affiliation(s)
- Kateryna Pierzynowska
- Department of Biology, Lund University, 223 62 Lund, Sweden;
- Department of Animal Physiology, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland; (K.Z.); (J.W.)
- Anara AB, 231 32 Trelleborg, Sweden; (P.W.); (J.D.)
| | - Piotr Wychowański
- Anara AB, 231 32 Trelleborg, Sweden; (P.W.); (J.D.)
- Department of Head and Neck and Sensory Organs, Division of Oral Surgery and Implantology, Institute of Clinical Dentistry, Gemelli Foundation for the University Policlinic, Catholic University of the “Sacred Heart”, 00168 Rome, Italy
- Department of Oral Surgery, Medical University of Gdańsk, 80-211 Gdańsk, Poland
- Specialized Private Implantology Clinic Wychowanski Stomatologia, 02-517 Warsaw, Poland
| | - Kamil Zaworski
- Department of Animal Physiology, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland; (K.Z.); (J.W.)
| | - Jarosław Woliński
- Department of Animal Physiology, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland; (K.Z.); (J.W.)
- Large Animal Models Laboratory, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jabłonna, Poland
| | - Janine Donaldson
- Anara AB, 231 32 Trelleborg, Sweden; (P.W.); (J.D.)
- School of Physiology, Faculty of Health Sciences, University of the Witwatersrand (WITS), Johannesburg 2050, South Africa
| | - Stefan Pierzynowski
- Department of Biology, Lund University, 223 62 Lund, Sweden;
- Anara AB, 231 32 Trelleborg, Sweden; (P.W.); (J.D.)
- Department of Medical Biology, Institute of Rural Health, 20-090 Lublin, Poland
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14
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Zhang X, Moran C, Wang R, Zhou Y, Brooks N. Salivary amylase gene (AMY1) copy number variation has only a minor correlation with body composition in Chinese adults. Genes Genomics 2023; 45:935-943. [PMID: 37043131 DOI: 10.1007/s13258-023-01381-x] [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: 09/06/2022] [Accepted: 03/26/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND According to the WHO, about 39% of the global adult population were overweight or obese in 2016. Obesity has high heritability, with more than 1000 variants so far identified. There have been reports indicating that salivary amylase gene (AMY1) copy number was one of these variants, yet its association with obesity remains controversial. OBJECTIVE Our research aimed to provide more evidence on the relationship of AMY1 copy number variation (CNV) with body mass index (BMI) and body composition. METHODS We recruited 133 Chinese adults (65 males, 68 females, 18-25 years old) with normal fasting blood glucose and blood pressure levels. 19 males were selected for a 10-week intervention to change body composition. After anthropometric measurements, BMI was calculated, and body composition was measured using dual energy X-ray absorptiometry (DEXA). For the 19 selected participants, we collected their height, weight, and body composition data one more time after intervention. All participants were required to leave their saliva samples and their AMY1 copy number was determined by real-time fluorescence quantitative PCR. RESULTS We failed to find any significant difference in BMI and body composition between different copy number groups. Only a weak correlation was found between body muscle mass and body fat mass. After adjusted for height and weight, AMY1 CNV explained 4.83% of the variance and one single increase in AMY1 CNV can increase 0.214 kg of the body muscle mass, while one single increase in AMY1 CNV can decrease 0.217 kg of the body fat mass and explained 4.69% of the variance. CONCLUSIONS As a genetic factor, the AMY1 gene copy number variation has only a minor correlation with BMI and body composition, and its effect can easily be hidden by other factors such as individual diet and exercise habit.
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Affiliation(s)
- Xinming Zhang
- School of Sport Science, Nantong University, Nantong, Jiangsu Province, China.
| | - Colin Moran
- School of Health Sciences and Sport, University of Stirling, Stirling, Scotland, UK
| | - Ruiyuan Wang
- Department of Exercise Physiology, Beijing Sport University, Beijing City, China
| | - Yue Zhou
- Department of Exercise Physiology, Beijing Sport University, Beijing City, China
| | - Naomi Brooks
- School of Health Sciences and Sport, University of Stirling, Stirling, Scotland, UK
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15
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Vázquez-Moreno MA, Cruz-López M. [From genotype to phenotype: amylase gene in childhood obesity]. REVISTA MEDICA DEL INSTITUTO MEXICANO DEL SEGURO SOCIAL 2023; 61:356-362. [PMID: 37216679 PMCID: PMC10437226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/21/2022] [Indexed: 05/24/2023]
Abstract
Worldwide, Mexico is one of the countries with the highest rate of obesity, which is a condition considered the main risk factor for type 2 diabetes. Among the mechanisms that predispose to obesity, the interaction between food intake and genetic components has been little explored. Recently we evidenced a significant association between the copy number (CN) of AMY1A and AMY2A genes, the enzymatic activity of salivary and pancreatic amylase, and the frequency of childhood obesity in Mexico, a particular population due to the high consumption of starch in the diet and the high prevalence of obesity in children and adults. This review aims to find a better understanding of the role of amylase in obesity through a description of the evolution of the CN of its genes, the association of its enzymatic activity with obesity, and the effect of its interaction with starch intake on Mexican children. In addition, it denotes the importance of the experimental perspectives of further investigation regarding the mechanism by which amylase could regulate the abundance of oligosaccharide-fermenting bacteria and producers of short-chain fatty acids and/or branched-chain amino acids that could contribute to the alteration of the physiological processes associated with intestinal inflammation and metabolic deregulation that predispose to the development of obesity.
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Affiliation(s)
- Miguel Alexander Vázquez-Moreno
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Hospital de Especialidades “Dr. Bernardo Sepúlveda Gutiérrez”, Unidad de Investigación Médica en Bioquímica. Ciudad de México, México Instituto Mexicano del Seguro SocialMéxico
| | - Miguel Cruz-López
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Hospital de Especialidades “Dr. Bernardo Sepúlveda Gutiérrez”, Unidad de Investigación Médica en Bioquímica. Ciudad de México, México Instituto Mexicano del Seguro SocialMéxico
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16
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Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. A draft human pangenome reference. Nature 2023; 617:312-324. [PMID: 37165242 PMCID: PMC10172123 DOI: 10.1038/s41586-023-05896-x] [Citation(s) in RCA: 258] [Impact Index Per Article: 258.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
Abstract
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
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Affiliation(s)
- Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Mobin Asri
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Doerr
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Marina Haukness
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - Julian K Lucas
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jean Monlong
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haley J Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Xian H Chang
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, Québec, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Charles Markello
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M Novak
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hugh E Olsen
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Trevor Pesout
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonas A Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Carl A Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Robert M Cook-Deegan
- Barrett and O'Connor Washington Center, Arizona State University, Washington, DC, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L Felsenfeld
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | | | - Jan O Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hugo Magalhães
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Alice B Popejoy
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I Schultz
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Michael W Smith
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J Sofia
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Karen H Miga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.
| | - Ira M Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, CA, USA.
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17
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Devarakonda SLS, Superdock DK, Ren J, Johnson LM, Loinard-Gonz Lez AAP, Poole AC. Gut microbial features and dietary fiber intake predict gut microbiota response to resistant starch supplementation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287665. [PMID: 37034622 PMCID: PMC10081390 DOI: 10.1101/2023.03.24.23287665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Resistant starch (RS) consumption can have beneficial effects on human health, but the response, in terms of effects on the gut microbiota and host physiology, varies between individuals. Factors predicting the response to RS are not yet established and would be useful for developing precision nutrition approaches that maximize the benefits of dietary fiber intake. We sought to identify predictors of gut microbiota response to RS supplementation. We enrolled 76 healthy adults into a seven-week crossover study. Participants consumed RS type 2 (RS2), RS type 4 (RS4), and a digestible starch, for ten days each with five-day washout periods in between. We collected fecal and saliva samples and food records before and during each treatment period. We performed 16S rRNA gene sequencing and measured fecal short-chain fatty acids (SCFAs), salivary amylase gene copy number, and salivary amylase activity (SAA). Dietary fiber intake was predictive of relative abundance of several amplicon sequence variants (ASVs) at the end of both RS treatments. Treatment order (the order of consumption of RS2 and RS4), alpha diversity, and a subset of ASVs were predictive of SCFA changes after RS supplementation. SAA was only predictive of the relative abundance of ASVs after digestible starch supplementation. Based on our findings, dietary fiber intake and gut microbiome composition would be informative if assessed prior to recommending RS supplementation. Using a precision nutrition approach to optimize the benefits of dietary fibers such as RS could be an effective strategy to compensate for the low consumption of dietary fiber nationwide.
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Nayema Z, Sato T, Kannon T, Tsujiguchi H, Hosomichi K, Nakamura H, Tajima A. Genetic factors associated with serum amylase in a Japanese population: combined analysis of copy-number and single-nucleotide variants. J Hum Genet 2023; 68:313-319. [PMID: 36599956 PMCID: PMC10125868 DOI: 10.1038/s10038-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
Amylase activity and levels in humans are heritable quantitative traits. Although many studies exist on the effects of copy-number variants (CNVs) in amylase genes (AMY) on human phenotypes, such as body mass index (BMI), the genetic factors controlling interindividual variation in amylase levels remain poorly understood. Here, we conducted a genome-wide association study (GWAS) of serum amylase levels (SAL) in 814 Japanese individuals to identify associated single-nucleotide variants (SNVs), after adjusting for non-genetic factors. Diploid copy numbers (CN) of AMY (AMY1, AMY2A, and AMY2B) were measured using droplet digital PCR to examine the association between each diploid CN and SAL. We further assessed the relative contribution of the GWAS-lead SNV and AMY CNVs to SAL. GWAS identified 14 significant SNVs (p < 5 × 10-8) within a linkage disequilibrium block near the AMY cluster on chromosome 1. The association analyses of AMY CNVs and SAL showed a significant association between AMY1 diploid CN and SAL (p = 1.89 × 10-19), while no significant association with SAL was found for AMY2A CN (p = 0.54) or AMY2B CN (p = 0.15). In a joint association analysis with SAL using the GWAS-lead SNV and AMY1 diploid CN, AMY1 CN remained significant (p = 5.4 ×10-13), while the association of the lead SNV was marginal (p = 0.08). We also found no association between AMY1 diploid CN and BMI (p = 0.14). Our results indicate that AMY1 CNV is the major genetic factor for Japanese SAL, with no significant association with BMI.
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Affiliation(s)
- Zannatun Nayema
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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19
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Lv Y, Liu R, Jia H, Sun X, Gong Y, Ma L, Qiu W, Wang X. Alterations of the gut microbiota in type 2 diabetics with or without subclinical hypothyroidism. PeerJ 2023; 11:e15193. [PMID: 37073275 PMCID: PMC10106085 DOI: 10.7717/peerj.15193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/15/2023] [Indexed: 04/20/2023] Open
Abstract
Background Diabetes and thyroid dysfunction are two closely related endocrine diseases. Increasing evidences show that gut microbiota plays an important role in both glucose metabolism and thyroid homeostasis. Meanwhile, copy number variation (CNV) of host salivary α-amylase gene (AMY1) has been shown to correlate with glucose homeostasis. Hence, we aim to characterize the gut microbiota and CNV of AMY1 in type 2 diabetes (T2D) patients with or without subclinical hypothyroidism (SCH). Methods High-throughput sequencing was used to analyze the gut microbiota of euthyroid T2D patients, T2D patients with SCH and healthy controls. Highly sensitive droplet digital PCR was used to measure AMY1 CN. Results Our results revealed that T2D patients have lower gut microbial diversity, no matter with or without SCH. The characteristic taxa of T2D patients were Coriobacteriales, Coriobacteriaceae, Peptostreptococcaceae, Pseudomonadaceae, Collinsella, Pseudomonas and Romboutsia. Meanwhile, Escherichia/Shigella, Lactobacillus_Oris, Parabacteroides Distasonis_ATCC_8503, Acetanaerobacterium, Lactonifactor, uncultured bacterium of Acetanaerobacterium were enriched in T2D patients with SCH. Moreover, serum levels of free triiodothyronine (FT3) and free thyroxine (FT4) in T2D patients were both negatively correlated with richness of gut microbiota. A number of specific taxa were also associated with clinical parameters at the phylum and genus level. In contrast, no correlation was found between AMY1 CN and T2D or T2D_SCH. Conclusion This study identified characteristic bacterial taxa in gut microbiota of T2D patients with or without SCH, as well as the taxa associated with clinical indices in T2D patients. These results might be exploited in the prevention, diagnosis and treatment of endocrine disorders in the future.
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Affiliation(s)
- Yanrong Lv
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Rong Liu
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Huaijie Jia
- State Key Laboratory of Veterinary of Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaolan Sun
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Yuhan Gong
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Wei Qiu
- Department of Endocrinology, Xinxiang First People’s Hospital, The Affiliated People’s Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaoxia Wang
- School of Public Health, Lanzhou University, Lanzhou, China
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20
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Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biol 2022; 20:245. [DOI: 10.1186/s12915-022-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
Results
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
Conclusions
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
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Zeng S, Wang S, Ross RP, Stanton C. The road not taken: host genetics in shaping intergenerational microbiomes. Trends Genet 2022; 38:1180-1192. [PMID: 35773025 DOI: 10.1016/j.tig.2022.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 02/09/2023]
Abstract
The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.
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Affiliation(s)
- Shuqin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China; APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China; APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
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22
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Christensen L, Hjorth MF, Krych L, Licht TR, Lauritzen L, Magkos F, Roager HM. Prevotella abundance and salivary amylase gene copy number predict fat loss in response to wholegrain diets. Front Nutr 2022; 9:947349. [PMID: 36071931 PMCID: PMC9441811 DOI: 10.3389/fnut.2022.947349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Background Salivary amylase (AMY1) gene copy number (CN) and Prevotella abundance in the gut are involved in carbohydrate digestion in the upper and lower gastrointestinal tract, respectively; and have been suggested as prognostic biomarkers for weight loss among overweight individuals consuming diets rich in fiber and wholegrains. Objective We hypothesized that Prevotella abundance would be linked to greater loss of body fat after wholegrain consumption among individuals with low AMY1 CN, but not in those with high AMY1 CN. Methods We reanalyzed data from two independent randomized ad libitum wholegrain interventions (fiber intake ∼33 g/d for 6–8 weeks), to investigate the relationship between baseline Prevotella abundance and body fat loss among healthy, overweight participants stratified into two groups by median AMY1 CN. Individuals with no detected Prevotella spp. were excluded from the main analysis. Results In both studies, individuals with low AMY1 CN exhibited a positive correlation between baseline Prevotella abundance and fat loss after consuming the wholegrain diet (r > 0.5, P < 0.05), but no correlation among participants with high AMY1 CN (P ≥ 0.6). Following consumption of the refined wheat control diets, there were no associations between baseline Prevotella abundance and changes in body fat in any of the AMY1 groups. Conclusion These results suggest that Prevotella abundance together with AMY1 CN can help predict fat loss in response to ad libitum wholegrain diets, highlighting the potential of these biomarkers in personalized obesity management.
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Affiliation(s)
- Lars Christensen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Lars Christensen,
| | | | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lotte Lauritzen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Faidon Magkos
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
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23
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Food as we knew it: Food processing as an evolutionary discourse. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Hasegawa T, Kakuta M, Yamaguchi R, Sato N, Mikami T, Murashita K, Nakaji S, Itoh K, Imoto S. Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population. Sci Rep 2022; 12:7628. [PMID: 35538098 PMCID: PMC9090785 DOI: 10.1038/s41598-022-11730-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/18/2022] [Indexed: 11/25/2022] Open
Abstract
Amylase genes reside in a structurally complex locus, and their copy numbers vary greatly, and several studies have reported their association with obesity. The mechanism of this effect was partially explained by changes in the oral and gut microbiome compositions; however, a detailed mechanism has been unclarified. In this study, we showed their association with diabetes in addition to obesity, and further discovered a plausible mechanism of this association based on the function of commensal bacteria. First, we confirmed that the amylase copy number in the population tends to be larger than that reported in other studies and that there is a positive association between obesity and diabetes (p = 1.89E-2 and 8.63E-3). Second, we identified that relative abundance of some genus level microbiome, Capnocytophaga, Dialister, and previously reported bacteria, were significantly associated with amylase copy numbers. Finally, through functional gene-set analysis using shotgun sequencing, we observed that the abundance of genes in the Acarbose pathway in the gut microbiome was significantly decreased with an increase in the amylase copy number (p-value = 5.80E-4). Our findings can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers.
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Affiliation(s)
- Takanori Hasegawa
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Masanori Kakuta
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Rui Yamaguchi
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Noriaki Sato
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tatsuya Mikami
- Innovation Center for Health Promotion, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Koichi Murashita
- COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori, Japan
| | - Shigeyuki Nakaji
- Department of Social Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Ken Itoh
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Seiya Imoto
- Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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25
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Al-Akl N, Thompson RI, Arredouani A. Elevated levels of salivary α- amylase activity in saliva associated with reduced odds of obesity in adult Qatari citizens: A cross-sectional study. PLoS One 2022; 17:e0264692. [PMID: 35271604 PMCID: PMC8912263 DOI: 10.1371/journal.pone.0264692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
The relationship between salivary α-amylase activity (ssAAa) and the risk of metabolic disorders remains equivocal. We aimed to assess this relationship in adults from Qatar, where obesity and type 2 diabetes are highly prevalent. We cross-sectionally quantified ssAAa in saliva and estimated AMY1 CN from whole-genome sequencing data from 1499 participants. Linear regression was used to assess the relationship between ssAAa and adiposity and glycemic markers. Logistic regression was used to examine the association between ssAAa and occurrence of obesity or diabetes. The mean and median ssAAa were significantly lower in obese individuals. There were significant inverse associations between ssAAa and BMI, and fat mass. We detected a marked effect of ssAAa on reduced odds of obesity after adjusting for age and sex, glucose, LDL, HLD, total cholesterol, and systolic and diastolic blood pressure (OR per ssAAa unit 0.998 [95% CI 0.996–0.999], p = 0.005), with ssAAa ranging between 6.8 and 422U/mL. The obesity odds were significantly lower in the upper half of the ssAAa distributional (OR 0.58 [95% CI 0.42–0.76], p<0.001) and lower in the top versus the bottom decile of the ssAAa distribution (OR 0.46 [95% CI 0.23–0.92], p = 0.03). Our findings suggest a potential beneficial relationship between high sAAa in saliva and low odds of obesity in Qatari adults.
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Affiliation(s)
- Neyla Al-Akl
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Richard I. Thompson
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Abdelilah Arredouani
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- * E-mail:
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Moreira VC, Silva CMS, Welker AF, da Silva ICR. Visceral Adipose Tissue Influence on Health Problem Development and Its Relationship with Serum Biochemical Parameters in Middle-Aged and Older Adults: A Literature Review. J Aging Res 2022; 2022:8350527. [PMID: 35492380 PMCID: PMC9042620 DOI: 10.1155/2022/8350527] [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: 07/02/2021] [Revised: 08/28/2021] [Accepted: 03/29/2022] [Indexed: 11/24/2022] Open
Abstract
Background The amount of visceral adipose tissue (VAT) tends to increase with age and is associated with several health problems, such as cardiometabolic diseases, increased infections, and overall mortality. Objectives This review provides a general assessment of how visceral adiposity correlates with the development of health problems and changes in serum biochemical parameters in middle-aged and older adults. Methods We searched specific terms in the Virtual Health Library (VHL) databases for VAT articles published in the English language between 2009 and 2019 related to older adults. Results The search found twenty-three publications in this period, of which nine were excluded. The publications had a population aged between 42 and 83 years and correlated the VAT area ratio with several comorbidities (such as pancreatitis, depression, cancer, and coronary heart disease) and serum biochemical parameters. Conclusion Further research on the association between visceral obesity and the emergence of health problems and the relationship between VAT and changes in serum biochemical parameters in older individuals should deepen the understanding of this connection and develop preventive actions.
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Affiliation(s)
- Vanessa C. Moreira
- Health Sciences and Technologies, University of Brasilia, Zip-Code: 72220-275, Brasilia, Brazil
| | - Calliandra M. S. Silva
- Health Sciences and Technologies, University of Brasilia, Zip-Code: 72220-275, Brasilia, Brazil
| | - Alexis F. Welker
- Health Sciences and Technologies, University of Brasilia, Zip-Code: 72220-275, Brasilia, Brazil
| | - Izabel C. R. da Silva
- Health Sciences and Technologies, University of Brasilia, Zip-Code: 72220-275, Brasilia, Brazil
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Dong J, Zhao H, Wang F, Jin J, Ji H, Yan X, Wang N, Zhang J, Hu S. Ferroptosis-Related Gene Contributes to Immunity, Stemness and Predicts Prognosis in Glioblastoma Multiforme. Front Neurol 2022; 13:829926. [PMID: 35359663 PMCID: PMC8960280 DOI: 10.3389/fneur.2022.829926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Ferroptosis, a recently discovered regulated programmed cell death, is associated with tumorigenesis and progression in glioblastoma. Based on widely recognized ferroptosis-related genes (FRGs), the regulation of ferroptosis patterns and corresponding characteristics of immune infiltration of 516 GBM samples with GSE13041, TCGA-GBM, and CGGA-325 were comprehensively analyzed. Here, we revealed the expression, mutations, and CNV of FRGs in GBM. We identified three distinct regulation patterns of ferroptosis and found the hub genes of immunity and stemness among DEGs in three patterns. A prognostic model was constructed based on five FRGs and verified at the mRNA and protein level. The risk score can not only predict the prognosis but also the degree of immune infiltration and ICB responsiveness by functional annotation. The overall assessment of FRGs in GBM patients will guide the direction of improved research and develop new prognostic prediction tools.
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Affiliation(s)
- Jiawei Dong
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongtao Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiaqi Jin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiuwei Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Nan Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiheng Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Shaoshan Hu
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28
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Butterworth PJ, Bajka BH, Edwards CH, Warren FJ, Ellis PR. Enzyme kinetic approach for mechanistic insight and predictions of in vivo starch digestibility and the glycaemic index of foods. Trends Food Sci Technol 2022; 120:254-264. [PMID: 35210697 PMCID: PMC8850932 DOI: 10.1016/j.tifs.2021.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Starch is a principal dietary source of digestible carbohydrate and energy. Glycaemic and insulinaemic responses to foods containing starch vary considerably and glucose responses to starchy foods are often described by the glycaemic index (GI) and/or glycaemic load (GL). Low GI/GL foods are beneficial in the management of cardiometabolic disorders (e.g., type 2 diabetes, cardiovascular disease). Differences in rates and extents of digestion of starch-containing foods will affect postprandial glycaemia. SCOPE AND APPROACH Amylolysis kinetics are influenced by structural properties of the food matrix and of starch itself. Native (raw) semi-crystalline starch is digested slowly but hydrothermal processing (cooking) gelatinises the starch and greatly increases its digestibility. In plants, starch granules are contained within cells and intact cell walls can limit accessibility of water and digestive enzymes hindering gelatinisation and digestibility. In vitro studies of starch digestion by α-amylase model early stages in digestion and can suggest likely rates of digestion in vivo and expected glycaemic responses. Reports that metabolic responses to dietary starch are influenced by α-amylase gene copy number, heightens interest in amylolysis. KEY FINDINGS AND CONCLUSIONS This review shows how enzyme kinetic strategies can provide explanations for differences in digestion rate of different starchy foods. Michaelis-Menten and Log of Slope analyses provide kinetic parameters (e.g., K m and k cat /K m ) for evaluating catalytic efficiency and ease of digestibility of starch by α-amylase. Suitable kinetic methods maximise the information that can be obtained from in vitro work for predictions of starch digestion and glycaemic responses in vivo.
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Key Words
- AMY1, human salivary α-amylase gene
- AMY2, human pancreatic α-amylase gene
- Alpha-amylase
- BMI, body mass index
- CE, catalytic efficiency
- CVD, cardiovascular disease
- Enzyme kinetics
- Fto, alpha-oxoglutarate-dependent dioxygenase gene
- GI, glycaemic index
- GIT, gastrointestinal tract
- GL, glycaemic load
- GLUT2, glucose transporter 2
- Gene copy number
- HI, hydrolysis index
- IC50, inhibitor concentration causing 50% inhibition
- LOS, logarithm of slope plot
- Metabolic significance
- RDS, rapidly digestible starch
- RS, resistant starch
- Resistant starch
- SCFAs, short chain fatty acids
- SDS, slowly digestible starch
- SGLT1, sodium-dependent glucose co-transporter
- Starch digestion
- XRD, X-ray diffraction
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Affiliation(s)
- Peter J. Butterworth
- Biopolymers Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Balázs H. Bajka
- Biopolymers Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Cathrina H. Edwards
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Frederick J. Warren
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Peter R. Ellis
- Biopolymers Group, Departments of Biochemistry and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
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Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Ramesh Babu J, Geetha T, Taneja V. Ethnic variability associating gut and oral microbiome with obesity in children. Gut Microbes 2022; 13:1-15. [PMID: 33596768 PMCID: PMC7894456 DOI: 10.1080/19490976.2021.1882926] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Obesity is a growing worldwide problem that generally starts in the early years of life and affects minorities more often than Whites. Thus, there is an urgency to determine factors that can be used as targets as indicators of obesity. In this study, we attempt to generate a profile of gut and oral microbial clades predictive of disease status in African American (AA) and European American (EA) children. 16S rDNA sequencing of the gut and saliva microbial profiles were correlated with salivary amylase, socioeconomic factors (e.g., education and family income), and obesity in both ethnic populations. Gut and oral microbial diversity between AA and EA children showed significant differences in alpha-, beta-, and taxa-level diversity. While gut microbial diversity between obese and non-obese was not evident in EA children, the abundance of gut Klebsiella and Magasphaera was associated with obesity in AA children. In contrast, an abundance of oral Aggregatibacter and Eikenella in obese EA children was observed. These observations suggest an ethnicity-specific association with gut and oral microbial profiles. Socioeconomic factors influenced microbiota in obesity, which were ethnicity dependent, suggesting that specific approaches to confront obesity are required for both populations.
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Affiliation(s)
| | - Vaithinathan Selvaraju
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Priscilla Ayine
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Lu Yang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jeganathan Ramesh Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA,Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA,Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA,Thangiah Geetha Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN, USA,CONTACT Veena Taneja Department of Immunology, Mayo Clinic, 200 First St SWRochester, MN55905, USA
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Abstract
The prevalence of obesity has tripled over the past four decades, imposing an enormous burden on people's health. Polygenic (or common) obesity and rare, severe, early-onset monogenic obesity are often polarized as distinct diseases. However, gene discovery studies for both forms of obesity show that they have shared genetic and biological underpinnings, pointing to a key role for the brain in the control of body weight. Genome-wide association studies (GWAS) with increasing sample sizes and advances in sequencing technology are the main drivers behind a recent flurry of new discoveries. However, it is the post-GWAS, cross-disciplinary collaborations, which combine new omics technologies and analytical approaches, that have started to facilitate translation of genetic loci into meaningful biology and new avenues for treatment.
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Affiliation(s)
- Ruth J. F. Loos
- grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark ,grid.59734.3c0000 0001 0670 2351Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Giles S. H. Yeo
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
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31
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Matusheski NV, Caffrey A, Christensen L, Mezgec S, Surendran S, Hjorth MF, McNulty H, Pentieva K, Roager HM, Seljak BK, Vimaleswaran KS, Remmers M, Péter S. Diets, nutrients, genes and the microbiome: recent advances in personalised nutrition. Br J Nutr 2021; 126:1489-1497. [PMID: 33509307 PMCID: PMC8524424 DOI: 10.1017/s0007114521000374] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 01/13/2021] [Accepted: 01/23/2021] [Indexed: 12/28/2022]
Abstract
As individuals seek increasingly individualised nutrition and lifestyle guidance, numerous apps and nutrition programmes have emerged. However, complex individual variations in dietary behaviours, genotypes, gene expression and composition of the microbiome are increasingly recognised. Advances in digital tools and artificial intelligence can help individuals more easily track nutrient intakes and identify nutritional gaps. However, the influence of these nutrients on health outcomes can vary widely among individuals depending upon life stage, genetics and microbial composition. For example, folate may elicit favourable epigenetic effects on brain development during a critical developmental time window of pregnancy. Genes affecting vitamin B12 metabolism may lead to cardiometabolic traits that play an essential role in the context of obesity. Finally, an individual's gut microbial composition can determine their response to dietary fibre interventions during weight loss. These recent advances in understanding can lead to a more complete and integrated approach to promoting optimal health through personalised nutrition, in clinical practice settings and for individuals in their daily lives. The purpose of this review is to summarise presentations made during the DSM Science and Technology Award Symposium at the 13th European Nutrition Conference, which focused on personalised nutrition and novel technologies for health in the modern world.
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Affiliation(s)
- Nathan V. Matusheski
- Nutrition Science and Advocacy, DSM Nutritional Products LLC, Parsippany, NJ, USA
| | - Aoife Caffrey
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, ColeraineBT52 1SA, Northern Republic of Ireland
| | - Lars Christensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Frederiksberg, Denmark
| | - Simon Mezgec
- Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000Ljubljana, Slovenia
| | - Shelini Surendran
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, University of Reading, Whiteknights, ReadingRG6 6DZ, UK
| | - Mads F. Hjorth
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Frederiksberg, Denmark
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, ColeraineBT52 1SA, Northern Republic of Ireland
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, ColeraineBT52 1SA, Northern Republic of Ireland
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Frederiksberg, Denmark
| | - Barbara Koroušić Seljak
- Computer Systems Department, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Ljubljana, Slovenia
| | | | | | - Szabolcs Péter
- Nutrition Innovation Center, DSM Nutritional Products Ltd, Kaiseraugst, Switzerland
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32
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Effect of AMY1 copy number variation and various doses of starch intake on glucose homeostasis: data from a cross-sectional observational study and a crossover meal study. GENES & NUTRITION 2021; 16:21. [PMID: 34789141 PMCID: PMC8596830 DOI: 10.1186/s12263-021-00701-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/31/2021] [Indexed: 12/16/2022]
Abstract
Background Copy number (CN) variation (CNV) of the salivary amylase gene (AMY1) influences the ability to digest starch and may influence glucose homeostasis, obesity and gut microbiota composition. Hence, the aim was to examine the association of AMY1 CNV with fasting glucose, BMI, and gut microbiota composition considering habitual starch intake and to investigate the effect of AMY1 CNV on the postprandial response after two different starch doses. Methods The Malmö Offspring Study (n = 1764, 18–71 years) was used to assess interaction effects between AMY1 CNV (genotyped by digital droplet polymerase chain reaction) and starch intake (assessed by 4-day food records) on fasting glucose, BMI, and 64 gut bacteria (16S rRNA sequencing). Participants with low (≤ 4 copies, n = 9) and high (≥ 10 copies, n = 10) AMY1 CN were recruited for a crossover meal study to compare postprandial glycemic and insulinemic responses to 40 g and 80 g starch from white wheat bread. Results In the observational study, no overall associations were found between AMY1 CNV and fasting glucose, BMI, or gut microbiota composition. However, interaction effects between AMY1 CNV and habitual starch intake on fasting glucose (P = 0.03) and BMI (P = 0.05) were observed, suggesting inverse associations between AMY1 CNV and fasting glucose and BMI at high starch intake levels and positive association at low starch intake levels. No associations with the gut microbiota were observed. In the meal study, increased postprandial glucose (P = 0.02) and insulin (P = 0.05) were observed in those with high AMY1 CN after consuming 40 g starch. This difference was smaller and nonsignificant after consuming 80 g starch. Conclusions Starch intake modified the observed association between AMY1 CNV and fasting glucose and BMI. Furthermore, depending on the starch dose, a higher postprandial glucose and insulin response was observed in individuals with high AMY1 CN than in those with low AMY1 CN. Trial registration ClinicalTrials.gov, NCT03974126. Registered 4 June 2019—retrospectively registered. Supplementary Information The online version contains supplementary material available at 10.1186/s12263-021-00701-8.
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Zhang YZ, Imoto S, Miyano S, Yamaguchi R. Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. PLoS Comput Biol 2021; 17:e1009186. [PMID: 34634042 PMCID: PMC8504719 DOI: 10.1371/journal.pcbi.1009186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 06/15/2021] [Indexed: 11/30/2022] Open
Abstract
Read-depths (RDs) are frequently used in identifying structural variants (SVs) from sequencing data. For existing RD-based SV callers, it is difficult for them to determine breakpoints in single-nucleotide resolution due to the noisiness of RD data and the bin-based calculation. In this paper, we propose to use the deep segmentation model UNet to learn base-wise RD patterns surrounding breakpoints of known SVs. We integrate model predictions with an RD-based SV caller to enhance breakpoints in single-nucleotide resolution. We show that UNet can be trained with a small amount of data and can be applied both in-sample and cross-sample. An enhancement pipeline named RDBKE significantly increases the number of SVs with more precise breakpoints on simulated and real data. The source code of RDBKE is freely available at https://github.com/yaozhong/deepIntraSV.
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Affiliation(s)
- Yao-Zhong Zhang
- Division of Health Medical Intelligence, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Division of Health Medical Intelligence, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rui Yamaguchi
- Division of Health Medical Intelligence, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Informatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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34
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Shin D, Lee KW. Dietary carbohydrates interact with AMY1 polymorphisms to influence the incidence of type 2 diabetes in Korean adults. Sci Rep 2021; 11:16788. [PMID: 34408213 PMCID: PMC8373941 DOI: 10.1038/s41598-021-96257-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/30/2021] [Indexed: 01/23/2023] Open
Abstract
The relationship between AMY1 single nucleotide polymorphisms (SNPs), dietary carbohydrates, and the risk of type 2 diabetes is unclear. We aimed to evaluate this association using an ongoing large-scale prospective study, namely the Korean Genome and Epidemiology Study. We selected six genetic variants of the AMY1 gene: rs10881197, rs4244372, rs6696797, rs1566154, rs1930212, and rs1999478. Baseline dietary data were obtained using a semi-quantitative food frequency questionnaire. Type 2 diabetes was defined according to the criteria of the World Health Organization and American Diabetes Association. During an average follow-up period of 12 years (651,780 person-years), 1082 out of 4552 (23.8%) patients had type 2 diabetes. Three AMY1 SNPs were significantly associated with diabetes incidence among patients with carbohydrate intake > 65% of total energy: rs6696797, rs4244372, and rs10881197. In multivariable Cox models, Korean women with the rs6696797 AG or AA genotype had 28% higher incidence of type 2 diabetes (hazard ratio 1.28, 95% confidence interval 1.06-1.55) than Korean women with the rs6696797 GG genotype. We did not observe significant associations between AMY1 SNPs, dietary carbohydrates, and diabetes incidence in Korean men. We conclude that AMY1 genetic variants and dietary carbohydrate intake influence the incidence of type 2 diabetes in Korean women only. Korean women who are minor carriers of the AMY1 rs6696797, rs4244372, and rs10881197 genotypes may benefit from a low-carbohydrate diet to prevent the future risk of type 2 diabetes.
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Affiliation(s)
- Dayeon Shin
- Department of Food and Nutrition, Inha University, Incheon, 22212, Republic of Korea
| | - Kyung Won Lee
- Department of Home Economics Education, Korea National University of Education, Cheongju, 28173, Republic of Korea.
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35
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Kang H, Zhao D, Xiang H, Li J, Zhao G, Li H. Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content. Genet Sel Evol 2021; 53:66. [PMID: 34399688 PMCID: PMC8369645 DOI: 10.1186/s12711-021-00656-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/15/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. RESULTS First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. CONCLUSIONS Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.
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Affiliation(s)
- Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Di Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Jing Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Guiping Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China. .,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China. .,Guangdong Tinoo's Foods Group Co., Ltd, Jiangkou, Feilaixia, Qingcheng, Qingyuan, 511827, Guangdong, People's Republic of China.
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Ko J, Skudder-Hill L, Cho J, Bharmal SH, Petrov MS. Pancreatic enzymes and abdominal adipose tissue distribution in new-onset prediabetes/diabetes after acute pancreatitis. World J Gastroenterol 2021; 27:3357-3371. [PMID: 34163117 PMCID: PMC8218354 DOI: 10.3748/wjg.v27.i23.3357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND New-onset prediabetes/diabetes after acute pancreatitis (NODAP) is the most common sequela of pancreatitis, and it differs from type 2 prediabetes/diabetes mellitus (T2DM).
AIM To study the associations between circulating levels of pancreatic amylase, pancreatic lipase, chymotrypsin and fat phenotypes in NODAP, T2DM, and health.
METHODS Individuals with NODAP (n = 30), T2DM (n = 30), and sex-matched healthy individuals (n = 30) were included. Five fat phenotypes (intra-pancreatic fat, liver fat, skeletal muscle fat, visceral fat, and subcutaneous fat) were determined using the same magnetic resonance imaging protocol and scanner magnet strength for all participants. One-way analysis of covariance, linear regression analysis, and relative importance analysis were conducted.
RESULTS Intra-pancreatic fat deposition (IPFD) was higher in NODAP (9.4% ± 1.8%) and T2DM (9.8% ± 1.1%) compared with healthy controls (7.8% ± 1.9%) after adjusting for covariates (P = 0.003). Similar findings were observed in regards to visceral fat volume (P = 0.005), but not subcutaneous fat volume, liver fat, or skeletal muscle fat. Both IPFD (β = -2.201, P = 0.023) and visceral fat volume (β = -0.004, P = 0.028) were significantly associated with circulating levels of pancreatic amylase in NODAP, but not in T2DM or healthy individuals. Of the five fat phenotypes, IPFD explained the highest amount of variance in pancreatic amylase concentration (R2 = 15.3% out of 41.2%). None of the phenotypes contributed meaningfully to the variance in pancreatic lipase or chymotrypsin.
CONCLUSION Both NODAP and T2DM are characterized by increased IPFD and visceral fat volume. However, only NODAP is characterized by significant inverse associations between the two fat phenotypes and pancreatic amylase.
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Affiliation(s)
- Juyeon Ko
- School of Medicine, University of Auckland, Auckland 1142, New Zealand
| | | | - Jaelim Cho
- School of Medicine, University of Auckland, Auckland 1142, New Zealand
| | - Sakina H Bharmal
- School of Medicine, University of Auckland, Auckland 1142, New Zealand
| | - Maxim S Petrov
- School of Medicine, University of Auckland, Auckland 1142, New Zealand
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DNA copy number and structural variation (CNV) contributions to adult and childhood obesity. Biochem Soc Trans 2021; 48:1819-1828. [PMID: 32726412 DOI: 10.1042/bst20200556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023]
Abstract
In recent years, obesity has reached epidemic proportions globally and has become a major public health concern. The development of obesity is likely caused by several behavioral, environmental, and genetic factors. Genomic variability among individuals is largely due to copy number variations (CNVs). Recent genome-wide association studies (GWAS) have successfully identified many loci containing CNV related to obesity. These obesity-related CNVs are informative to the diagnosis and treatment of genomic diseases. A more comprehensive classification of CNVs may provide the basis for determining how genomic diversity impacts the mechanisms of expression for obesity in children and adults of a variety of genders and ethnicities. In this review, we summarize current knowledge on the relationship between obesity and the CNV of several genomic regions, with an emphasis on genes at the following loci: 11q11, 1p21.1, 10q11.22, 10q26.3, 16q12.2, 16p12.3, and 4q25.
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Al-Akl NS, Thompson RI, Arredouani A. Reduced odds of diabetes associated with high plasma salivary α-amylase activity in Qatari women: a cross-sectional study. Sci Rep 2021; 11:11495. [PMID: 34075145 PMCID: PMC8169920 DOI: 10.1038/s41598-021-90977-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 05/13/2021] [Indexed: 11/11/2022] Open
Abstract
The association of salivary α-amylase activity (SAA) activity or low copy number of its coding gene AMY1 with diabetes remains controversial. We aimed to reinvestigate the association of these factors with diabetes in Qatar, where diabetes prevalence is about 16%. We obtained cross-sectional data of 929 Qataris (age > 18 years) from the Qatar Biobank. We estimated AMY1 copy number variants (CNV) from whole-genome data, and quantified the SAA activity in plasma (pSAA). We used adjusted logistic regression to examine the association between pSAA activity or AMY1 CNV and diabetes odds. We found a significant association between high pSAA activity, but not AMY1 CNV, and reduced odds of diabetes in Qatari women. The OR per pSAA activity unit was 0.95 [95% CI 0.92, 0.98] (p = 0.002) (pSAA activity range: 4.7 U/L to 65 U/L) in women. The association is driven largely by the highest levels of pSAA activity. The probability of having diabetes was significantly lower in the fifth pSAA activity quintile relative to the first (0.21 ± 0.03 (Q1) versus 0.82 ± 0.02 (Q5)), resulting in significantly reduced diabetes prevalence in Q5 in women. Our study indicates a beneficial effect of high pSAA activity, but not AMY1 CN, on diabetes odds in Qatari women, and suggests pSAA activity levels as a potential marker to predict future diabetes in Qatari women.
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Affiliation(s)
- Neyla S Al-Akl
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), PO Box: 34110, Doha, Qatar
| | - Richard Ian Thompson
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), PO Box: 34110, Doha, Qatar
| | - Abdelilah Arredouani
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), PO Box: 34110, Doha, Qatar.
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar.
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39
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Hariharan R, Mousa A, de Courten B. Influence of AMY1A copy number variations on obesity and other cardiometabolic risk factors: A review of the evidence. Obes Rev 2021; 22:e13205. [PMID: 33432778 DOI: 10.1111/obr.13205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/01/2022]
Abstract
The rising incidence of obesity and type 2 diabetes is contributing to the escalating burden of disease globally. These metabolic disorders are closely linked with diet and in particular with carbohydrate consumption; hence, it is important to understand the underlying mechanisms that influence carbohydrate metabolism. Amylase, the enzyme responsible for the digestion of starch, is coded by the genes AMY1A, AMY1B, and AMY1C (salivary amylase) and AMY2A and AMY2B (pancreatic amylase). Previous studies demonstrate wide variations in AMY1A copy numbers, which can be attributed to several genetic, nutritional, and geographical diversities seen in populations globally. Current literature suggests that AMY1A copy number variations are important in obesity and other cardiometabolic disorders through their effects on glucose and lipid homeostasis, inflammatory markers, and the gut microbiome. This review synthesizes the available evidence to improve understanding of the role of AMY1A in obesity and related cardiometabolic risk factors and disorders including insulin resistance and type 2 diabetes, cardiovascular risk and inflammation, and the gut microbiome.
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Affiliation(s)
- Rohit Hariharan
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia
| | - Aya Mousa
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Clayton, Australia
| | - Barbora de Courten
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia
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40
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Bouchard C. Genetics of Obesity: What We Have Learned Over Decades of Research. Obesity (Silver Spring) 2021; 29:802-820. [PMID: 33899337 DOI: 10.1002/oby.23116] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
There is a genetic component to human obesity that accounts for 40% to 50% of the variability in body weight status but that is lower among normal weight individuals (about 30%) and substantially higher in the subpopulation of individuals with obesity and severe obesity (about 60%-80%). The appreciation that heritability varies across classes of BMI represents an important advance. After controlling for BMI, ectopic fat and fat distribution traits are characterized by heritability levels ranging from 30% to 55%. Defects in at least 15 genes are the cause of monogenic obesity cases, resulting mostly from deficiencies in the leptin-melanocortin signaling pathway. Approximately two-thirds of the BMI heritability can be imputed to common DNA variants, whereas low-frequency and rare variants explain the remaining fraction. Diminishing allele effect size is observed as the number of obesity-associated variants expands, with most BMI-increasing or -decreasing alleles contributing only a few grams or less to body weight. Obesity-promoting alleles exert minimal effects in normal weight individuals but have larger effects in individuals with a proneness to obesity, suggesting a higher penetrance; however, it is not known whether these larger effect sizes precede obesity or are caused by an obese state. The obesity genetic risk is conditioned by thousands of DNA variants that make genetically based obesity prevention and treatment a major challenge.
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Affiliation(s)
- Claude Bouchard
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
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Cole JW, Adigun T, Akinyemi R, Akpa OM, Bell S, Chen B, Jimenez Conde J, Lazcano Dobao U, Fernandez I, Fornage M, Gallego-Fabrega C, Jern C, Krawczak M, Lindgren A, Markus HS, Melander O, Owolabi M, Schlicht K, Söderholm M, Srinivasasainagendra V, Soriano Tárraga C, Stenman M, Tiwari H, Corasaniti M, Fecteau N, Guizzardi B, Lopez H, Nguyen K, Gaynor B, O’Connor T, Stine OC, Kittner SJ, McArdle P, Mitchell BD, Xu H, Grond-Ginsbach C. The copy number variation and stroke (CaNVAS) risk and outcome study. PLoS One 2021; 16:e0248791. [PMID: 33872305 PMCID: PMC8055008 DOI: 10.1371/journal.pone.0248791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND PURPOSE The role of copy number variation (CNV) variation in stroke susceptibility and outcome has yet to be explored. The Copy Number Variation and Stroke (CaNVAS) Risk and Outcome study addresses this knowledge gap. METHODS Over 24,500 well-phenotyped IS cases, including IS subtypes, and over 43,500 controls have been identified, all with readily available genotyping on GWAS and exome arrays, with case measures of stroke outcome. To evaluate CNV-associated stroke risk and stroke outcome it is planned to: 1) perform Risk Discovery using several analytic approaches to identify CNVs that are associated with the risk of IS and its subtypes, across the age-, sex- and ethnicity-spectrums; 2) perform Risk Replication and Extension to determine whether the identified stroke-associated CNVs replicate in other ethnically diverse datasets and use biomarker data (e.g. methylation, proteomic, RNA, miRNA, etc.) to evaluate how the identified CNVs exert their effects on stroke risk, and lastly; 3) perform outcome-based Replication and Extension analyses of recent findings demonstrating an inverse relationship between CNV burden and stroke outcome at 3 months (mRS), and then determine the key CNV drivers responsible for these associations using existing biomarker data. RESULTS The results of an initial CNV evaluation of 50 samples from each participating dataset are presented demonstrating that the existing GWAS and exome chip data are excellent for the planned CNV analyses. Further, some samples will require additional considerations for analysis, however such samples can readily be identified, as demonstrated by a sample demonstrating clonal mosaicism. CONCLUSION The CaNVAS study will cost-effectively leverage the numerous advantages of using existing case-control data sets, exploring the relationships between CNV and IS and its subtypes, and outcome at 3 months, in both men and women, in those of African and European-Caucasian descent, this, across the entire adult-age spectrum.
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Affiliation(s)
- John W. Cole
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | | | | | | | - Steven Bell
- Unversity of Cambridge, Cambridge, England, United Kingdom
| | - Bowang Chen
- National Center for Cardiovascular Diseases, Beijing, China
| | | | - Uxue Lazcano Dobao
- IMIM-Hospital del Mar; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Israel Fernandez
- Institute of Research Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
| | - Myriam Fornage
- University of Texas Health Science at Houston, Institute of Molecular Medicine & School of Public Health, Houston, TX, United States of America
| | | | | | - Michael Krawczak
- Institute of Medical Statistics and Informatics, University of Kiel, Kiel, Germany
| | | | - Hugh S. Markus
- Unversity of Cambridge, Cambridge, England, United Kingdom
| | | | | | - Kristina Schlicht
- Institute of Medical Statistics and Informatics, University of Kiel, Kiel, Germany
| | - Martin Söderholm
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital Malmö and Lund, Lund, Sweden
| | | | | | | | - Hemant Tiwari
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Margaret Corasaniti
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Natalie Fecteau
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Beth Guizzardi
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Haley Lopez
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Kevin Nguyen
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Brady Gaynor
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Timothy O’Connor
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - O. Colin Stine
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Steven J. Kittner
- Veterans Affairs Maryland Health Care System, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Patrick McArdle
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Braxton D. Mitchell
- University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Huichun Xu
- University of Maryland School of Medicine, Baltimore, MD, United States of America
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Relationship between Mediterranean Diet Adherence and Saliva Composition. Nutrients 2021; 13:nu13041246. [PMID: 33920127 PMCID: PMC8068872 DOI: 10.3390/nu13041246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 01/22/2023] Open
Abstract
Dietary polyphenol exposure is known to change protein saliva composition in rodents, but less is known in humans. The present study aimed to assess the relationship between saliva protein composition and adherence to Mediterranean Diet (MD) and polyphenol intake levels. Participants were assessed for their dietary habits, which were converted in Mediterranean adherence level, according to Mediterranean Diet Adherence Score (MEDAS) score. Total polyphenol and total flavanol intakes were extrapolated from dietary data, using Phenol explorer database. Whole saliva was collected, and proteins were separated by SDS-PAGE. Salivary S-type cystatins were highly expressed in the group with medium adherence to MD, being positively correlated with wine intake in overweight individuals. The association between salivary amylase and MD adherence also depended on Body Mass Index (BMI), with a positive association only in normal weight individuals. Polyphenol intake was positively associated with S-type cystatins levels, particularly when flavanols were considered separately. These results show that saliva relationship with MD adherence depend on BMI, suggesting that normal weight and overweight individuals may have different salivary responses to diet. Moreover, these results reinforce the link between saliva and dietary polyphenols (flavanols) levels, leading to the hypothesis that salivary proteome can have a role in polyphenol-rich foods acceptance.
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Stangvaltaite-Mouhat L, Pūrienė A, Aleksejūnienė J, Stankeviciene I, Tommeras B, Al-Haroni M. Amylase Alpha 1 Gene (AMY1) Copy Number Variation and Dental Caries Experience: A Pilot Study among Adults in Lithuania. Caries Res 2021; 55:174-182. [PMID: 33735865 DOI: 10.1159/000514667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/24/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Genetic biomarkers have the potential to be used in personalised dentistry for improved prevention and decision-making in caries management. The amylase alpha 1 gene (AMY1) encodes salivary α-amylase and may be one such biomarker. We examined the association between AMY1 copy number variation (CNV) and dental caries experience in adults. MATERIALS AND METHODS A stratified random sample of 193 participants from the Lithuanian National Oral Health Survey (LNOHS) agreed to provide saliva samples and were included in this analysis (age 35-44 years; participation rate 43%). Information on socio-demographic and behavioural characteristics was taken from the LNHOS, which used the self-administered World Health Organisation (WHO) questionnaire. Data on fluoride levels in drinking water at the recruitment areas was recorded based on information provided by water suppliers. Dental caries experience was recorded at a surface level (smooth-surface and occlusal-surface decayed, missing, filled surfaces [D3MFS] score) by one trained and calibrated examiner using WHO criteria, and subsequently dichotomised for the statistical analyses. DNA extracted from saliva samples was used to investigate AMY1 CNV using the QX200 droplet digital PCR system. Bivariate and multivariable statistical analyses were employed. RESULTS When compared to participants with an AMY1 copy number (CN) of 2-3, higher odds of smooth-surface D3MFS >14 was observed for participants with a CN of 4-5 (OR 13.3, 95% CI 2.1-86.3), 6-9 (OR 7.0, 95% CI 1.4-34.1), and 10-16 (OR 5.8, 95% CI 1.2-32.2). Female sex was independently associated with a smooth-surface D3MFS >14 (OR 5.7, 95% CI 1.9-17.2). CONCLUSIONS Our study demonstrated an association between AMY1 CNV and high smooth-surface caries experience. Studies with larger sample sizes are needed to validate this association.
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Affiliation(s)
- Lina Stangvaltaite-Mouhat
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway, .,Oral Health Centre of Expertise in Eastern Norway, Oslo, Norway,
| | - Alina Pūrienė
- Institute of Dentistry, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Jolanta Aleksejūnienė
- Department of Oral Health Sciences, Faculty of Dentistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Indre Stankeviciene
- Institute of Dentistry, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Berit Tommeras
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.,Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
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Jauhal AA, Newcomb RD. Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO. Mol Ecol Resour 2021; 21:1416-1421. [PMID: 33629477 DOI: 10.1111/1755-0998.13364] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/16/2021] [Indexed: 12/21/2022]
Abstract
With the ever-increasing number of publicly available eukaryotic genome assemblies and user-friendly bioinformatics tools, there are increasing opportunities for researchers to use genomic resources in their research. While there are multiple dimensions to genome quality, it is often reduced to a single score that may not be correlated with other metrics, or appropriate for all applications of an assembly. To assess whether the commonly reported N50 value could reliably predict a separate dimension of genome quality, gene space completeness, we performed a meta-analysis of 611 published articles on eukaryotic genomes that used BUSCO scores, in addition to the typical N50 score. We found that although assemblies with relatively high contig and scaffold N50 values consistently had high BUSCO scores, a high BUSCO score could also be obtained from assemblies with a low N50. This reinforces that despite its ubiquity, N50 is not a perfect proxy for all measures of genome accuracy. Our data also suggests that variations in BUSCO scores among assemblies with poor N50 scores may be related to the number of introns in conserved eukaryotic genes. We stress the importance of screening and evaluating assembly quality based on the appropriate tools and urge increased reporting of additional genome assessment metrics in addition to N50. We also discuss the potential limitations of BUSCO and suggest improvements for assessing gene space within genome assemblies.
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Affiliation(s)
- April A Jauhal
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The New Zealand Institute for Plant & Food Research, Auckland, New Zealand
| | - Richard D Newcomb
- The New Zealand Institute for Plant & Food Research, Auckland, New Zealand
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Ben-Dor M, Sirtoli R, Barkai R. The evolution of the human trophic level during the Pleistocene. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175 Suppl 72:27-56. [PMID: 33675083 DOI: 10.1002/ajpa.24247] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/07/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Abstract
The human trophic level (HTL) during the Pleistocene and its degree of variability serve, explicitly or tacitly, as the basis of many explanations for human evolution, behavior, and culture. Previous attempts to reconstruct the HTL have relied heavily on an analogy with recent hunter-gatherer groups' diets. In addition to technological differences, recent findings of substantial ecological differences between the Pleistocene and the Anthropocene cast doubt regarding that analogy's validity. Surprisingly little systematic evolution-guided evidence served to reconstruct HTL. Here, we reconstruct the HTL during the Pleistocene by reviewing evidence for the impact of the HTL on the biological, ecological, and behavioral systems derived from various existing studies. We adapt a paleobiological and paleoecological approach, including evidence from human physiology and genetics, archaeology, paleontology, and zoology, and identified 25 sources of evidence in total. The evidence shows that the trophic level of the Homo lineage that most probably led to modern humans evolved from a low base to a high, carnivorous position during the Pleistocene, beginning with Homo habilis and peaking in Homo erectus. A reversal of that trend appears in the Upper Paleolithic, strengthening in the Mesolithic/Epipaleolithic and Neolithic, and culminating with the advent of agriculture. We conclude that it is possible to reach a credible reconstruction of the HTL without relying on a simple analogy with recent hunter-gatherers' diets. The memory of an adaptation to a trophic level that is embedded in modern humans' biology in the form of genetics, metabolism, and morphology is a fruitful line of investigation of past HTLs, whose potential we have only started to explore.
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Affiliation(s)
- Miki Ben-Dor
- Department of Archaeology, Tel Aviv University, Tel Aviv, Israel
| | | | - Ran Barkai
- Department of Archaeology, Tel Aviv University, Tel Aviv, Israel
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46
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Minoche AE, Lundie B, Peters GB, Ohnesorg T, Pinese M, Thomas DM, Zankl A, Roscioli T, Schonrock N, Kummerfeld S, Burnett L, Dinger ME, Cowley MJ. ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data. Genome Med 2021; 13:32. [PMID: 33632298 PMCID: PMC7908648 DOI: 10.1186/s13073-021-00841-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/02/2021] [Indexed: 01/09/2023] Open
Abstract
Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5-4.5%) and reproducibility high (95-99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35-63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .
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Affiliation(s)
- Andre E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
| | - Ben Lundie
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
| | - Greg B Peters
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Hawkesbury Road & Hainsworth Street, Westmead, NSW, Australia
| | - Thomas Ohnesorg
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
| | - Mark Pinese
- Children's Cancer Institute, University of New South Wales, Randwick, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia
| | - David M Thomas
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
| | - Andreas Zankl
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Hawkesbury Road, Westmead, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Tony Roscioli
- NSW Health Pathology Randwick, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, University of New South Wales, Randwick, Sydney, NSW, Australia
| | - Nicole Schonrock
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
| | - Sarah Kummerfeld
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Leslie Burnett
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia
- Genome.One, Darlinghurst, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, 370 Victoria Street, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
- Children's Cancer Institute, University of New South Wales, Randwick, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW, Sydney, NSW, Australia.
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Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank. NPJ Genom Med 2021; 6:8. [PMID: 33563995 PMCID: PMC7873199 DOI: 10.1038/s41525-021-00170-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Studies assessing the impact of amylase genes copy number (CN) on adiposity report conflicting findings in different global populations, likely reflecting the impact of ancestral and ethnic-specific environment and lifestyle on selection at the amylase loci. Here, we leverage population size and detailed adiposity measures from a large population biobank to resolve confounding effects and determine the relationship between salivary (AMY1) and pancreatic (AMY2A) amylase genes CN and adiposity in 2935 Qatari individuals who underwent whole-genome sequencing (WGS) as part of the Qatar Genome Programme. We observe a negative association between AMY1 CNs and trunk fat percentage in the Qatari population (P = 7.50 × 10-3) and show that Qataris of Arab descent have significantly lower CN at AMY1 (P = 1.32 × 10-10) as well as less favorable adiposity and metabolic profiles (P < 1.34 × 10-8) than Qataris with Persian ancestry. Indeed, lower AMY1 CN was associated with increased total and trunk fat percentages in Arabs (P < 4.60 × 10-3) but not in Persians. Notably, overweight and obese Persians reported a significant trend towards dietary restraint following weight gain compared to Arabs (P = 4.29 × 10-5), with AMY1 CN showing negative association with dietary self-restraint (P = 3.22 × 10-3). This study reports an association between amylase gene CN and adiposity traits in a large Middle Eastern population. Importantly, we leverage rich biobank data to demonstrate that the strength of this association varies with ethnicity, and may be influenced by population-specific behaviors that also contribute to adiposity traits.
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Romdhane L, Mezzi N, Dallali H, Messaoud O, Shan J, Fakhro KA, Kefi R, Chouchane L, Abdelhak S. A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa. NPJ Genom Med 2021; 6:3. [PMID: 33420067 PMCID: PMC7794582 DOI: 10.1038/s41525-020-00166-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022] Open
Abstract
Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.
- Department of Biology, Faculty of Science of Bizerte, Jarzouna, Tunisia.
| | - Nessrine Mezzi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rym Kefi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
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Hamid AK, Andersson-Assarsson J, Ericson U, Sonestedt E. Interaction Effect Between Copy Number Variation in Salivary Amylase Locus ( AMY1) and Starch Intake on Glucose Homeostasis in the Malmö Diet and Cancer Cohort. Front Nutr 2021; 7:598850. [PMID: 33490099 PMCID: PMC7817815 DOI: 10.3389/fnut.2020.598850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Salivary amylase initiates the digestion of starch and it has been hypothesized that salivary amylase may play a role in the development of insulin resistance and type 2 diabetes. The aim was to examine the interaction between copy number variation in the salivary amylase gene AMY1 and starch intake. We studied 3,624 adults without diabetes or elevated blood glucose in the Malmö Diet Cancer cohort. We assessed the associations and interactions between starch intake, AMY1 copies and glucose homeostasis traits (i.e., fasting plasma glucose, insulin and HOMA-IR) and risk of type 2 diabetes over an average of 18 follow-up years. AMY1 copy number was not associated with glucose, insulin or HOMA-IR. We observed a significant interaction between starch intake and AMY1 copies on insulin and HOMA-IR after adjusting for potential confounders (p < 0.05). The inverse association between starch intake and insulin and HOMA-IR was stronger in the group with 10 or more copies (P trend < 0.001). In addition, we observed an inverse association between starch intake and type 2 diabetes in the group with 10 or more copies (p trend = 0.003), but not in the other groups. This cross-sectional observational study suggests that AMY1 copy numbers might interact with starch intake on glucose homeostasis traits. Interventional studies are required to determine whether individuals with high AMY1 copy numbers may benefit from a high starch intake.
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Affiliation(s)
- Aida Koder Hamid
- Nutritional Epidemiology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Johanna Andersson-Assarsson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Ericson
- Diabetes and Cardiovascular Disease - Genetic Epidemiology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Emily Sonestedt
- Nutritional Epidemiology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
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50
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Zhan F, Chen J, Yan H, Wang S, Zhao M, Zhang S, Lan X, Maekawa M. Association of Serum Amylase Activity and the Copy Number Variation of AMY1/2A/2B with Metabolic Syndrome in Chinese Adults. Diabetes Metab Syndr Obes 2021; 14:4705-4714. [PMID: 34880639 PMCID: PMC8648087 DOI: 10.2147/dmso.s339604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Low serum amylase activity and copy number (CN) variation (CNV) of the salivary amylase gene (AMY1) are reportedly associated with obesity and abnormal glucose metabolism; however, this association remains controversial. We aimed to clarify the relationship between serum amylase activity and the CNV of AMY1/2A/2B with the occurrence of metabolic syndrome (MetS) in Chinese adults. PATIENTS AND METHODS Anthropometry, metabolic risk factors, and serum amylase activity were assessed in 560 subjects (260 MetS patients; 300 healthy controls). AMY1/2A/2B CNs were evaluated using the highly sensitive droplet digital PCR. RESULTS The serum total, pancreatic, and salivary amylase activity, but not the AMY1/2A/2B CNs, was significantly lower in MetS patients than that in the control subjects. Patients <45 y had a lower AMY1 CN, compared to that in healthy controls. Low serum amylase activity was significantly associated with high MetS prevalence (p < 0.001). In the receiver operating characteristic curve analysis, serum amylase activity was a significant diagnostic indicator for MetS. The diagnostic value of total amylase was second only to that of γ-glutamyl transpeptidase; it was higher than that of alanine aminotransferase and uric acid. CONCLUSION Low serum amylase activity was significantly associated with increased risk of MetS in Chinese adults. Therefore, amylase could be a potential biomarker for predicting MetS.
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Affiliation(s)
- Fangjie Zhan
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Jin Chen
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Huihui Yan
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Shuiliang Wang
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Meng Zhao
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Shenghang Zhang
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Xiaopeng Lan
- Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
- Correspondence: Xiaopeng Lan Department of Clinical Laboratory Medicine, The 900th Hospital of Joint Logistics Support Force, 156th, Xierhuan Road, Fuzhou, 350025, People’s Republic of ChinaTel +86 591 22859482 Email
| | - Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Masato Maekawa Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1, Handayama, Higashi-ku, Hamamatsu, 431-3192, JapanTel +81-53-435-2721Fax +81-53-435-2096 Email
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