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Sawyers C, Sheerin C, Moore AA, Neigh G, Hettema JM, Roberson-Nay R. Genetic and environmental influences on alpha amylase stress reactivity and shared genetic covariation with cortisol. Psychoneuroendocrinology 2024; 161:106922. [PMID: 38101095 PMCID: PMC10842877 DOI: 10.1016/j.psyneuen.2023.106922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Salivary alpha amylase (sAA) is a common measure of stress reactivity, primarily reflecting sympathetic nervous system activity. Salivary cortisol is also a reliable, frequently used biomarker of stress and reflects the hypothalamic-pituitary-adrenal (HPA) axis response. This study examined heritability across varying metrics of sAA in response to a social evaluative stressor, the Trier Social Stress Test (TSST). The goal of this study was to estimate genetic and environmental influences on measurements of sAA stress reactivity. Moreover, we evaluated the shared genetic covariation between sAA and cortisol. Participants included twins aged 15-20 years (54% female). We measured alpha amylase and cortisol reactivity to the TSST via serial salivary cortisol samples collected pre- and post-TSST. Modest to moderate heritability estimates (11-64%) were observed across measures purported to capture alpha amylase stress reactivity (peak, area under the curve, baseline-to-peak change). Findings also indicate that sAA baseline and peak are primarily influenced by a shared genetic factor. There was no evidence of shared genetic influences between sAA and cortisol. These findings suggest the genetic control of the HPA and Sympathetic Adreno-Medullar axis are genetically independent of one another despite both playing a role in response to stressors.
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Affiliation(s)
- Chelsea Sawyers
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA; Department of Psychiatry, Virginia Commonwealth University, USA.
| | - Christina Sheerin
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA; Department of Psychiatry, Virginia Commonwealth University, USA
| | - Ashlee A Moore
- Department of Psychology, State University of New York at Oswego, USA
| | - Gretchen Neigh
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, USA
| | - John M Hettema
- Department of Psychiatry, Texas A&M Health Sciences Center, USA
| | - Roxann Roberson-Nay
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, USA; Department of Psychiatry, Virginia Commonwealth University, USA
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Mauricio-Castillo R, Valdevit A, Gonzalez-Davalos L, Dominguez-Perez RA, Garcia-Solis P, Vazquez-Martinez O, Hernandez-Montiel HL, Solis-Sainz JC. Dental caries prevalence and severity positively associate with AMY1 gene copy number. Clin Oral Investig 2023; 28:25. [PMID: 38147184 DOI: 10.1007/s00784-023-05435-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
OBJECTIVE To establish the possible relation between total caries (TC) and caries severity (CS) with the AMY1 gene copy number (AMY1GCN). MATERIALS AND METHODS This was an observational, cross-sectional, population-based, and association study with 303 participants. Each participant underwent a complete anamnesis and stomatological check-up, and peripheral blood was obtained to extract gDNA. TC and CS were determined as the number of caries at the dental exploration and the number of dental surfaces affected by caries, respectively, and AMY1GCN was determined by qPCR. RESULTS We found an elevated caries prevalence (92.7%); TC and CS were 8 ± 10 and 10 ± 13 (median ± IR). There were higher TC and CS in those participants with AMY1GCN above the mean value (0.02 and 0.01 p values, respectively). A positive correlation between TC and CS with AMY1GCN (0.11 and 0.125 r values, 0.03 and 0.01 p values, respectively) was found, in addition to an association between TC and CS with AMY1GCN (1.5 and 1.6 OR values, 0.48 and 0.26 p values, respectively). CONCLUSION TC and CS were positively related to the AMY1GCN. CLINICAL RELEVANCE Dental caries has a high prevalence and a multifactorial etiology and has been related to a genetic component. Indeed, the salivary enzyme alpha-amylase could play a significant role in caries susceptibility, considering that its codifying gene (AMY1) can show variation in its gene copy number. This can be considered an important factor for the development of caries at a genetic level.
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Affiliation(s)
- Rubi Mauricio-Castillo
- PhD. program in Biomedical Sciences, School of Medicine, Autonomous University of Queretaro, Querétaro, Mexico
| | - Andres Valdevit
- Department of Biomedical Research, School of Medicine, Autonomous University of Queretaro, Clavel 200, Col. Prados de la Capilla, 76170, Querétaro, Mexico
| | - Laura Gonzalez-Davalos
- Department of Cellular and Molecular Neurobiology, Institute of Neurobiology, National Autonomous University of México, UAQ-Juriquilla Campus, Querétaro, Mexico
| | - Rubén Abraham Dominguez-Perez
- Laboratory of Multidisciplinary Dentistry Research, School of Medicine, Autonomous University of Queretaro, Querétaro, Mexico
| | - Pablo Garcia-Solis
- Department of Biomedical Research, School of Medicine, Autonomous University of Queretaro, Clavel 200, Col. Prados de la Capilla, 76170, Querétaro, Mexico
| | - Olivia Vazquez-Martinez
- Department of Cellular and Molecular Neurobiology, Institute of Neurobiology, National Autonomous University of México, UAQ-Juriquilla Campus, Querétaro, Mexico
| | - Hebert Luis Hernandez-Montiel
- Department of Biomedical Research, School of Medicine, Autonomous University of Queretaro, Clavel 200, Col. Prados de la Capilla, 76170, Querétaro, Mexico
| | - Juan Carlos Solis-Sainz
- Department of Biomedical Research, School of Medicine, Autonomous University of Queretaro, Clavel 200, Col. Prados de la Capilla, 76170, Querétaro, Mexico.
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Vázquez-Moreno MA, Cruz-López M. [From genotype to phenotype: amylase gene in childhood obesity]. Rev Med Inst Mex Seguro Soc 2023; 61:356-362. [PMID: 37216679 PMCID: PMC10437226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [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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Li H, Borné Y, Wang Y, Sonestedt E. Starch intake, amylase gene copy number variation, plasma proteins, and risk of cardiovascular disease and mortality. BMC Med 2023; 21:27. [PMID: 36691017 PMCID: PMC9872432 DOI: 10.1186/s12916-022-02706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/12/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Salivary amylase, encoded by the AMY1 gene, initiate the digestion of starch. Whether starch intake or AMY1 copy number is related to disease risk is currently rather unknown. The aim was to investigate the association between starch intake and AMY1 copy number and risk of cardiovascular disease (CVD) and mortality and whether there is an interaction. In addition, we aim to identify CVD-related plasma proteins associated with starch intake and AMY1 copy number. METHODS This prospective cohort study used data from 21,268 participants from the Malmö Diet and Cancer Study. Dietary data were collected through a modified diet history method and incident CVD and mortality were ascertained through registers. AMY1 gene copy number was determined by droplet digital polymerase chain reaction, a risk score of 10 genetic variants in AMY1 was measured, and a total of 88 selected CVD-related proteins were measured. Cox proportional hazards regression was used to analyze the associations of starch intake and AMY1 copy number with disease risk. Linear regression was used to identify plasma proteins associated with starch intake and AMY1 copy number. RESULTS Over a median of 23 years' follow-up, 4443 individuals developed CVD event and 8125 died. After adjusting for potential confounders, a U-shape association between starch intake and risk of CVD (P-nonlinearity = 0.001) and all-cause mortality (P-nonlinearity = 0.03) was observed. No significant association was found between AMY1 copy number and risk of CVD and mortality, and there were no interactions between starch intake and AMY1 copy number (P interaction > 0.23). Among the 88 plasma proteins, adrenomedullin, interleukin-1 receptor antagonist protein, fatty acid-binding protein, leptin, and C-C motif chemokine 20 were associated with starch intake after adjusting for multiple testing. CONCLUSIONS In this large prospective study among Swedish adults, a U-shaped association between starch intake and risk of CVD and all-cause mortality was found. Several plasma proteins were identified which might provide information on potential pathways for such association. AMY1 copy number was not associated with CVD risk or any of the plasma proteins, and there was no interaction between starch intake and AMY1 copy number on disease risk.
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Affiliation(s)
- Huiping Li
- School of Public Health, Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin, 300070, China.
- Nutritional Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden.
| | - Yan Borné
- Nutritional Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden
| | - Yaogang Wang
- School of Public Health, Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin, 300070, China
| | - Emily Sonestedt
- Nutritional Epidemiology, Department of Clinical Sciences in Malmö, Lund University, Malmö, Sweden.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barber TM, Bhatti AA, Elder PJD, Ball SP, Calvez R, Ramsden DB, Cuthbertson DJ, Pfeiffer AF, Burnett D, Weickert MO. AMY1 Gene Copy Number Correlates With Glucose Absorption and Visceral Fat Volume, but Not with Insulin Resistance. J Clin Endocrinol Metab 2020; 105:5875080. [PMID: 32697825 DOI: 10.1210/clinem/dgaa473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/17/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND The human amylase gene (AMY1) has a broad copy number (CN) variation that may associate with body mass index. METHODS Deoxyribonucleic acid was extracted from urine (n = 74) and serum (n = 6) samples (Protein, Fiber and Metabolic Syndrome [ProFiMet] cohort), and buccal (n = 17) samples (Oral Starch Challenge [OSC] cohort), and assessed for AMY1 CN by droplet digital polymerase chain reaction. The association of AMY1 CN with comprehensive markers of metabolic status (ProFiMet cohort) were analyzed with Pearson's correlation coefficient (CC). For the healthy, euglycemic OSC cohort, glycemic response to OSC was analyzed with independent sample t-tests (subgroups: high AMY1 CN 9-12, n = 10; low AMY1 CN 4-6, n = 7). RESULTS There were significant inverse correlations of AMY1 CN with total visceral fat volume (CC -0.33; P = 0.004) and positive correlations of AMY1 CN with oral glucose insulin sensitivity score (derived from an oral glucose tolerance test, CC 0.26; P = 0.02), serum HDL-cholesterol (CC 0.325; P = 0.003), and serum adiponectin (CC 0.249; P = 0.026). Linear regression multivariate analysis (adiponectin as dependent variable), showed independent association of adiponectin with AMY1 CN (Beta = 0.29; P = 0.03). There were no significant associations between AMY1 CN and clamp-derived M-value, homeostasis model assessment of insulin resistance (IR), hepatic endogenous glucose production, fecal floral signature, or macronutrient dietary preference. Delta (mean) change in blood glucose concentration (fasting to 30-minutes post-OSC) was significantly greater in the high versus low AMY1 CN subgroups (mean 1.7 mmol/l [SEM 0.6] vs 0.9 mmol/l [SEM 0.9], respectively; P = 0.016). CONCLUSIONS High AMY1 CN associates with a favorable metabolic profile (lower visceral fat volume, higher serum adiponectin, enhanced glucose absorption following oral glucose, and OSC), but not with whole-body or hepatic IR.
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Affiliation(s)
- Thomas M Barber
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Ahsan A Bhatti
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Patrick J D Elder
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
| | - Sarah P Ball
- Micropathology Ltd., University of Warwick Science Park, Coventry, UK
| | - Ronan Calvez
- Micropathology Ltd., University of Warwick Science Park, Coventry, UK
| | - David B Ramsden
- Institute of Metabolism and Systems Research, Medical School, University of Birmingham, Birmingham, UK
| | - Dan J Cuthbertson
- Department of Obesity and Endocrinology; Clinical Sciences Centre, University Hospital Aintree, Liverpool, UK
| | - Andreas F Pfeiffer
- German Institute of Human Nutrition, Department of Clinical Nutrition, Potsdam-Rehbruecke, Germany
- Department of Endocrinology, Diabetes and Nutrition, Campus Benjamin Franklin, Charité-University-Medicine Berlin, Berlin, Germany
| | - David Burnett
- Micropathology Ltd., University of Warwick Science Park, Coventry, UK
| | - Martin O Weickert
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire, Coventry, UK
- German Institute of Human Nutrition, Department of Clinical Nutrition, Potsdam-Rehbruecke, Germany
- Department of Endocrinology, Diabetes and Nutrition, Campus Benjamin Franklin, Charité-University-Medicine Berlin, Berlin, Germany
- Centre of Applied Biological & Exercise Sciences, Faculty of Health & Life Sciences, Coventry University, Coventry, UK
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Grammatikopoulou MG, Gkiouras K, Markaki AG, Gkouskou KK, Aivaliotis M, Stylianou K, Bogdanos DP. AMY1 diploid copy number among end-stage renal disease patients. Hormones (Athens) 2020; 19:369-376. [PMID: 32405930 DOI: 10.1007/s42000-020-00199-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE The salivary amylase gene (AMY1) copy number variation (CNV) is increased as a human adaptation to starch-enriched nutritional patterns. The purpose of this study was to evaluate the relationship between AMY1 CNV, dietary starch consumption, and anthropometric indices among a known population with elevated cardiovascular risk, being end-stage renal disease (ESRD) patients. METHODS A total of 43 ESRD patients were recruited based on the following inclusion criteria: being (1) adults, (2) on hemodialysis for more than 3 months, (3) able to communicate effectively, and (4) willing to participate. Anthropometric measurements were performed, dietary intake was recorded via food-frequency questionnaires, and AMY1 CNV was quantified in blood samples DNA via real-time PCR. RESULTS Median AMY1 CNV was 4.0 (2.0-17.0). A total of 21 patients had an even, and 22 had an odd AMY1 copy number (CN). Independent samples t tests revealed that AMY1-odd diploid CN is associated with increased body weight, waist and hip circumferences, and fat mass compared to the respective even diploid CN carrier group. No differences were observed for BMI or nutritional intake. Multiple regression analysis revealed that AMY1-odd diploid CN was positively associated with increased hip circumference (ß = 7.87, 95% CI = 0.34 to 15.39) and absolute fat mass (ß = 6.66, 95% CI = 0.98 to 12.34); however, after applying the Bonferroni correction for multiplicity, all regression analyses lost their significance. CONCLUSIONS AMY1-odd diploid CN appears to be associated with selected adiposity variables among hemodialysis patients. However, more research is needed to verify this finding in this population with known increased cardiovascular risk.
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Affiliation(s)
- Maria G Grammatikopoulou
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece.
| | - Konstantinos Gkiouras
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Anastasia G Markaki
- Department of Nutrition & Dietetics, Faculty of Health Sciences, Hellenic Mediterranean University, Sitia, Greece
| | - Kalliopi K Gkouskou
- Department of Medical Laboratories, Faculty of Health and Caring Professions, University of West Attica, Athens, Greece
- Embiodiagnostics, Biology Research Company, Melissinon and Damvergidon Str, Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas (FORTH), Heraklion, Crete, Greece
| | | | - Dimitrios P Bogdanos
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
- Division of Transplantation, Immunology and Mucosal Biology, MRC Centre for Transplantation, King's College London Medical School, London, UK
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Heianza Y, Zhou T, Yuhang C, Huang T, Willett WC, Hu FB, Bray GA, Sacks FM, Qi L. Starch Digestion-Related Amylase Genetic Variants, Diet, and Changes in Adiposity: Analyses in Prospective Cohort Studies and a Randomized Dietary Intervention. Diabetes 2020; 69:1917-1926. [PMID: 32493715 PMCID: PMC7458037 DOI: 10.2337/db19-1257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/29/2020] [Indexed: 01/18/2023]
Abstract
Salivary amylase, encoded by the AMY1 gene, is responsible for the digestion of carbohydrates. We investigated associations of AMY1 genetic variations with general and central adiposity changes considering dietary carbohydrate intake among 32,054 adults from four prospective cohort studies. A genetic risk score (GRS) was calculated based on nine AMY1 single-nucleotide polymorphisms, with higher AMY1-GRS indicating higher activity of salivary amylase. We meta-analyzed interactions between AMY1-GRS and dietary intake for changes in general and central adiposity over 5.5-10 years. We found that carbohydrate food intake significantly altered associations of AMY1-GRS with changes in BMI (P interaction = 0.001) and waist circumference (P interaction < 0.001). Results were consistent and significant in female cohorts rather than in male cohorts. Among women, higher AMY1-GRS was associated with more increases in adiposity if dietary carbohydrate food intake was high, while higher AMY1-GRS was associated with less gains in adiposity when the dietary intake was low. Also, in a 2-year randomized dietary intervention trial, associations of AMY1-GRS with changes in weight (P interaction = 0.023) and waist circumference (P interaction = 0.037) were significantly modified by carbohydrate intake. Our results suggest the importance of precision nutrition strategies considering participants' genetic adaptation to carbohydrate-rich diets in regulating general and central adiposity.
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Affiliation(s)
- Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Tao Zhou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Chen Yuhang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Tao Huang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Walter C Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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9
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Liu Y, Smith CE, Parnell LD, Lee YC, An P, Straka RJ, Tiwari HK, Wood AC, Kabagambe EK, Hidalgo B, Hopkins PN, Province MA, Arnett DK, Tucker KL, Ordovas JM, Lai CQ. Salivary AMY1 Copy Number Variation Modifies Age-Related Type 2 Diabetes Risk. Clin Chem 2020; 66:718-726. [PMID: 32337541 PMCID: PMC7192522 DOI: 10.1093/clinchem/hvaa072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/28/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND Copy number variation (CNV) in the salivary amylase gene (AMY1) modulates salivary α-amylase levels and is associated with postprandial glycemic traits. Whether AMY1-CNV plays a role in age-mediated change in insulin resistance (IR) is uncertain. METHODS We measured AMY1-CNV using duplex quantitative real-time polymerase chain reaction in two studies, the Boston Puerto Rican Health Study (BPRHS, n = 749) and the Genetics of Lipid-Lowering Drug and Diet Network study (GOLDN, n = 980), and plasma metabolomic profiles in the BPRHS. We examined the interaction between AMY1-CNV and age by assessing the relationship between age with glycemic traits and type 2 diabetes (T2D) according to high or low copy numbers of the AMY1 gene. Furthermore, we investigated associations between metabolites and interacting effects of AMY1-CNV and age on T2D risk. RESULTS We found positive associations of IR with age among subjects with low AMY1-copy-numbers in both studies. T2D was marginally correlated with age in participants with low AMY1-copy-numbers but not with high AMY1-copy-numbers in the BPRHS. Metabolic pathway enrichment analysis identified the pentose metabolic pathway based on metabolites that were associated with both IR and the interactions between AMY1-CNV and age. Moreover, in older participants, high AMY1-copy-numbers tended to be associated with lower levels of ribonic acid, erythronic acid, and arabinonic acid, all of which were positively associated with IR. CONCLUSIONS We found evidence supporting a role of AMY1-CNV in modifying the relationship between age and IR. Individuals with low AMY1-copy-numbers tend to have increased IR with advancing age.
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Affiliation(s)
- Yuwei Liu
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
- School of Public Health, Fudan University, Shanghai, China
| | - Caren E Smith
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Laurence D Parnell
- USDA Agricultural Research Service, Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Yu-Chi Lee
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Ping An
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL
| | - Alexis C Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | | | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - Paul N Hopkins
- Division of Cardiovascular Medicine, University of Utah, Salt Lake City, UT
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY
| | - Katherine L Tucker
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Chao-Qiang Lai
- USDA Agricultural Research Service, Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
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Date K, Yamazaki T, Toyoda Y, Hoshi K, Ogawa H. α-Amylase expressed in human small intestinal epithelial cells is essential for cell proliferation and differentiation. J Cell Biochem 2020; 121:1238-1249. [PMID: 31478242 PMCID: PMC6973164 DOI: 10.1002/jcb.29357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
α-Amylase, which plays an essential role in starch degradation, is expressed mainly in the pancreas and salivary glands. Human α-amylase is also detected in other tissues, but it is unclear whether the α-amylase is endogenously expressed in each tissue or mixed exogenously with one expressed by the pancreas or salivary glands. Furthermore, the biological significance of these α-amylases detected in tissues other than the pancreas and salivary glands has not been elucidated. We discovered that human α-amylase is expressed in intestinal epithelial cells and analyzed the effects of suppressing α-amylase expression. α-Amylase was found to be expressed at the second-highest messenger RNA level in the duodenum in human normal tissues after the pancreas. α-Amylase was detected in the cell extract of Caco-2 intestinal epithelial cells but not secreted into the culture medium. The amount of α-amylase expressed increased depending on the length of the culture of Caco-2 cells, suggesting that α-amylase is expressed in small intestine epithelial cells rather than the colon because the cells differentiate spontaneously upon reaching confluence in culture to exhibit the characteristics of small intestinal epithelial cells rather than colon cells. The α-amylase expressed in Caco-2 cells had enzymatic activity and was identified as AMY2B, one of the two isoforms of pancreatic α-amylase. The suppression of α-amylase expression by small interfering RNA inhibited cell differentiation and proliferation. These results demonstrate for the first time that α-amylase is expressed in human intestinal epithelial cells and affects cell proliferation and differentiation. This α-amylase may induce the proliferation and differentiation of small intestine epithelial cells, supporting a rapid turnover of cells to maintain a healthy intestinal lumen.
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Affiliation(s)
- Kimie Date
- Institute for Human Life InnovationOchanomizu University, Ohtsuka, Bunkyo‐kuTokyoJapan
| | - Tomomi Yamazaki
- National Institute of Health and NutritionNational Institutes of Biomedical Innovation, Health and Nutrition, Toyama, Shinjuku‐kuTokyoJapan
| | - Yoko Toyoda
- Graduate School of Humanities and SciencesOchanomizu University, Ohtsuka, Bunkyo‐kuTokyoJapan
| | - Kumi Hoshi
- Graduate School of Humanities and SciencesOchanomizu University, Ohtsuka, Bunkyo‐kuTokyoJapan
| | - Haruko Ogawa
- Institute for Human Life InnovationOchanomizu University, Ohtsuka, Bunkyo‐kuTokyoJapan
- Graduate School of Humanities and SciencesOchanomizu University, Ohtsuka, Bunkyo‐kuTokyoJapan
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Venkatapoorna CMK, Ayine P, Parra EP, Koenigs T, Phillips M, Babu JR, Sandey M, Geetha T. Association of Salivary Amylase ( AMY1) Gene Copy Number with Obesity in Alabama Elementary School Children. Nutrients 2019; 11:nu11061379. [PMID: 31248128 PMCID: PMC6627241 DOI: 10.3390/nu11061379] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 01/14/2023] Open
Abstract
Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of starch. Recently studies have shown that the copy number of AMY1 is associated with obesity; however, the data varies with location. One-third of children are overweight/obese in Alabama. In this study, we aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in children from Alabama. One hundred twenty-seven children aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Genomic DNA was extracted from saliva, and the copy number of the AMY1 gene was estimated by digital PCR. The association between AMY1 copy number and obesity measurements was analyzed by linear regression. The mean AMY1 copy number significantly decreased in overweight/obese (6.21 ± 1.48) compared to normal weight (7.97 ± 2.35) children. AMY1 copy number inversely associated with the obesity measurements. African Americans had a stronger association between low AMY1 copy number and obesity compared to white/European Americans. Our findings suggest that overweight/obese children have a low AMY1 copy number and the effect is more prominent in African Americans.
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Affiliation(s)
- Chandra M K Venkatapoorna
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Priscilla Ayine
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Emily P Parra
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Taylor Koenigs
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Megan Phillips
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Jeganathan R Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA.
| | - Maninder Sandey
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA.
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12
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Byman E, Schultz N, Fex M, Wennström M. Brain alpha-amylase: a novel energy regulator important in Alzheimer disease? Brain Pathol 2018; 28:920-932. [PMID: 29485701 PMCID: PMC8028266 DOI: 10.1111/bpa.12597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/16/2018] [Indexed: 12/11/2022] Open
Abstract
Reduced glucose metabolism and formation of polyglucosan bodies (PGB) are, beside amyloid beta plaques and neurofibrillary tangles, well-known pathological findings associated with Alzheimer's disease (AD). Since both glucose availability and PGB are regulated by enzymatic degradation of glycogen, we hypothesize that dysfunctional glycogen degradation is a critical event in AD progression. We therefore investigated whether alpha (α)-amylase, an enzyme known to efficiently degrade polysaccharides in the gastrointestinal tract, is expressed in the hippocampal CA1/subiculum and if the expression is altered in AD patients. Using immunohistochemical staining techniques, we show the presence of the α-amylase isotypes AMY1A and AMY2A in neuronal dendritic spines, pericytes and astrocytes. Moreover, AD patients showed reduced gene expression of α-amylase, but conversely increased protein levels of α-amylase as well as increased activity of the enzyme compared with non-demented controls. Lastly, we observed increased, albeit not significant, load of periodic acid-Schiff positive PGB in the brain of AD patients, which correlated with increased α-amylase activity. These findings show that α-amylase is expressed and active in the human brain, and suggest the enzyme to be affected, alternatively play a role, in the neurodegenerative Alzheimer's disease pathology.
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Affiliation(s)
- Elin Byman
- Clinical Memory Research Unit, Department of Clinical Sciences MalmöLund UniversityMalmöSweden
| | - Nina Schultz
- Clinical Memory Research Unit, Department of Clinical Sciences MalmöLund UniversityMalmöSweden
| | | | - Malin Fex
- Unit for Molecular Metabolism, Lund University Diabetes Centre, Department of Clinical Sciences, Lund UniversityMalmöSweden
| | - Malin Wennström
- Clinical Memory Research Unit, Department of Clinical Sciences MalmöLund UniversityMalmöSweden
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León-Mimila P, Villamil-Ramírez H, López-Contreras BE, Morán-Ramos S, Macias-Kauffer LR, Acuña-Alonzo V, Del Río-Navarro BE, Salmerón J, Velazquez-Cruz R, Villarreal-Molina T, Aguilar-Salinas CA, Canizales-Quinteros S. Low Salivary Amylase Gene ( AMY1) Copy Number Is Associated with Obesity and Gut Prevotella Abundance in Mexican Children and Adults. Nutrients 2018; 10:nu10111607. [PMID: 30388780 PMCID: PMC6266693 DOI: 10.3390/nu10111607] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified copy number variants (CNVs) associated with obesity in chromosomal regions 1p31.1, 10q11.22, 11q11, 16p12.3, and recently 1p21.1, which contains the salivary amylase gene (AMY1). Recent evidence suggests this enzyme may influence gut microbiota composition through carbohydrate (mainly starch) degradation. The role of these CNVs in obesity has been scarcely explored in the Latino population, and thus the aim of our study was to evaluate the association of 1p31.1, 10q11.22, 11q11, 16p12.3 and 1p21.1 CNVs with obesity in 921 Mexican children, to replicate significant associations in 920 Mexican adults, and to analyze the association of AMY1 copy number with gut microbiota in 75 children and 45 adults. Of the five CNVs analyzed, 1q11 CNV was significantly associated with obesity in children, but not in adults. Only AMY1 CNV was significantly associated with obesity in both age groups. Moreover, gut microbiota analyses revealed a positive correlation between AMY1 copy number and Prevotella abundance. This genus has enzymes and gene clusters essential for complex polysaccharide degradation and utilization. To our knowledge, this is the first study to analyze the association of these five CNVs in the Mexican population and to report a correlation between AMY1 CN and gut microbiota in humans.
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Affiliation(s)
- Paola León-Mimila
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
| | - Hugo Villamil-Ramírez
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
| | - Blanca E López-Contreras
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
| | - Sofía Morán-Ramos
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico City 03940, Mexico.
| | - Luis R Macias-Kauffer
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
| | - Víctor Acuña-Alonzo
- Escuela Nacional de Antropología e Historia, Laboratorio de genética molecular, Mexico City 14030, Mexico.
| | - Blanca E Del Río-Navarro
- Departamento de Alergia e Inmunología Clínica, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico.
| | - Jorge Salmerón
- Unidad Académica de Investigación Epidemiológica del Centro de Investigación en Políticas, Población y Salud, Facultad de Medicina-UNAM, Mexico City 04510, Mexico.
| | | | | | - Carlos A Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14000, Mexico.
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo León 64710, Mexico.
| | - Samuel Canizales-Quinteros
- Facultad de Química, Unidad de Genómica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
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14
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Abstract
INTRODUCTION Humans have multiple genes encoding amylase that are broadly divided into salivary (AMY1) and pancreatic (AMY2) genes. They exhibit some of the greatest copy numbers of any human gene, an expansion possibly driven by increased dietary starch intake. Within the population, amylase gene copy number is highly variable and there is evidence of an inverse association between AMY1 copy number and BMI. AREAS COVERED We examine the evidence for the link between AMY1 and BMI, its potential mechanisms, and the metabolic effects of salivary and pancreatic amylase, both in the gastrointestinal tract and the blood EXPERT COMMENTARY Salivary amylase may influence postprandial 'cephalic phase' insulin release, which improves glucose tolerance, while serum amylase may have insulin-sensitizing properties. This could explain the favorable metabolic status associated with higher AMY1 copy number. The association with BMI is harder to explain and is potentially mediated by increased flux of undigested starch into the ileum, with resultant effects on short-chain fatty acids (SCFAs), changes in gut microbiota and effects on appetite and energy expenditure in those with low copy number. Future research on the role of amylase as a determinant of metabolic health and BMI may lead to novel therapies to target obesity.
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Affiliation(s)
- Patrick J D Elder
- a Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire , Coventry , UK
| | - David B Ramsden
- b Institute of Metabolism and Systems Research, The Medical School, University of Birmingham , Birmingham , UK
| | - David Burnett
- c Micropathology Ltd, University of Warwick Science Park , Coventry , UK
| | - Martin O Weickert
- a Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire , Coventry , UK
- d Division of Biomedical Sciences , Warwick Medical School, University of Warwick , Coventry , UK
- e Centre of Applied Biological & Exercise Sciences, Faculty of Health & Life Sciences , Coventry University , Coventry , UK
| | - Thomas M Barber
- a Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism, University Hospitals Coventry and Warwickshire , Coventry , UK
- d Division of Biomedical Sciences , Warwick Medical School, University of Warwick , Coventry , UK
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Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A. AMYCNE: Confident copy number assessment using whole genome sequencing data. PLoS One 2018; 13:e0189710. [PMID: 29579039 PMCID: PMC5868770 DOI: 10.1371/journal.pone.0189710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/30/2017] [Indexed: 11/18/2022] Open
Abstract
Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection. None of these tools are designed specifically to accurately estimate copy numbers of complex regions in a small cohort or clinical setting. Herein, we present AMYCNE (automatic modeling functionality for copy number estimation), a CNV analysis tool using WGS data. AMYCNE is multifunctional and performs copy number estimation of complex regions, annotation of VCF files, and CNV detection on individual samples. The performance of AMYCNE was evaluated using AMY1A ddPCR measurements from 86 unrelated individuals. In addition, we validated the accuracy of AMYCNE copy number predictions on two additional genes (FCGR3A and FCGR3B) using datasets available through the 1000 genomes consortium. Finally, we simulated levels of mosaic loss and gain of chromosome X and used this dataset for benchmarking AMYCNE. The results show a high concordance between AMYCNE and ddPCR, validating the use of AMYCNE to measure tandem AMY1 repeats with high accuracy. This opens up new possibilities for the use of WGS for accurate copy number determination of other complex regions in the genome in small cohorts or single individuals.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- * E-mail:
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | | | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Ooi DSQ, Tan VMH, Ong SG, Chan YH, Heng CK, Lee YS. Differences in AMY1 Gene Copy Numbers Derived from Blood, Buccal Cells and Saliva Using Quantitative and Droplet Digital PCR Methods: Flagging the Pitfall. PLoS One 2017; 12:e0170767. [PMID: 28125683 PMCID: PMC5268653 DOI: 10.1371/journal.pone.0170767] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/10/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction The human salivary (AMY1) gene, encoding salivary α-amylase, has variable copy number variants (CNVs) in the human genome. We aimed to determine if real-time quantitative polymerase chain reaction (qPCR) and the more recently available Droplet Digital PCR (ddPCR) can provide a precise quantification of the AMY1 gene copy number in blood, buccal cells and saliva samples derived from the same individual. Methods Seven participants were recruited and DNA was extracted from the blood, buccal cells and saliva samples provided by each participant. Taqman assay real-time qPCR and ddPCR were conducted to quantify AMY1 gene copy numbers. Statistical analysis was carried out to determine the difference in AMY1 gene copy number between the different biological specimens and different assay methods. Results We found significant within-individual difference (p<0.01) in AMY1 gene copy number between different biological samples as determined by qPCR. However, there was no significant within-individual difference in AMY1 gene copy number between different biological samples as determined by ddPCR. We also found that AMY1 gene copy number of blood samples were comparable between qPCR and ddPCR, while there is a significant difference (p<0.01) between AMY1 gene copy numbers measured by qPCR and ddPCR for both buccal swab and saliva samples. Conclusions Despite buccal cells and saliva samples being possible sources of DNA, it is pertinent that ddPCR or a single biological sample, preferably blood sample, be used for determining highly polymorphic gene copy numbers like AMY1, due to the large within-individual variability between different biological samples if real time qPCR is employed.
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Affiliation(s)
- Delicia Shu Qin Ooi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Verena Ming Hui Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
| | - Siong Gim Ong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Yiong Huak Chan
- Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chew Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Yung Seng Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
- * E-mail:
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Arredouani A, Stocchero M, Culeddu N, Moustafa JES, Tichet J, Balkau B, Brousseau T, Manca M, Falchi M. Metabolomic Profile of Low-Copy Number Carriers at the Salivary α-Amylase Gene Suggests a Metabolic Shift Toward Lipid-Based Energy Production. Diabetes 2016; 65:3362-3368. [PMID: 27436124 DOI: 10.2337/db16-0315] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/06/2016] [Indexed: 12/28/2022]
Abstract
Low serum salivary amylase levels have been associated with a range of metabolic abnormalities, including obesity and insulin resistance. We recently suggested that a low copy number at the AMY1 gene, associated with lower enzyme levels, also increases susceptibility to obesity. To advance our understanding of the effect of AMY1 copy number variation on metabolism, we compared the metabolomic signatures of high- and low-copy number carriers. We analyzed, using mass spectrometry and nuclear magnetic resonance (NMR), the sera of healthy normal-weight women carrying either low-AMY1 copies (LAs: four or fewer copies; n = 50) or high-AMY1 copies (HAs: eight or more copies; n = 50). Best-fitting multivariate models (empirical P < 1 × 10-3) of mass spectrometry and NMR data were concordant in showing differences in lipid metabolism between the two groups. In particular, LA carriers showed lower levels of long- and medium-chain fatty acids, and higher levels of dicarboxylic fatty acids and 2-hydroxybutyrate (a known marker of glucose malabsorption). Taken together, these observations suggest increased metabolic reliance on fatty acids in LA carriers through β- and ω-oxidation and reduced cellular glucose uptake with consequent diversion of acetyl-CoA into ketogenesis. Our observations are in line with previously reported delayed glucose uptake in LA carriers after starch consumption. Further functional studies are needed to extrapolate from our findings to implications for biochemical pathways.
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Affiliation(s)
- Abdelilah Arredouani
- Hamad Ben Khalifa University, Qatar Biomedical Research Institute, Diabetes Research Centre, Qatar Foundation, Doha, Qatar
- Department of Genomics of Common Disease, Imperial College London, U.K
| | | | - Nicola Culeddu
- Istituto di Chimica Biomolecolare, Laboratory of Nuclear Magnetic Resonance, Consiglio Nazionale delle Ricerche, Sassari, Italy
| | - Julia El-Sayed Moustafa
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital Campus, London, U.K
| | | | - Jean Tichet
- Institut Inter-Régional Pour la Santé, La Riche, France
| | - Beverley Balkau
- Centre de Recherche en Epidémiologie et Santé des Populations, Le Centre de Recherche en Epidémiologie et Santé des Populations, INSERM U1018, Renal and Cardiovascular Epidemiology, Villejuif, France
- Universities Versailles-St. Quentin and Paris-Sud, UMRS 1018, Villejuif, France
| | - Thierry Brousseau
- UF8832, Biochimie Automatisée, Pôle de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Marco Manca
- Experimental Vascular Pathology, Cardiovascular Research Institute Maastricht, University of Maastricht, Maastricht, the Netherlands
- Accelerators & Technology Sector, CERN, Geneva, Switzerland
| | - Mario Falchi
- Department of Genomics of Common Disease, Imperial College London, U.K.
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital Campus, London, U.K
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18
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Affiliation(s)
- Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
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19
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Choi YJ, Nam YS, Yun JM, Park JH, Cho BL, Son HY, Kim JI, Yun JW. Association between salivary amylase (AMY1) gene copy numbers and insulin resistance in asymptomatic Korean men. Diabet Med 2015; 32:1588-95. [PMID: 25996848 DOI: 10.1111/dme.12808] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 12/13/2022]
Abstract
AIMS Salivary amylase gene (AMY1) copy number variations (CNVs) correlate directly with salivary amylase activity and serum amylase levels. Previously, individuals with high AMY1 CNVs exhibited low postprandial glucose levels and postprandial early insulin surge, suggesting that high AMY1 gene copy numbers may play a role in lowering the risk of insulin resistance. METHODS We verified the relationship between AMY1 CNVs and homeostatic model assessment-insulin resistance (HOMA-IR) in a cohort of 1257 Korean men aged 20-65 years who visited two medical centres for regular health check-ups, and in subgroups of current smokers and regular alcohol drinkers. Individuals with fasting plasma glucose levels > 10.0 mmol/l, HbA1c ≥ 64 mmol/mol (8.0%) or who used oral hypoglycaemic agents or insulin were excluded. RESULTS AMY1 CNVs correlated negatively with HOMA-IR even after adjusting for covariates (e.g. BMI, systolic blood pressure, triacylglycerol, alcohol consumption, smoking and physical activity). When the participants were divided according to current smoking and alcohol consumption habits, negative correlations between AMY1 CNVs and HOMA-IR were more evident among non-smokers and regular drinkers and were non-significant among smokers and non-regular drinkers. CONCLUSIONS Low AMY1 CNVs correlated with high insulin resistance in asymptomatic Korean men, and such a relationship presented differently according to the status of smoking and alcohol consumption.
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Affiliation(s)
- Y-J Choi
- Department of Family Medicine, Seoul National University Hospital, Seoul, Korea
| | - Y-S Nam
- Department of Family Medicine, Seoul National University Hospital, Seoul, Korea
| | - J M Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, Korea
| | - J H Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, Korea
| | - B L Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, Korea
| | - H-Y Son
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - J I Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - J W Yun
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
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Mejía-Benítez MA, Bonnefond A, Yengo L, Huyvaert M, Dechaume A, Peralta-Romero J, Klünder-Klünder M, García Mena J, El-Sayed Moustafa JS, Falchi M, Cruz M, Froguel P. Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children. Diabetologia 2015; 58:290-4. [PMID: 25394825 DOI: 10.1007/s00125-014-3441-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/29/2014] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Childhood obesity is a major public health problem in Mexico, affecting one in every three children. Genome-wide association studies identified genetic variants associated with childhood obesity, but a large missing heritability remains to be elucidated. We have recently shown a strong association between a highly polymorphic copy number variant encompassing the salivary amylase gene (AMY1 also known as AMY1A) and obesity in European and Asian adults. In the present study, we aimed to evaluate the association between AMY1 copy number and obesity in Mexican children. METHODS We evaluated the number of AMY1 copies in 597 Mexican children (293 obese children and 304 normal weight controls) through highly sensitive digital PCR. The effect of AMY1 copy number on obesity status was assessed using a logistic regression model adjusted for age and sex. RESULTS We identified a marked effect of AMY1 copy number on reduced risk of obesity (OR per estimated copy 0.84, with the number of copies ranging from one to 16 in this population; p = 4.25 × 10(-6)). The global association between AMY1 copy number and reduced risk of obesity seemed to be mostly driven by the contribution of the highest AMY1 copy number. Strikingly, all children with >10 AMY1 copies were normal weight controls. CONCLUSIONS/INTERPRETATION Salivary amylase initiates the digestion of dietary starch, which is highly consumed in Mexico. Our current study suggests putative benefits of high number of AMY1 copies (and related production of salivary amylase) on energy metabolism in Mexican children.
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Affiliation(s)
- María A Mejía-Benítez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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Yang ZM, Lin J, Chen LH, Zhang M, Chen WW, Yang XR. The roles of AMY1 copies and protein expression in human salivary α-amylase activity. Physiol Behav 2015; 138:173-8. [PMID: 25446200 DOI: 10.1016/j.physbeh.2014.10.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/21/2014] [Accepted: 10/27/2014] [Indexed: 11/11/2022]
Abstract
Salivary α-amylase (sAA) activity has been extensively investigated in nutrition and psychology. But few studies were performed to assess the role played by sAA gene (AMY1) copies and protein expression in basal and stimulus-induced sAA activity. The sAA activity, amount and AMY1 copy number were determined from 184 saliva samples pre- and post-citric acid stimulation. Our findings showed that citric acid could induce significant increase in sAA activity, total sAA amount, and glycosylated sAA amount, among which the glycosylated sAA amount had the largest response. The correlation analysis showed that AMY1 copy number, total sAA amount and AMY1 copy number×total sAA amount had significantly positive and successively increasing correlations with sAA activity in unstimulated and stimulated saliva, respectively, and furthermore, we observed higher correlations in unstimulated saliva when compared with the corresponding correlations in stimulated saliva. We also observed significant correlations between glycosylated sAA amount and sAA activity in unstimulated and stimulated saliva, respectively. Interestingly, the correlations were higher in stimulated saliva than in unstimulated saliva, and the correlations between glycosylated sAA amount and sAA activity were higher than that of between total sAA amount and sAA activity in stimulated saliva. Moreover, total sAA amount ratio and glycosylated sAA amount ratio showed significantly positive correlation with sAA activity ratio. AMY1 copy number had no correlation with sAA activity ratio. These findings suggested that AMY1 copy number and sAA amount played crucial roles in sAA activity; however, the roles were attenuated after stimulation due to fortified release of glycosylated sAA.
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Affiliation(s)
- Ze-Min Yang
- School of Basic Courses, Guangdong Pharmaceutical University, China.
| | - Jing Lin
- School of Basic Courses, Guangdong Pharmaceutical University, China
| | - Long-Hui Chen
- Pi-Wei Institute, Guangzhou University of Chinese Medicine, China
| | - Min Zhang
- Pediatrics of Traditional Chinese Medicine, Haizhu Maternal and Child Health Hospital, China
| | - Wei-Wen Chen
- Pi-Wei Institute, Guangzhou University of Chinese Medicine, China
| | - Xiao-Rong Yang
- Clinical Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, China
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Kawauchi D, Robinson G, Uziel T, Gibson P, Rehg J, Gao C, Finkelstein D, Qu C, Pounds S, Ellison DW, Gilbertson RJ, Roussel MF. A mouse model of the most aggressive subgroup of human medulloblastoma. Cancer Cell 2012; 21:168-80. [PMID: 22340591 PMCID: PMC3285412 DOI: 10.1016/j.ccr.2011.12.023] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 11/02/2011] [Accepted: 12/20/2011] [Indexed: 12/23/2022]
Abstract
Medulloblastomas that display a large cell/anaplastic morphology and overexpress the cellular c-MYC gene are highly aggressive and carry a very poor prognosis. This so-called MYC-subgroup differs in its histopathology, gene expression profile, and clinical behavior from other forms of medulloblastoma. We generated a mouse model of MYC-subgroup medulloblastoma by transducing Trp53-null cerebellar progenitor cells with Myc. The cardinal features of these mouse medulloblastomas closely mimic those of human MYC-subgroup tumors and significantly differ from mouse models of the Sonic-Hedgehog- and WNT-disease subgroups. This mouse model should significantly accelerate understanding and treatment of the most aggressive form of medulloblastoma and infers distinct roles for MYC and MYCN in tumorigenesis.
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Affiliation(s)
- Daisuke Kawauchi
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Giles Robinson
- Department of Oncology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Tamar Uziel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Paul Gibson
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Jerold Rehg
- Department of Pathology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Cuilan Gao
- Department of Biostatistics, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - David Finkelstein
- Department of Biostatistics, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Chunxu Qu
- Department of Information Sciences, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - David W. Ellison
- Department of Pathology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Richard J. Gilbertson
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
- Richard J. Gilbertson, MD, PhD, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA. Tel: 901-595-3913; FAX: 901-595-2270;
| | - Martine F. Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262, Danny Thomas Place, Memphis, Tennessee, 38105, USA
- to whom requests should be submitted: Martine F. Roussel, PhD, Department of Tumor Cell Biology, Danny Thomas Research Center, DTRC 5006C, 262, Danny Thomas Place, Memphis, Tennessee, 38105. Tel: 901-595-3481; FAX: 901-595-2381;
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