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Karvela M, Golden CT, Bell N, Martin-Li S, Bedzo-Nutakor J, Bosnic N, DeBeaudrap P, de Mateo-Lopez S, Alajrami A, Qin Y, Eze M, Hon TK, Simón-Sánchez J, Sahoo R, Pearson-Stuttard J, Soon-Shiong P, Toumazou C, Oliver N. Assessment of the impact of a personalised nutrition intervention in impaired glucose regulation over 26 weeks: a randomised controlled trial. Sci Rep 2024; 14:5428. [PMID: 38443427 PMCID: PMC10914757 DOI: 10.1038/s41598-024-55105-6] [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: 10/30/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Dietary interventions can reduce progression to type 2 diabetes mellitus (T2DM) in people with non-diabetic hyperglycaemia. In this study we aimed to determine the impact of a DNA-personalised nutrition intervention in people with non-diabetic hyperglycaemia over 26 weeks. ASPIRE-DNA was a pilot study. Participants were randomised into three arms to receive either (i) Control arm: standard care (NICE guidelines) (n = 51), (ii) Intervention arm: DNA-personalised dietary advice (n = 50), or (iii) Exploratory arm: DNA-personalised dietary advice via a self-guided app and wearable device (n = 46). The primary outcome was the difference in fasting plasma glucose (FPG) between the Control and Intervention arms after 6 weeks. 180 people were recruited, of whom 148 people were randomised, mean age of 59 years (SD = 11), 69% of whom were female. There was no significant difference in the FPG change between the Control and Intervention arms at 6 weeks (- 0.13 mmol/L (95% CI [- 0.37, 0.11]), p = 0.29), however, we found that a DNA-personalised dietary intervention led to a significant reduction of FPG at 26 weeks in the Intervention arm when compared to standard care (- 0.019 (SD = 0.008), p = 0.01), as did the Exploratory arm (- 0.021 (SD = 0.008), p = 0.006). HbA1c at 26 weeks was significantly reduced in the Intervention arm when compared to standard care (- 0.038 (SD = 0.018), p = 0.04). There was some evidence suggesting prevention of progression to T2DM across the groups that received a DNA-based intervention (p = 0.06). Personalisation of dietary advice based on DNA did not result in glucose changes within the first 6 weeks but was associated with significant reduction of FPG and HbA1c at 26 weeks when compared to standard care. The DNA-based diet was effective regardless of intervention type, though results should be interpreted with caution due to the low sample size. These findings suggest that DNA-based dietary guidance is an effective intervention compared to standard care, but there is still a minimum timeframe of adherence to the intervention before changes in clinical outcomes become apparent.Trial Registration: www.clinicaltrials.gov.uk Ref: NCT03702465.
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Affiliation(s)
- Maria Karvela
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Caroline T Golden
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Nikeysha Bell
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Stephanie Martin-Li
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Judith Bedzo-Nutakor
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Natalie Bosnic
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Pierre DeBeaudrap
- Centre for Population and Development (Ceped), French National Institute for Sustainable Development (IRD), and Paris University, Inserm ERL, 1244, Paris, France
| | - Sara de Mateo-Lopez
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Ahmed Alajrami
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Yun Qin
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Maria Eze
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Tsz-Kin Hon
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Javier Simón-Sánchez
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | - Rashmita Sahoo
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK
| | | | - Patrick Soon-Shiong
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Christofer Toumazou
- Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, UK.
- DnaNudge Ltd, Scale Space, Imperial College London, White City Campus, London, UK.
| | - Nick Oliver
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
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Ramos-Lopez O. Genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus. World J Diabetes 2024; 15:142-153. [PMID: 38464367 PMCID: PMC10921165 DOI: 10.4239/wjd.v15.i2.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Globally, type 2 diabetes mellitus (T2DM) is one of the most common metabolic disorders. T2DM physiopathology is influenced by complex interrelationships between genetic, metabolic and lifestyle factors (including diet), which differ between populations and geographic regions. In fact, excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM, whereas habitual intakes of plant-based healthy diets usually exert a protective effect. Moreover, genomic studies have allowed the characterization of sequence DNA variants across the human genome, some of which may affect gene expression and protein functions relevant for glucose homeostasis. This comprehensive literature review covers the impact of gene-diet interactions on T2DM susceptibility and disease progression, some of which have demonstrated a value as biomarkers of personal responses to certain nutritional interventions. Also, novel genotype-based dietary strategies have been developed for improving T2DM control in comparison to general lifestyle recommendations. Furthermore, progresses in other omics areas (epigenomics, metagenomics, proteomics, and metabolomics) are improving current understanding of genetic insights in T2DM clinical outcomes. Although more investigation is still needed, the analysis of the genetic make-up may help to decipher new paradigms in the pathophysiology of T2DM as well as offer further opportunities to personalize the screening, prevention, diagnosis, management, and prognosis of T2DM through precision nutrition.
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Affiliation(s)
- Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana 22390, Baja California, Mexico
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3
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Ozcelik F, Arslan S, Ozguc Caliskan B, Kardas F, Ozkul Y, Dundar M. PPM1K defects cause mild maple syrup urine disease: The second case in the literature. Am J Med Genet A 2023; 191:1360-1365. [PMID: 36706222 DOI: 10.1002/ajmg.a.63129] [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: 10/09/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/29/2023]
Abstract
Maple syrup urine disease (MSUD) is an inborn error of metabolism caused by the insufficient catabolism of branched-chain amino acids. BCKDHA, BCKDHB, DBT, and DLD encode the subunits of the branched-chain α-ketoacid dehydrogenase complex, which is responsible for the catabolism of these amino acids. Biallelic pathogenic variants in BCKDHA, BCKDHB, or DBT are characteristic of MSUD. In addition, a patient with a PPM1K defect was previously reported. PPM1K dephosphorylates and activates the enzyme complex. We report a patient with MSUD with mild findings and elevated BCAA levels carrying a novel homozygous start-loss variant in PPM1K. Our study offers further evidence that PPM1K variants cause mild MSUD.
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Affiliation(s)
- Firat Ozcelik
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | - Sezai Arslan
- Division of Nutrition and Metabolism, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | | | - Fatih Kardas
- Division of Nutrition and Metabolism, Department of Pediatrics, Erciyes University, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University, Kayseri, Turkey
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4
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Lutter D, Sachs S, Walter M, Kerege A, Perreault L, Kahn DE, Wolide AD, Kleinert M, Bergman BC, Hofmann SM. Skeletal muscle and intermuscular adipose tissue gene expression profiling identifies new biomarkers with prognostic significance for insulin resistance progression and intervention response. Diabetologia 2023; 66:873-883. [PMID: 36790478 PMCID: PMC10036433 DOI: 10.1007/s00125-023-05874-y] [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: 07/15/2022] [Accepted: 12/06/2022] [Indexed: 02/16/2023]
Abstract
AIMS/HYPOTHESIS Although insulin resistance often leads to type 2 diabetes mellitus, its early stages are often unrecognised, thus reducing the probability of successful prevention and intervention. Moreover, treatment efficacy is affected by the genetics of the individual. We used gene expression profiles from a cross-sectional study to identify potential candidate genes for the prediction of diabetes risk and intervention response. METHODS Using a multivariate regression model, we linked gene expression profiles of human skeletal muscle and intermuscular adipose tissue (IMAT) to fasting glucose levels and glucose infusion rate. Based on the expression patterns of the top predictive genes, we characterised and compared individual gene expression with clinical classifications using k-nearest neighbour clustering. The predictive potential of the candidate genes identified was validated using muscle gene expression data from a longitudinal intervention study. RESULTS We found that genes with a strong association with clinical measures clustered into three distinct expression patterns. Their predictive values for insulin resistance varied substantially between skeletal muscle and IMAT. Moreover, we discovered that individual gene expression-based classifications may differ from classifications based predominantly on clinical variables, indicating that participant stratification may be imprecise if only clinical variables are used for classification. Of the 15 top candidate genes, ST3GAL2, AASS, ARF1 and the transcription factor SIN3A are novel candidates for predicting a refined diabetes risk and intervention response. CONCLUSION/INTERPRETATION Our results confirm that disease progression and successful intervention depend on individual gene expression states. We anticipate that our findings may lead to a better understanding and prediction of individual diabetes risk and may help to develop individualised intervention strategies.
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Affiliation(s)
- Dominik Lutter
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Stephan Sachs
- Institute for Diabetes and Regeneration (IDR-H), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marc Walter
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Diabetes and Regeneration (IDR-H), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anna Kerege
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Leigh Perreault
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Darcy E Kahn
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Amare D Wolide
- Computational Discovery Research, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Metabolic Diseases, Department of Medicine, Technische Universität München (TUM), Munich, Germany
| | - Maximilian Kleinert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Drug Development Unit, Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Group of Muscle Physiology and Metabolism, German Institute of Human Nutrition, Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Bryan C Bergman
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susanna M Hofmann
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Institute for Diabetes and Regeneration (IDR-H), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
- Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany.
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5
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Dimou A, Tsimihodimos V, Bairaktari E. The Critical Role of the Branched Chain Amino Acids (BCAAs) Catabolism-Regulating Enzymes, Branched-Chain Aminotransferase (BCAT) and Branched-Chain α-Keto Acid Dehydrogenase (BCKD), in Human Pathophysiology. Int J Mol Sci 2022; 23:ijms23074022. [PMID: 35409380 PMCID: PMC8999875 DOI: 10.3390/ijms23074022] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 12/26/2022] Open
Abstract
Branched chain amino acids (BCAAs), leucine, isoleucine and valine, are essential amino acids widely studied for their crucial role in the regulation of protein synthesis mainly through the activation of the mTOR signaling pathway and their emerging recognition as players in the regulation of various physiological and metabolic processes, such as glucose homeostasis. BCAA supplementation is primarily used as a beneficial nutritional intervention in chronic liver and kidney disease as well as in muscle wasting disorders. However, downregulated/upregulated plasma BCAAs and their defective catabolism in various tissues, mainly due to altered enzymatic activity of the first two enzymes in their catabolic pathway, BCAA aminotransferase (BCAT) and branched-chain α-keto acid dehydrogenase (BCKD), have been investigated in many nutritional and disease states. The current review focused on the underlying mechanisms of altered BCAA catabolism and its contribution to the pathogenesis of a numerous pathological conditions such as diabetes, heart failure and cancer. In addition, we summarize findings that indicate that the recovery of the dysregulated BCAA catabolism may be associated with an improved outcome and the prevention of serious disease complications.
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Affiliation(s)
- Aikaterini Dimou
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
| | - Vasilis Tsimihodimos
- Department of Internal Medicine, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
| | - Eleni Bairaktari
- Laboratory of Clinical Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
- Correspondence: ; Tel.: +30-26510-07620
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6
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Gkouskou KK, Grammatikopoulou MG, Lazou E, Sanoudou D, Goulis DG, Eliopoulos AG. Genetically-Guided Medical Nutrition Therapy in Type 2 Diabetes Mellitus and Pre-diabetes: A Series of n-of-1 Superiority Trials. Front Nutr 2022; 9:772243. [PMID: 35265654 PMCID: PMC8899711 DOI: 10.3389/fnut.2022.772243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a heterogeneous metabolic disorder of multifactorial etiology that includes genetic and dietary influences. By addressing the latter, medical nutrition therapy (MNT) contributes to the management of T2DM or pre-diabetes toward achieving glycaemic control and improved insulin sensitivity. However, the clinical outcomes of MNT vary and may further benefit from personalized nutritional plans that take into consideration genetic variations associated with individual responses to macronutrients. The aim of the present series of n-of-1 trials was to assess the effects of genetically-guided vs. conventional MNT on patients with pre-diabetes or T2DM. A quasi-experimental, cross-over design was adopted in three Caucasian adult men with either diagnosis. Complete diet, bioclinical and anthropometric assessment was performed and a conventional MNT, based on the clinical practice guidelines was applied for 8 weeks. After a week of “wash-out,” a precision MNT was prescribed for an additional 8-week period, based on the genetic characteristics of each patient. Outcomes of interest included changes in body weight (BW), fasting plasma glucose (FPG), and blood pressure (BP). Collectively, the trials indicated improvements in BW, FPG, BP, and glycosylated hemoglobin (HbA1c) following the genetically-guided precision MNT intervention. Moreover, both patients with pre-diabetes experienced remission of the condition. We conclude that improved BW loss and glycemic control can be achieved in patients with pre-diabetes/T2DM, by coupling MNT to their genetic makeup, guiding optimal diet, macronutrient composition, exercise and oral nutrient supplementation in a personalized manner.
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Affiliation(s)
- Kalliopi K Gkouskou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Embiodiagnostics Biology Research Company, Heraklion, Greece
| | - Maria G Grammatikopoulou
- Unit of Reproductive Endocrinology, First Department of Obstetrics and Gynecology, Faculty of Health Sciences, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Nutritional Sciences and Dietetics, Faculty of Health Sciences, International Hellenic University, Thessaloniki, Greece
| | - Evgenia Lazou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Despina Sanoudou
- Clinical Genomics and Pharmacogenomics Unit, Fourth Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dimitrios G Goulis
- Unit of Reproductive Endocrinology, First Department of Obstetrics and Gynecology, Faculty of Health Sciences, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aristides G Eliopoulos
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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7
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Three Different Genetic Risk Scores Based on Fatty Liver Index, Magnetic Resonance Imaging and Lipidomic for a Nutrigenetic Personalized Management of NAFLD: The Fatty Liver in Obesity Study. Diagnostics (Basel) 2021; 11:diagnostics11061083. [PMID: 34199237 PMCID: PMC8231822 DOI: 10.3390/diagnostics11061083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) affects 25% of the global population. The pathogenesis of NAFLD is complex; available data reveal that genetics and ascribed interactions with environmental factors may play an important role in the development of this morbid condition. The purpose of this investigation was to assess genetic and non-genetic determinants putatively involved in the onset and progression of NAFLD after a 6-month weight loss nutritional treatment. A group of 86 overweight/obese subjects with NAFLD from the Fatty Liver in Obesity (FLiO) study were enrolled and metabolically evaluated at baseline and after 6 months. A pre-designed panel of 95 genetic variants related to obesity and weight loss was applied and analyzed. Three genetic risk scores (GRS) concerning the improvement on hepatic health evaluated by minimally invasive methods such as the fatty liver index (FLI) (GRSFLI), lipidomic-OWLiver®-test (GRSOWL) and magnetic resonance imaging (MRI) (GRSMRI), were derived by adding the risk alleles genotypes. Body composition, liver injury-related markers and dietary intake were also monitored. Overall, 23 SNPs were independently associated with the change in FLI, 16 SNPs with OWLiver®-test and 8 SNPs with MRI, which were specific for every diagnosis tool. After adjusting for gender, age and other related predictors (insulin resistance, inflammatory biomarkers and dietary intake at baseline) the calculated GRSFLI, GRSOWL and GRSMRI were major contributors of the improvement in hepatic status. Thus, fitted linear regression models showed a variance of 53% (adj. R2 = 0.53) in hepatic functionality (FLI), 16% (adj. R2 = 0.16) in lipidomic metabolism (OWLiver®-test) and 34% (adj. R2 = 0.34) in liver fat content (MRI). These results demonstrate that three different genetic scores can be useful for the personalized management of NAFLD, whose treatment must rely on specific dietary recommendations guided by the measurement of specific genetic biomarkers.
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8
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Fan J, Wang X, Xiao R, Li M. Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data. PLoS Genet 2021; 17:e1009080. [PMID: 33661921 PMCID: PMC7963069 DOI: 10.1371/journal.pgen.1009080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/16/2021] [Accepted: 02/09/2021] [Indexed: 12/27/2022] Open
Abstract
Allelic expression imbalance (AEI), quantified by the relative expression of two alleles of a gene in a diploid organism, can help explain phenotypic variations among individuals. Traditional methods detect AEI using bulk RNA sequencing (RNA-seq) data, a data type that averages out cell-to-cell heterogeneity in gene expression across cell types. Since the patterns of AEI may vary across different cell types, it is desirable to study AEI in a cell-type-specific manner. Although this can be achieved by single-cell RNA sequencing (scRNA-seq), it requires full-length transcript to be sequenced in single cells of a large number of individuals, which are still cost prohibitive to generate. To overcome this limitation and utilize the vast amount of existing disease relevant bulk tissue RNA-seq data, we developed BSCET, which enables the characterization of cell-type-specific AEI in bulk RNA-seq data by integrating cell type composition information inferred from a small set of scRNA-seq samples, possibly obtained from an external dataset. By modeling covariate effect, BSCET can also detect genes whose cell-type-specific AEI are associated with clinical factors. Through extensive benchmark evaluations, we show that BSCET correctly detected genes with cell-type-specific AEI and differential AEI between healthy and diseased samples using bulk RNA-seq data. BSCET also uncovered cell-type-specific AEIs that were missed in bulk data analysis when the directions of AEI are opposite in different cell types. We further applied BSCET to two pancreatic islet bulk RNA-seq datasets, and detected genes showing cell-type-specific AEI that are related to the progression of type 2 diabetes. Since bulk RNA-seq data are easily accessible, BSCET provides a convenient tool to integrate information from scRNA-seq data to gain insight on AEI with cell type resolution. Results from such analysis will advance our understanding of cell type contributions in human diseases. Detection of allelic expression imbalance (AEI), a phenomenon where the two alleles of a gene differ in their expression magnitude, is a key step towards the understanding of phenotypic variations among individuals. Existing methods detect AEI using bulk RNA sequencing (RNA-seq) data and ignore AEI variations among different cell types. Although single-cell RNA sequencing (scRNA-seq) has enabled the characterization of cell-to-cell heterogeneity in gene expression, the high costs have limited its application in AEI analysis. To overcome this limitation, we developed BSCET to characterize cell-type-specific AEI using the widely available bulk RNA-seq data by integrating cell-type composition information inferred from scRNA-seq samples. Since the degree of AEI may vary with disease phenotypes, we further extended BSCET to detect genes whose cell-type-specific AEIs are associated with clinical factors. Through extensive benchmark evaluations and analyses of two pancreatic islet bulk RNA-seq datasets, we demonstrated BSCET’s ability to refine bulk-level AEI to cell-type resolution, and to identify genes whose cell-type-specific AEIs are associated with the progression of type 2 diabetes. With the vast amount of easily accessible bulk RNA-seq data, we believe BSCET will be a valuable tool for elucidating cell type contributions in human diseases.
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Affiliation(s)
- Jiaxin Fan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Xuran Wang
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rui Xiao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RX); (ML)
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RX); (ML)
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9
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Sievenpiper JL. Low-carbohydrate diets and cardiometabolic health: the importance of carbohydrate quality over quantity. Nutr Rev 2021; 78:69-77. [PMID: 32728757 DOI: 10.1093/nutrit/nuz082] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Carbohydrates are increasingly being implicated in the epidemics of obesity, diabetes, and their downstream cardiometabolic diseases. The "carbohydrate-insulin model" has been proposed to explain this role of carbohydrates. It posits that a high intake of carbohydrate induces endocrine deregulation marked by hyperinsulinemia, leading to energy partitioning with increased storage of energy in adipose tissue resulting in adaptive increases in food intake and decreases in energy expenditure. Whether all carbohydrate foods under real-world feeding conditions directly contribute to weight gain and its complications or whether this model can explain these clinical phenomena requires close inspection. The aim of this review is to assess the evidence for the role of carbohydrate quantity vs quality in cardiometabolic health. Although the clinical investigations of the "carbohydrate-insulin model" have shown the requisite decreases in insulin secretion and increases in fat oxidation, there has been a failure to achieve the expected fat loss under low-carbohydrate feeding. Systematic reviews with pairwise and network meta-analyses of the best available evidence have failed to show the superiority of low-carbohydrate diets on long-term clinical weight loss outcomes or that all sources of carbohydrate behave equally. High-carbohydrate diets that emphasize foods containing important nutrients and substances, including high-quality carbohydrate such as whole grains (especially oats and barley), pulses, or fruit; low glycemic index and load; or high fiber (especially viscous fiber sources) decrease intermediate cardiometabolic risk factors in randomized trials and are associated with weight loss and decreased incidence of diabetes, cardiovascular disease, and cardiovascular mortality in prospective cohort studies. The evidence for sugars as a marker of carbohydrate quality appears to be highly dependent on energy control (comparator) and food source (matrix), with sugar-sweetened beverages providing excess energy showing evidence of harm, and with high-quality carbohydrate food sources containing sugars such as fruit, 100% fruit juice, yogurt, and breakfast cereals showing evidence of benefit in energy-matched substitutions for refined starches (low-quality carbohydrate food sources). These data reflect the current shift in dietary guidance that allows for flexibility in the proportion of macronutrients (including carbohydrates) in the diet, with a focus on quality over quantity and dietary patterns over single nutrients.
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Affiliation(s)
- John L Sievenpiper
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto; and with the Division of Endocrinology & Metabolism; the Department of Medicine; the Li Ka Shing Knowledge Institute; and the Toronto 3D Knowledge Synthesis & Clinical Trials Unit, Clinical Nutrition and Risk Factor Modification Centre; St. Michael's Hospital, Toronto, Ontario, Canada
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10
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Gkouskou K, Lazou E, Skoufas E, Eliopoulos AG. Genetically Guided Mediterranean Diet for the Personalized Nutritional Management of Type 2 Diabetes Mellitus. Nutrients 2021; 13:nu13020355. [PMID: 33503923 PMCID: PMC7912380 DOI: 10.3390/nu13020355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The current consensus for the prevention and management of type 2 diabetes mellitus (T2DM) is that high-quality diets and adherence to a healthy lifestyle provide significant health benefits. Remarkably, however, there is little agreement on the proportions of macronutrients in the diet that should be recommended to people suffering from pre-diabetes or T2DM. We herein discuss emerging evidence that underscores the importance of gene-diet interactions in the improvement of glycemic biomarkers in T2DM. We propose that we can achieve better glycemic control in T2DM patients by coupling Mediterranean diets to genetic information as a predictor for optimal diet macronutrient composition in a personalized manner. We provide evidence to support this concept by presenting a case study of a T2DM patient who achieved rapid glycemic control when adhered to a personalized, genetically-guided Mediterranean Diet.
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Affiliation(s)
- Kalliopi Gkouskou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Mikras Asias 75, 11527 Athens, Greece; (E.L.); (E.S.)
- Embiodiagnostics Biology Research Company, 71305 Heraklion, Greece
- Correspondence: (K.G.); (A.G.E.); Tel.: +30-2107462356 (A.G.E.)
| | - Evgenia Lazou
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Mikras Asias 75, 11527 Athens, Greece; (E.L.); (E.S.)
| | - Efstathios Skoufas
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Mikras Asias 75, 11527 Athens, Greece; (E.L.); (E.S.)
| | - Aristides G. Eliopoulos
- Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Mikras Asias 75, 11527 Athens, Greece; (E.L.); (E.S.)
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Correspondence: (K.G.); (A.G.E.); Tel.: +30-2107462356 (A.G.E.)
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11
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Castro-Barquero S, Ruiz-León AM, Sierra-Pérez M, Estruch R, Casas R. Dietary Strategies for Metabolic Syndrome: A Comprehensive Review. Nutrients 2020; 12:nu12102983. [PMID: 33003472 PMCID: PMC7600579 DOI: 10.3390/nu12102983] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
Metabolic syndrome is a cluster of metabolic risk factors, characterized by abdominal obesity, dyslipidemia, low levels of high-density lipoprotein cholesterol (HDL-c), hypertension, and insulin resistance. Lifestyle modifications, especially dietary habits, are the main therapeutic strategy for the treatment and management of metabolic syndrome, but the most effective dietary pattern for its management has not been established. Specific dietary modifications, such as improving the quality of the foods or changing macronutrient distribution, showed beneficial effects on metabolic syndrome conditions and individual parameters. On comparing low-fat and restricted diets, the scientific evidence supports the use of the Mediterranean Dietary Approaches to Stop Hypertension (DASH) diet intervention as the new paradigm for metabolic syndrome prevention and treatment. The nutritional distribution and quality of these healthy diets allows health professionals to provide easy-to-follow dietary advice without the need for restricted diets. Nonetheless, energy-restricted dietary patterns and improvements in physical activity are crucial to improve the metabolic disturbances observed in metabolic syndrome patients.
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Affiliation(s)
- Sara Castro-Barquero
- Department of Medicine, Faculty of Medicine and Life Sciences, University of Barcelona, 08036 Barcelona, Spain; (S.C.-B.); (M.S.-P.); (R.E.)
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red, Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana María Ruiz-León
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red, Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria Sierra-Pérez
- Department of Medicine, Faculty of Medicine and Life Sciences, University of Barcelona, 08036 Barcelona, Spain; (S.C.-B.); (M.S.-P.); (R.E.)
| | - Ramon Estruch
- Department of Medicine, Faculty of Medicine and Life Sciences, University of Barcelona, 08036 Barcelona, Spain; (S.C.-B.); (M.S.-P.); (R.E.)
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red, Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosa Casas
- Department of Medicine, Faculty of Medicine and Life Sciences, University of Barcelona, 08036 Barcelona, Spain; (S.C.-B.); (M.S.-P.); (R.E.)
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red, Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-932275400; Fax: +34-932272907
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12
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Associations between Genotype-Diet Interactions and Weight Loss-A Systematic Review. Nutrients 2020; 12:nu12092891. [PMID: 32971836 PMCID: PMC7551578 DOI: 10.3390/nu12092891] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Studies on the interactions between single nucleotide polymorphisms (SNPs) and macronutrient consumption on weight loss are rare and heterogeneous. This review aimed to conduct a systematic literature search to investigate genotype–diet interactions on weight loss. Four databases were searched with keywords on genetics, nutrition, and weight loss (PROSPERO: CRD42019139571). Articles in languages other than English and trials investigating special groups (e.g., pregnant women, people with severe diseases) were excluded. In total, 20,542 articles were identified, and, after removal of duplicates and further screening steps, 27 articles were included. Eligible articles were based on eight trials with 91 SNPs in 63 genetic loci. All articles examined the interaction between genotype and macronutrients (carbohydrates, fat, protein) on the extent of weight loss. However, in most cases, the interaction results were not significant and represented single findings that lack replication. The publications most frequently analyzed genotype–fat intake interaction on weight loss. Since the majority of interactions were not significant and not replicated, a final evaluation of the genotype–diet interactions on weight loss was not possible. In conclusion, no evidence was found that genotype–diet interaction is a main determinant of obesity treatment success, but this needs to be addressed in future studies.
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13
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Barrea L, Annunziata G, Bordoni L, Muscogiuri G, Colao A, Savastano S. Nutrigenetics-personalized nutrition in obesity and cardiovascular diseases. INTERNATIONAL JOURNAL OF OBESITY SUPPLEMENTS 2020; 10:1-13. [PMID: 32714508 PMCID: PMC7371677 DOI: 10.1038/s41367-020-0014-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epidemiological data support the view that both obesity and cardiovascular diseases (CVD) account for a high proportion of total morbidity and mortality in adults throughout the world. Obesity and CVD have complex interplay mechanisms of genetic and environmental factors, including diet. Nutrition is an environmental factor and it has a predominant and recognizable role in health management and in the prevention of obesity and obesity-related diseases, including CVD. However, there is a marked variation in CVD in patients with obesity and the same dietary pattern. The different genetic polymorphisms could explain this variation, which leads to the emergence of the concept of nutrigenetics. Nutritional genomics or nutrigenetics is the science that studies and characterizes gene variants associated with differential response to specific nutrients and relating this variation to various diseases, such as CVD related to obesity. Thus, the personalized nutrition recommendations, based on the knowledge of an individual's genetic background, might improve the outcomes of a specific dietary intervention and represent a new dietary approach to improve health, reducing obesity and CVD. Given these premises, it is intuitive to suppose that the elucidation of diet and gene interactions could support more specific and effective dietary interventions in both obesity and CVD prevention through personalized nutrition based on nutrigenetics. This review aims to briefly summarize the role of the most important genes associated with obesity and CVD and to clarify the knowledge about the relation between nutrition and gene expression and the role of the main nutrition-related genes in obesity and CVD.
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Affiliation(s)
- Luigi Barrea
- Dipartimento di Medicina Clinica e Chirurgia, Unit of Endocrinology, Federico II University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giuseppe Annunziata
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Laura Bordoni
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, 62032 Camerino, Macerata Italy
| | - Giovanna Muscogiuri
- Dipartimento di Medicina Clinica e Chirurgia, Unit of Endocrinology, Federico II University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Annamaria Colao
- Dipartimento di Medicina Clinica e Chirurgia, Unit of Endocrinology, Federico II University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Silvia Savastano
- Dipartimento di Medicina Clinica e Chirurgia, Unit of Endocrinology, Federico II University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
| | - on behalf of Obesity Programs of nutrition, Education, Research and Assessment (OPERA) Group
- Dipartimento di Medicina Clinica e Chirurgia, Unit of Endocrinology, Federico II University Medical School of Naples, Via Sergio Pansini 5, 80131 Naples, Italy
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, 62032 Camerino, Macerata Italy
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14
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Distinct genetic subtypes of adiposity and glycemic changes in response to weight-loss diet intervention: the POUNDS Lost trial. Eur J Nutr 2020; 60:249-258. [PMID: 32274554 DOI: 10.1007/s00394-020-02244-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
PURPOSE Obesity is a heterogeneous condition and distinct adiposity subtypes may differentially affect type 2 diabetes risk. We assessed relations between genetically determined subtypes of adiposity and changes in glycemic traits in a dietary intervention trial. METHODS The four genetic subtypes of adiposity including waist-hip ratio-increase only (WHRonly+), body mass index-increase only (BMIonly+), WHR-increase and BMI-increase (BMI+WHR+), and WHR-decrease and BMI-increase (BMI+WHR-) were assessed by polygenetic scores (PGSs), calculated based on 159 single nucleotide polymorphisms related to BMI and/or WHR. We examined the associations between the four PGSs and changes in fasting glucose, insulin, β-cell function (HOMA-B) and insulin resistance (HOMA-IR) in 692 overweight participants (84% white Americans) who were randomly assigned to one of four weight-loss diets in a 2-year intervention trial. RESULTS Higher BMI+WHR-PGS was associated with a greater decrease in 2-year changes in waist circumference in white participants (P = 0.002). We also found significant interactions between WHRonly+PGS and dietary protein in 2-year changes in fasting glucose and HOMA-B (P = 0.0007 and < 0.0001, respectively). When consuming an average-protein diet, participants with higher WHRonly+PGS showed less increased fasting glucose (β = - 0.46, P = 0.006) and less reduction in HOMA-B (β = 0.02, P = 0.005) compared with lower WHRonly+PGS. Conversely, eating high-protein diet was associated with less decreased HOMA-B among individuals with lower than higher WHRonly+PGS (β = - 0.02, P = 0.006). CONCLUSIONS Distinct genetically determined adiposity subtypes may differentially modify the effects of weight-loss diets on improving glucose metabolism in white Americans. This trial was registered at clinicaltrials.gov as NCT00072995.
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15
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Interplay of an Obesity-Based Genetic Risk Score with Dietary and Endocrine Factors on Insulin Resistance. Nutrients 2019; 12:nu12010033. [PMID: 31877696 PMCID: PMC7019905 DOI: 10.3390/nu12010033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/17/2022] Open
Abstract
This study aimed to nutrigenetically screen gene-diet and gene-metabolic interactions influencing insulin resistance (IR) phenotypes. A total of 232 obese or overweight adults were categorized by IR status: non-IR (HOMA-IR (homeostatic model assessment - insulin resistance) index ≤ 2.5) and IR (HOMA-IR index > 2.5). A weighted genetic risk score (wGRS) was constructed using 95 single nucleotide polymorphisms related to energy homeostasis, which were genotyped by a next generation sequencing system. Body composition, the metabolic profile and lifestyle variables were evaluated, where individuals with IR showed worse metabolic outcomes. Overall, 16 obesity-predisposing genetic variants were associated with IR (p < 0.10 in the multivariate model). The wGRS strongly associated with the HOMA-IR index (adj. R squared = 0.2705, p < 0.0001). Moreover, the wGRS positively interacted with dietary intake of cholesterol (P int. = 0.002), and with serum concentrations of C-reactive protein (P int. = 0.008) regarding IR status, whereas a negative interaction was found regarding adiponectin blood levels (P int. = 0.006). In conclusion, this study suggests that interactions between an adiposity-based wGRS with nutritional and metabolic/endocrine features influence IR phenotypes, which could facilitate the prescription of personalized nutrition recommendations for precision prevention and management of IR and diabetes.
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16
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Zhou M, Shao J, Wu CY, Shu L, Dong W, Liu Y, Chen M, Wynn RM, Wang J, Wang J, Gui WJ, Qi X, Lusis AJ, Li Z, Wang W, Ning G, Yang X, Chuang DT, Wang Y, Sun H. Targeting BCAA Catabolism to Treat Obesity-Associated Insulin Resistance. Diabetes 2019; 68:1730-1746. [PMID: 31167878 PMCID: PMC6702639 DOI: 10.2337/db18-0927] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Recent studies implicate a strong association between elevated plasma branched-chain amino acids (BCAAs) and insulin resistance (IR). However, a causal relationship and whether interrupted BCAA homeostasis can serve as a therapeutic target for diabetes remain to be established experimentally. In this study, unbiased integrative pathway analyses identified a unique genetic link between obesity-associated IR and BCAA catabolic gene expression at the pathway level in human and mouse populations. In genetically obese (ob/ob) mice, rate-limiting branched-chain α-keto acid (BCKA) dehydrogenase deficiency (i.e., BCAA and BCKA accumulation), a metabolic feature, accompanied the systemic suppression of BCAA catabolic genes. Restoring BCAA catabolic flux with a pharmacological inhibitor of BCKA dehydrogenase kinase (BCKDK) ( a suppressor of BCKA dehydrogenase) reduced the abundance of BCAA and BCKA and markedly attenuated IR in ob/ob mice. Similar outcomes were achieved by reducing protein (and thus BCAA) intake, whereas increasing BCAA intake did the opposite; this corroborates the pathogenic roles of BCAAs and BCKAs in IR in ob/ob mice. Like BCAAs, BCKAs also suppressed insulin signaling via activation of mammalian target of rapamycin complex 1. Finally, the small-molecule BCKDK inhibitor significantly attenuated IR in high-fat diet-induced obese mice. Collectively, these data demonstrate a pivotal causal role of a BCAA catabolic defect and elevated abundance of BCAAs and BCKAs in obesity-associated IR and provide proof-of-concept evidence for the therapeutic validity of manipulating BCAA metabolism for treating diabetes.
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Affiliation(s)
- Meiyi Zhou
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Shao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng-Yang Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Weibing Dong
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxia Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengping Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiqiu Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Jun Gui
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiangbing Qi
- Chemistry Center, National Institute of Biological Science, Beijing, China
| | - Aldons J Lusis
- Departments of Medicine, Microbiology, and Human Genetics, University of California at Los Angeles, Los Angeles, CA
| | - Zhaoping Li
- Department of Clinical Nutrition, University of California at Los Angeles, Los Angeles, CA
| | - Weiqing Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Haipeng Sun
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
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17
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Haydar S, Grigorescu F, Vintilă M, Cogne Y, Lautier C, Tutuncu Y, Brun JF, Robine JM, Pugeat M, Normand C, Poucheret P, Gheorghiu ML, Georgescu C, Badiu C, Băculescu N, Renard E, Ylli D, Badiou S, Sutra T, Cristol JP, Mercier J, Gomis R, Macias JM, Litvinov S, Khusnutdinova E, Poiana C, Pasquali R, Lauro D, Sesti G, Prudente S, Trischitta V, Tsatsoulis A, Abdelhak S, Barakat A, Zenati A, Ylli A, Satman I, Kanninen T, Rinato Y, Missoni S. Fine-scale haplotype mapping of MUT, AACS, SLC6A15 and PRKCA genes indicates association with insulin resistance of metabolic syndrome and relationship with branched chain amino acid metabolism or regulation. PLoS One 2019; 14:e0214122. [PMID: 30913280 PMCID: PMC6435171 DOI: 10.1371/journal.pone.0214122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/07/2019] [Indexed: 12/15/2022] Open
Abstract
Branched chain amino acids (BCAA) are essential elements of the human diet, which display increased plasma levels in obesity and regained particular interest as potential biomarkers for development of diabetes. To define determinants of insulin resistance (IR) we investigated 73 genes involved in BCAA metabolism or regulation by fine-scale haplotype mapping in two European populations with metabolic syndrome. French and Romanians (n = 465) were genotyped for SNPs (Affymetrix) and enriched by imputation (BEAGLE 4.1) at 1000 genome project density. Initial association hits detected by sliding window were refined (HAPLOVIEW 3.1 and PHASE 2.1) and correlated to homeostasis model assessment (HOMAIR) index, in vivo insulin sensitivity (SI) and BCAA plasma levels (ANOVA). Four genomic regions were associated with IR located downstream of MUT, AACS, SLC6A15 and PRKCA genes (P between 9.3 and 3.7 x 10-5). Inferred haplotypes up to 13 SNPs length were associated with IR (e.g. MUT gene with P < 4.9 x 10-5; Bonferroni 1.3 x 10-3) and synergistic to HOMAIR. SNPs in the same regions were also associated with one order of magnitude lower P values (e.g. rs20167284 in the MUT gene with P < 1.27 x 10-4) and replicated in Mediterranean samples (n = 832). In French, influential haplotypes (OR > 2.0) were correlated with in vivo insulin sensitivity (1/SI) except for SLC6A15 gene. Association of these genes with BCAA levels was variable, but influential haplotypes confirmed implication of MUT from BCAA metabolism as well as a role of regulatory genes (AACS and PRKCA) and suggested potential changes in transcriptional activity. These data drive attention towards new regulatory regions involved in IR in relation with BCAA and show the ability of haplotypes in phased DNA to detect signals complimentary to SNPs, which may be useful in designing genetic markers for clinical applications in ethnic populations.
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Affiliation(s)
- Sara Haydar
- University of Montpellier, UMR204 NUTRIPASS (IRD, UM, SupAgro), Montpellier, France
| | - Florin Grigorescu
- University of Montpellier, UMR204 NUTRIPASS (IRD, UM, SupAgro), Montpellier, France
| | - Mădălina Vintilă
- Universitatea de Medicina si Farmacie Carol Davila, Department of Endocrinology, Bucharest, Romania
| | - Yannick Cogne
- University of Montpellier, UMR204 NUTRIPASS (IRD, UM, SupAgro), Montpellier, France
| | - Corinne Lautier
- University of Montpellier, UMR204 NUTRIPASS (IRD, UM, SupAgro), Montpellier, France
| | - Yildiz Tutuncu
- Istanbul University, Department of Internal Medicine, Istanbul, Turkey
| | - Jean Frederic Brun
- University of Montpellier, PhyMedExp, INSERM, CNRS, Department of Biochemistry and Hormonology, CHRU Montpellier, Montpellier, France
| | | | - Michel Pugeat
- University Claude Bernard de Lyon 1, Lyon-Bron, France
| | - Christophe Normand
- University of Montpellier, UMR204 NUTRIPASS (IRD, UM, SupAgro), Montpellier, France
| | | | - Monica Livia Gheorghiu
- Universitatea de Medicina si Farmacie Carol Davila, Department of Endocrinology, Bucharest, Romania
| | - Carmen Georgescu
- Universitatea de Medicina si Farmacie Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Corin Badiu
- Universitatea de Medicina si Farmacie Carol Davila, Department of Endocrinology, Bucharest, Romania
| | - Nicoleta Băculescu
- Universitatea de Medicina si Farmacie Carol Davila, Department of Endocrinology, Bucharest, Romania
| | - Eric Renard
- Centre Hospitalier Regional Universitaire de Montpellier, Departement d'Endocrinologie, Diabète, Nutrition, Hôpital Lapeyronie, Montpellier, France
| | - Dorina Ylli
- Mjekesise University of Tirana, Tirana, Albania
| | - Stephanie Badiou
- University of Montpellier, PhyMedExp, INSERM, CNRS, Department of Biochemistry and Hormonology, CHRU Montpellier, Montpellier, France
| | - Thibault Sutra
- University of Montpellier, PhyMedExp, INSERM, CNRS, Department of Biochemistry and Hormonology, CHRU Montpellier, Montpellier, France
| | - Jean Paul Cristol
- University of Montpellier, PhyMedExp, INSERM, CNRS, Department of Biochemistry and Hormonology, CHRU Montpellier, Montpellier, France
| | - Jacques Mercier
- University of Montpellier, PhyMedExp, INSERM, CNRS, Department of Biochemistry and Hormonology, CHRU Montpellier, Montpellier, France
| | - Ramon Gomis
- Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | | | | | | | - Catalina Poiana
- Universitatea de Medicina si Farmacie Carol Davila, Department of Endocrinology, Bucharest, Romania
| | - Renato Pasquali
- University Alma Mater Studiorum, Division of Endocrinology, Bologna, Italy
| | - Davide Lauro
- Universita degli Studi di Roma Tor Vergata, Roma, Italy
| | - Giorgio Sesti
- University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Sabrina Prudente
- Scientific Institute Casa Sollievo della Sofferenza, San Giovani Rotondo, Italy
| | - Vincenzo Trischitta
- Scientific Institute Casa Sollievo della Sofferenza, San Giovani Rotondo, Italy
| | - Agathocles Tsatsoulis
- University of Ioannina School of Medicine, Department of Endocrinology, Ioannina, Greece
| | - Sonia Abdelhak
- Institut Pasteur de Tunis, Laboratory of Biomedical Genomics and Oncogenetics, Tunis, Tunisia
| | | | - Akila Zenati
- Universite d'Alger, CHU Bab-El-Oued, Alger, Algeria
| | - Agron Ylli
- Mjekesise University of Tirana, Tirana, Albania
| | - Ilhan Satman
- Istanbul University, Department of Internal Medicine, Istanbul, Turkey
| | | | | | - Sasa Missoni
- Institute for Anthropological Research, Zagreb, Croatia
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