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Pérez-Gutiérrez AM, Carmona R, Loucera C, Cervilla JA, Gutiérrez B, Molina E, Lopez-Lopez D, Pérez-Florido J, Zarza-Rebollo JA, López-Isac E, Dopazo J, Martínez-González LJ, Rivera M. Mutational landscape of risk variants in comorbid depression and obesity: a next-generation sequencing approach. Mol Psychiatry 2024:10.1038/s41380-024-02609-2. [PMID: 38806690 DOI: 10.1038/s41380-024-02609-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
Major depression (MD) and obesity are complex genetic disorders that are frequently comorbid. However, the study of both diseases concurrently remains poorly addressed and therefore the underlying genetic mechanisms involved in this comorbidity remain largely unknown. Here we examine the contribution of common and rare variants to this comorbidity through a next-generation sequencing (NGS) approach. Specific genomic regions of interest in MD and obesity were sequenced in a group of 654 individuals from the PISMA-ep epidemiological study. We obtained variants across the entire frequency spectrum and assessed their association with comorbid MD and obesity, both at variant and gene levels. We identified 55 independent common variants and a burden of rare variants in 4 genes (PARK2, FGF21, HIST1H3D and RSRC1) associated with the comorbid phenotype. Follow-up analyses revealed significantly enriched gene-sets associated with biological processes and pathways involved in metabolic dysregulation, hormone signaling and cell cycle regulation. Our results suggest that, while risk variants specific to the comorbid phenotype have been identified, the genes functionally impacted by the risk variants share cell biological processes and signaling pathways with MD and obesity phenotypes separately. To the best of our knowledge, this is the first study involving a targeted sequencing approach toward the study of the comorbid MD and obesity. The framework presented here allowed a deep characterization of the genetics of the co-occurring MD and obesity, revealing insights into the mutational and functional profile that underlies this comorbidity and contributing to a better understanding of the relationship between these two disabling disorders.
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Affiliation(s)
- Ana M Pérez-Gutiérrez
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Rosario Carmona
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Jorge A Cervilla
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Psychiatry, Faculty of Medicine, University of Granada, Granada, Spain
| | - Blanca Gutiérrez
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Psychiatry, Faculty of Medicine, University of Granada, Granada, Spain
| | - Esther Molina
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
- Department of Nursing, Faculty of Health Sciences, University of Granada, Granada, Spain
| | - Daniel Lopez-Lopez
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Javier Pérez-Florido
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Juan Antonio Zarza-Rebollo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Elena López-Isac
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
| | - Luis Javier Martínez-González
- Genomics Unit, Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Margarita Rivera
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain.
- Institute of Neurosciences "Federico Olóriz", Biomedical Research Center (CIBM), University of Granada, Granada, Spain.
- Instituto de Investigación Biosanitaria, Ibs Granada, Granada, Spain.
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Mayman N, Wei J, Cai S, Soman R, Raynes H, La Vega-Talbott M, He C, Naidich T, Raju GP, Kathiresu Nageshwaran S. Case report: A novel biallelic FTO variant causing multisystem anomalies with severe epilepsy, widening the spectrum of FTO syndrome. SAGE Open Med Case Rep 2023; 11:2050313X231188883. [PMID: 37529081 PMCID: PMC10387762 DOI: 10.1177/2050313x231188883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
The fat mass and obesity-associated gene (FTO) codes for a DNA/RNA demethylase. Pathological variants in this gene are rare, with only three reports in the literature, all with mutations in the catalytic domain. We report the first biallelic human variant in fat mass and obesity-associated gene (c.287G>C, p.Arg96Pro/R96P) outside the catalytic site, causing numerous abnormalities across multiple organ systems, affecting respiratory, cardiovascular, and neurological function. Biochemical assays of cells with the patient's variant were performed to further quantify the effect of the variant on function. Loss-of-function resulting from the patient's R96P missense variant was demonstrated with in vitro biochemical characterization of demethylase activity, resulting in a 90% reduction in function of the fat mass and obesity-associated protein compared to wild-type. Our findings demonstrate a novel fat mass and obesity-associated gene non-catalytic site variant with a unique patient phenotype of bilateral multifocal epilepsy and multisystem congenital anomalies.
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Affiliation(s)
- Naomi Mayman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jiangbo Wei
- Department of Chemistry, University of Chicago, IL, USA
| | - Shangjun Cai
- Department of Chemistry, University of Chicago, IL, USA
| | - Rohan Soman
- Weill Cornell/Rockefeller/Sloan Kettering MD/PhD Tri-institutional Program, New York, NY, USA
| | - Hillary Raynes
- Department of Pediatrics, Mount Sinai, New York, NY, USA
- Department of Neurology, Mount Sinai, New York, NY, USA
| | - Maite La Vega-Talbott
- Department of Pediatrics, Mount Sinai, New York, NY, USA
- Department of Neurology, Mount Sinai, New York, NY, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, IL, USA
| | | | - G. Praveen Raju
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Mount Sinai, New York, NY, USA
- Department of Neurology, Mount Sinai, New York, NY, USA
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Li J, Wu N, Yang Y, Zhai X, Yuan F, Zhang F, Yu N, Li D, Wang R, Wang J, Zhang L, Shi Y, He G, Liu B. Unique genetic variants of lean nonalcoholic fatty liver disease: a retrospective cohort study. BMC Endocr Disord 2023; 23:11. [PMID: 36627697 PMCID: PMC9830772 DOI: 10.1186/s12902-022-01234-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/30/2022] [Indexed: 01/12/2023] Open
Abstract
We investigated the prevalence and clinical metabolic characteristics of lean nonalcoholic fatty liver disease (NAFLD) in an elderly Chinese population and assessed the relevance of lipid markers and genetic variation. All 5,338 community subjects underwent detailed clinical and laboratory examinations and were divided into three groups: lean (Body mass index (BMI) < 23 kg/m2, n = 2,012), overweight (BMI = 23-24.9 kg/m2, n = 1,354), and obese (BMI ≥ 25 kg/m2, n = 1,972). Single nucleotide polymorphisms were selected based on those reported in previous NAFLD or obesity genome-wide association studies. The frequencies of alleles and genotypes were calculated and statistically analyzed with Pearson's χ2 tests. One-way ANCOVA was used to test the association between positive SNPs and metabolic parameters in lean NAFLD individuals. Our results showed that the C allele frequency of rs2279026, the G allele of rs2279028, the C allele of rs780093, and the C allele frequency of rs1260326 were higher in obese NAFLD than in lean NAFLD (P < 0.05). In addition, we observed an association between the CC of rs1421085, TT of rs3751812, AA of rs8050136, and AA of rs9939609 genotypes in the FTO gene and low-density lipoprotein levels (P < 0.05). In conclusion, our findings provide a unique perspective on the prevalence, genetic characteristics, and metabolic profile of NAFLD in older lean individuals in China. This is the first study to examine the association between genetic variants in the FTO, TFAP2B and GCKR genes and NAFLD in a cohort of lean individuals.
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Affiliation(s)
- Jie Li
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Na Wu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Yukun Yang
- Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiangyu Zhai
- Graduate School of Sport Sciences, Waseda University, Saitama, Japan
| | - Fan Yuan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Fengwei Zhang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ning Yu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dong Li
- Zhangjiang Community Health Service Center of Pudong New District, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jianying Wang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lei Zhang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China.
| | - Baocheng Liu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, School of Public Health, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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Souza Junior MLF, de Sousa JV, Guerreiro JF. Analysis of coding variants in the human FTO gene from the gnomAD database. PLoS One 2022; 17:e0248610. [PMID: 34990463 PMCID: PMC8735611 DOI: 10.1371/journal.pone.0248610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the first intron of the FTO gene reported in 2007 continue to be the known variants with the greatest effect on adiposity in different human populations. Coding variants in the FTO gene, on the other hand, have been little explored, although data from complete sequencing of the exomes of various populations are available in public databases and provide an excellent opportunity to investigate potential functional variants in FTO. In this context, this study aimed to track nonsynonymous variants in the exons of the FTO gene in different population groups employing the gnomAD database and analyze the potential functional impact of these variants on the FTO protein using five publicly available pathogenicity prediction programs. The findings revealed 345 rare mutations, of which 321 are missense (93%), 19 are stop gained (5.6%) and five mutations are located in the splice region (1.4%). Of these, 134 (38.8%) were classified as pathogenic, 144 (41.7%) as benign and 67 (19.5%) as unknown. The available data, however, suggest that these variants are probably not associated with BMI and obesity, but instead, with other diseases. Functional studies are, therefore, required to identify the role of these variants in disease genesis.
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Affiliation(s)
| | | | - João Farias Guerreiro
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
- * E-mail:
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Relier S, Rivals E, David A. The multifaceted functions of the Fat mass and Obesity-associated protein (FTO) in normal and cancer cells. RNA Biol 2021; 19:132-142. [PMID: 35067178 PMCID: PMC8786332 DOI: 10.1080/15476286.2021.2016203] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/02/2021] [Indexed: 01/25/2023] Open
Abstract
The last decade has seen mRNA modification emerge as a new layer of gene expression regulation. The Fat mass and obesity-associated protein (FTO) was the first identified eraser of N6-methyladenosine (m6A) adducts, the most widespread modification in eukaryotic messenger RNA. This discovery, of a reversible and dynamic RNA modification, aided by recent technological advances in RNA mass spectrometry and sequencing has led to the birth of the field of epitranscriptomics. FTO crystallized much of the attention of epitranscriptomics researchers and resulted in the publication of numerous, yet contradictory, studies describing the regulatory role of FTO in gene expression and central biological processes. These incongruities may be explained by a wide spectrum of FTO substrates and RNA sequence preferences: FTO binds multiple RNA species (mRNA, snRNA and tRNA) and can demethylate internal m6A in mRNA and snRNA, N6,2'-O-dimethyladenosine (m6Am) adjacent to the mRNA cap, and N1-methyladenosine (m1A) in tRNA. Here, we review current knowledge related to FTO function in healthy and cancer cells. In particular, we emphasize the divergent role(s) attributed to FTO in different tissues and subcellular and molecular contexts.
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Affiliation(s)
| | - Eric Rivals
- LIRMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Alexandre David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
- IRMB-PPC, Univ Montpellier, INSERM, CHU Montpellier, CNRS, Montpellier, France
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Kumar SU, Rajan B, Kumar DT, Cathryn RH, Das S, Zayed H, Emmanuel Jebaraj Walter C, Ramanathan G, Priya Doss C G. Comparison of potential inhibitors and targeting fat mass and obesity-associated protein causing diabesity through docking and molecular dynamics strategies. J Cell Biochem 2021; 122:1625-1638. [PMID: 34289159 DOI: 10.1002/jcb.30109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have identified an association between polymorphisms in the FTO gene and obesity. The FTO: rs9939609, an intronic variant, is considered a risk allele for developing diabesity in homozygous and heterozygous forms. This study aimed to investigate the molecular structure of the available inhibitors specific to the FTO mutations along with the rs9939609 variant. We identified the best-suited inhibitor molecules for each mutant type containing the rs9939609 risk allele. Missense mutations unique to obesity and containing the risk allele of rs9939609 were retrieved from dbSNP for this study. Further stability testing for the mutations were carried out using DynaMut and iStable tools. Three mutations (G187A, M223V, and I492V) were highly destabilizing the FTO structure. These three mutants and native FTO were docked with each of the nine-inhibitor molecules collected from literature studies with the help of PyRx and AutoDock. Further structural behavior of the mutants and native FTO were identified with molecular dynamics simulations and MM-PBSA analyses, along with the 19complex inhibitor compound. We found the compound 19complex exhibited better binding interactions and is the top candidate inhibitor for the M223V and I492V mutants. This study provided insights into the structural changes caused due to mutations in FTO, and the binding mechanism of the inhibitor molecules. It could aid in developing antiobesity drugs for treating patients with mutations and risk alleles predisposing to obesity.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Bithia Rajan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - D Thirumal Kumar
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, India
| | - R Hephzibah Cathryn
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Samprita Das
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Charles Emmanuel Jebaraj Walter
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, Tamil Nadu, India
| | - Gnanasambandan Ramanathan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.,Department of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - George Priya Doss C
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Chauhdary Z, Rehman K, Akash MSH. The composite alliance of FTO locus with obesity-related genetic variants. Clin Exp Pharmacol Physiol 2021; 48:954-965. [PMID: 33735452 DOI: 10.1111/1440-1681.13498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Obesity has become a genuine global pandemic due to lifestyle and environmental modifications, and is associated with chronic lethal comorbidities. Various environmental factors such as lack of physical activity due to modernization and higher intake of energy-rich diets are primary obesogenic factors in pathogenesis of obesity. Genome-wide association study has identified the crucial role of FTO (fat mass and obesity) in human obesity. A bunch of SNPs in the first intron of FTO has been identified and subsequently correlated to body mass index and body composition. Findings of in silico, in vitro, and in vivo studies have manifested the robust role of FTO in regulation of energy expenditure and food consumption. Numerous studies have highlighted the mechanistic pathways behind the concomitant functions of FTO in adipogenesis and body size. Current investigation has also revealed the link of FTO neighbouring genes i.e., RPGRIP1L, IRX3 and IRX5 and epigenetic factors with obesity phenotypes. The motive behind this review is to cite the consequences of FTO on obesity vulnerability.
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Affiliation(s)
- Zunera Chauhdary
- Department of Pharmaceutical Chemistry, Government College University, Faisalabad, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, University of Agriculture, Faisalabad, Pakistan
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KANLI A, KASAP M, AKPINAR G, YANAR S. Fat Mass and Obesity Associated (FTO) Protein Ekspresyonunun Neden Olduğu SH-SY5Y Hücrelerinin Proteomunda Meydana Gelen Değişiklikler, FTO Proteininin Çok Yönlü Özellikleri Ortaya Çıkarır. KOCAELI ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2020. [DOI: 10.30934/kusbed.666084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Mosca P, Leheup B, Dreumont N. Nutrigenomics and RNA methylation: Role of micronutrients. Biochimie 2019; 164:53-59. [DOI: 10.1016/j.biochi.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/06/2019] [Indexed: 12/24/2022]
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10
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Waheed SO, Ramanan R, Chaturvedi SS, Ainsley J, Evison M, Ames JM, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Conformational flexibility influences structure-function relationships in nucleic acid N-methyl demethylases. Org Biomol Chem 2019; 17:2223-2231. [PMID: 30720838 DOI: 10.1039/c9ob00162j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
N-Methylation of DNA/RNA bases can be regulatory or damaging and is linked to diseases including cancer and genetic disorders. Bacterial AlkB and human FTO are DNA/RNA demethylases belonging to the Fe(ii) and 2-oxoglutarate oxygenase superfamily. Modelling studies reveal conformational dynamics influence structure-function relationships of AlkB and FTO, e.g. why 1-methyladenine is a better substrate for AlkB than 6-methyladenine. Simulations show that the flexibility of the double stranded DNA substrate in AlkB influences correlated motions, including between the core jelly-roll fold and an active site loop involved in substrate binding. The FTO N- and C-terminal domains move in respect to one another in a manner likely important for substrate binding. Substitutions, including clinically observed ones, influencing catalysis contribute to the network of correlated motions in AlkB and FTO. Overall, the calculations highlight the importance of the overall protein environment and its flexibility to the geometry of the reactant complexes.
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Affiliation(s)
- Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, USA.
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Beysel S, Eyerci N, Ulubay M, Caliskan M, Kizilgul M, Hafızoğlu M, Cakal E. Maternal genetic contribution to pre-pregnancy obesity, gestational weight gain, and gestational diabetes mellitus. Diabetol Metab Syndr 2019; 11:37. [PMID: 31114636 PMCID: PMC6518700 DOI: 10.1186/s13098-019-0434-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION Pre-pregnancy obesity, gestational diabetes mellitus (GDM), and gestational weight gain (GWG) are associated with each other. This is the first study to investigate whether genetic variants were associated with having GDM, and whether genetic variants-related GDM were associated with adiposity including pre-pregnancy obesity and excessive GWG in Turkish women. PATIENTS AND METHODS Women with GDM (n = 160) and without GDM (n = 145) were included in case-controlled study. Genotyping of the HNF1A gene (p.I27L rs1169288, p.98V rs1800574, p.S487N rs2464196), the VDR gene (p.BsmI rs1544410, p.ApaI rs7975232, p.TaqI rs731236, p.FokI rs2228570), and FTO gene (rs9939609) SNPs were performed by using RT-PCR. RESULTS The FTO AA genotype was associated with an increased risk of having GDM (AA vs. AT + TT, 24.4% vs. 12.4%, OR = 2.27, 95% CI [1.23-4.19], p = 0.007). The HNF1A p.I27L GT/TT genotype was associated with increased GDM risk (GT + TT vs. GG-wild, 79.4% vs. 65.5%, OR = 2.02, 95% CI 1.21-3.38], p = 0.007). However, all VDR gene SNPs and the HNF1A p.A98V, p.S487N were not associated with having GDM (p > 0.05). The FTO AA genotype was associated with an increased risk for pre-pregnancy overweight/obesity (OR = 1.43, 95% CI [1.25-3.4], p = 0.035), but not associated with excessive GWG after adjusting for pre-pregnancy weight (p > 0.05). Pre-pregnancy weight, weight at delivery, and GWG did not differ in both VDR and HNF1A gene carriers (p > 0.05). HOMA-IR and HbA1c were increased in both p.I27L TT and FTO AA genotype carriers (p < 0.05). CONCLUSION The adiposity-related gene FTO is associated with GDM by the effect of FTO on pre-pregnancy obesity. The diabetes-related p.I27L gene is associated with GDM by increasing insulin resistance.
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Affiliation(s)
- Selvihan Beysel
- Department of Endocrinology and Metabolism, Ankara Diskapi Yildirim Beyazit Teaching and Training Research Hospital, Ankara, Turkey
- Department of Medical Biology, Baskent University, Ankara, Turkey
- Department of Endocrinology and Metabolism, Afyonkarahisar Saglik Bilimleri University, Afyon, Turkey
| | - Nilnur Eyerci
- Department of Genetic Research, Ankara Diskapi Yildirim Beyazit Teaching and Training Research Hospital, Ankara, Turkey
| | - Mustafa Ulubay
- Department of Obstetrics and Gynecology, Gulhane School of Medicine, Ankara, Turkey
| | - Mustafa Caliskan
- Department of Endocrinology and Metabolism, Ankara Diskapi Yildirim Beyazit Teaching and Training Research Hospital, Ankara, Turkey
| | - Muhammed Kizilgul
- Department of Endocrinology and Metabolism, Ankara Diskapi Yildirim Beyazit Teaching and Training Research Hospital, Ankara, Turkey
| | - Merve Hafızoğlu
- Department of İnternal Medicine, Afyonkarahisar Saglik Bilimleri University, Afyon, Turkey
| | - Erman Cakal
- Department of Endocrinology and Metabolism, Ankara Diskapi Yildirim Beyazit Teaching and Training Research Hospital, Ankara, Turkey
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Fat Mass and Obesity Associated ( FTO) Gene and Hepatic Glucose and Lipid Metabolism. Nutrients 2018; 10:nu10111600. [PMID: 30388740 PMCID: PMC6266206 DOI: 10.3390/nu10111600] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/20/2018] [Accepted: 10/20/2018] [Indexed: 01/17/2023] Open
Abstract
Common genetic variants of the fat mass and obesity associated (FTO) gene are strongly associated with obesity and type 2 diabetes. FTO is ubiquitously expressed. Earlier studies have focused on the role of hypothalamic FTO in the regulation of metabolism. However, recent studies suggest that expression of hepatic FTO is regulated by metabolic signals, such as nutrients and hormones, and altered FTO levels in the liver affect glucose and lipid metabolism. This review outlines recent findings on hepatic FTO in the regulation of metabolism, with particular focus on hepatic glucose and lipid metabolism. It is proposed that abnormal activity of hepatic signaling pathways involving FTO links metabolic impairments such as obesity, type 2 diabetes and nonalcoholic fatty liver disease (NAFLD). Therefore, a better understanding of these pathways may lead to therapeutic approaches to treat these metabolic diseases by targeting hepatic FTO. The overall goal of this review is to place FTO within the context of hepatic regulation of metabolism.
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Martin Carli JF, LeDuc CA, Zhang Y, Stratigopoulos G, Leibel RL. FTO mediates cell-autonomous effects on adipogenesis and adipocyte lipid content by regulating gene expression via 6mA DNA modifications. J Lipid Res 2018; 59:1446-1460. [PMID: 29934339 DOI: 10.1194/jlr.m085555] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/30/2018] [Indexed: 12/18/2022] Open
Abstract
SNPs in the first intron of α-ketoglutarate-dependent dioxygenase (FTO) convey effects on adiposity by mechanisms that remain unclear, but appear to include modulation of expression of FTO itself, as well as other genes in cisFTO expression is lower in fibroblasts and iPSC-derived neurons of individuals segregating for FTO obesity risk alleles. We employed in vitro adipogenesis models to investigate the molecular mechanisms by which Fto affects adipocyte development and function. Fto expression was upregulated during adipogenesis, and was required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreased the number of 3T3-L1 cells that differentiated into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming was conveyed, in part, by modulation of CCAAT enhancer binding protein (C/ebp)β-regulated transcription. We found that Fto also affected Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele.
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Affiliation(s)
| | | | - Yiying Zhang
- Columbia University Medical Center, New York, NY 10032
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14
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Howard SR, Guasti L, Poliandri A, David A, Cabrera CP, Barnes MR, Wehkalampi K, O’Rahilly S, Aiken CE, Coll AP, Ma M, Rimmington D, Yeo GSH, Dunkel L. Contributions of Function-Altering Variants in Genes Implicated in Pubertal Timing and Body Mass for Self-Limited Delayed Puberty. J Clin Endocrinol Metab 2018; 103:649-659. [PMID: 29161441 PMCID: PMC5800831 DOI: 10.1210/jc.2017-02147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/13/2017] [Indexed: 11/19/2022]
Abstract
CONTEXT Self-limited delayed puberty (DP) is often associated with a delay in physical maturation, but although highly heritable the causal genetic factors remain elusive. Genome-wide association studies of the timing of puberty have identified multiple loci for age at menarche in females and voice break in males, particularly in pathways controlling energy balance. OBJECTIVE/MAIN OUTCOME MEASURES We sought to assess the contribution of rare variants in such genes to the phenotype of familial DP. DESIGN/PATIENTS We performed whole-exome sequencing in 67 pedigrees (125 individuals with DP and 35 unaffected controls) from our unique cohort of familial self-limited DP. Using a whole-exome sequencing filtering pipeline one candidate gene [fat mass and obesity-associated gene (FTO)] was identified. In silico, in vitro, and mouse model studies were performed to investigate the pathogenicity of FTO variants and timing of puberty in FTO+/- mice. RESULTS We identified potentially pathogenic, rare variants in genes in linkage disequilibrium with genome-wide association studies of age at menarche loci in 283 genes. Of these, five genes were implicated in the control of body mass. After filtering for segregation with trait, one candidate, FTO, was retained. Two FTO variants, found in 14 affected individuals from three families, were also associated with leanness in these patients with DP. One variant (p.Leu44Val) demonstrated altered demethylation activity of the mutant protein in vitro. Fto+/- mice displayed a significantly delayed timing of pubertal onset (P < 0.05). CONCLUSIONS Mutations in genes implicated in body mass and timing of puberty in the general population may contribute to the pathogenesis of self-limited DP.
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Affiliation(s)
- Sasha R. Howard
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Leonardo Guasti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Ariel Poliandri
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Alessia David
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claudia P. Cabrera
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Michael R. Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Karoliina Wehkalampi
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, FIN-00029 HUS Helsinki, Finland
| | - Stephen O’Rahilly
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Catherine E. Aiken
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge CB2 0SW, United Kingdom
- National Institute for Health Research, Cambridge Comprehensive Biomedical Research Centre, Cambridge CB2 0SW, United Kingdom
| | - Anthony P. Coll
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Marcella Ma
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Debra Rimmington
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Giles S. H. Yeo
- University of Cambridge Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Leo Dunkel
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom
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15
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Giuranna J, Diebels I, Hinney A. Polygene Varianten und Epigenetik bei Adipositas. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0156-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zusammenfassung
Hintergrund
Durch molekulargenetische Analysen wurde eine kleine Anzahl von Hauptgenen identifiziert, die Übergewicht (Body Mass Index, BMI ≥ 25 kg/m2) und Adipositas (BMI ≥ 30 kg/m2) bei Menschen mit bedingen können. Die zugrunde liegenden Mutationen sind selten. Die genetische Prädisposition zur Entwicklung einer Adipositas ist meist polygener Natur.
Ziel der Arbeit
Darstellung der polygenen Formen der Adipositas und epigenetischer Befunde.
Material und Methoden
Literaturübersicht.
Ergebnisse und Diskussion
Metaanalysen genomweiter Assoziationsstudien (GWAMA) haben bisher mehr als 100 Polygene oder polygene Loci identifiziert, die genomweit mit dem BMI assoziiert sind. Jedes einzelne Polygen leistet nur einen kleinen Beitrag zur Entwicklung einer Adipositas. Effektstärken liegen im Bereich von ca. 100 g bis 1,5 kg. Eine Reihe solcher prädisponierenden Genvarianten (Allele) findet sich bei adipösen Probanden. Allerdings tragen auch normalgewichtige und schlanke Individuen diese Allele, wenn auch in geringerer Frequenz. Diese Allele können durch statistische Analysen als Adipositas-Risikoallele identifiziert und validiert werden. Vor Kurzem haben sogenannte Cross-Disorder- und Cross-Phänotyp-Analysen zur Identifizierung von Genen geführt, die nicht allein durch Analysen der einzelnen Erkrankungen/Phänotypen nachgewiesen werden konnten. Funktionelle in-vitro- und in-vivo-Studien der GWAS-abgeleiteten Polygene könnten zu einem besseren Verständnis der molekulargenetischen Mechanismen der Körpergewichtsregulation führen. Erste genomweite Methylierungsmusteranalysen und Studien zu metastabilen Epiallelen tragen zudem zu einem besseren Verständnis der Pathomechanismen der Adipositas bei.
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Affiliation(s)
- Johanna Giuranna
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
| | - Inga Diebels
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
| | - Anke Hinney
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
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Abstract
The ciliopathies Bardet-Biedl syndrome and Alström syndrome cause obesity. How ciliary dysfunction leads to obesity has remained mysterious, partly because of a lack of understanding of the physiological roles of primary cilia in the organs and pathways involved in the regulation of metabolism and energy homeostasis. Historically, the study of rare monogenetic disorders that present with obesity has informed our molecular understanding of the mechanisms involved in nonsyndromic forms of obesity. Here, we present a framework, based on genetic studies in mice and humans, of the molecular and cellular pathways underlying long-term regulation of energy homeostasis. We focus on recent progress linking these pathways to the function of the primary cilia with a particular emphasis on the roles of neuronal primary cilia in the regulation of satiety.
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Affiliation(s)
- Christian Vaisse
- Diabetes Center and Department of Medicine, University of California San Francisco, San Francisco, California 94143
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158
| | - Nicolas F Berbari
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
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Exogenous Expressions of FTO Wild-Type and R316Q Mutant Proteins Caused an Increase in HNRPK Levels in 3T3-L1 Cells as Demonstrated by DIGE Analysis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8216180. [PMID: 28555196 PMCID: PMC5438842 DOI: 10.1155/2017/8216180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/08/2017] [Accepted: 03/27/2017] [Indexed: 01/16/2023]
Abstract
Fat mass and obesity-associated protein is an enzyme that oxidatively demethylates DNA. Although there are numerous studies regarding the catalytic function of FTO, the overall existence or absence of FTO on cellular proteome has not been investigated. This study investigated the changes in the soluble proteome of 3T3-L1 cells upon expression of the WT and the mutant (R316Q) FTO proteins. Protein extracts prepared from 3T3-L1 cells expressing either the WT or the mutant FTO proteins were used in DIGE experiments. Analysis of the data revealed the number of spots matched to every member and there were 350 ± 20 spots with 30.5% overall mean coefficient of variation. Eleven regulated protein spots were excised from the gels and identified by MALDI-TOF/TOF. One of the identified proteins was heterogeneous nuclear ribonucleoprotein K, which displayed more than 2.6- and 3.7-fold increases in its abundance in the WT and the mutant FTO expressing cells, respectively. Western blot analysis validated these observations. This is the first study revealing the presence of a parallel increase in expressions of FTO and HNRNPK proteins. This increase may codictate the metabolic changes occurring in the cell and may attribute a significance to HNRNPK in FTO-associated transformations.
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Yang Q, Xiao T, Guo J, Su Z. Complex Relationship between Obesity and the Fat Mass and Obesity Locus. Int J Biol Sci 2017; 13:615-629. [PMID: 28539834 PMCID: PMC5441178 DOI: 10.7150/ijbs.17051] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 03/24/2017] [Indexed: 12/15/2022] Open
Abstract
In the 21st century, obesity has become a serious problem because of increasing obese patients and numerous metabolic complications. The primary reasons for this situation are environmental and genetic factors. In 2007, FTO (fat mass and obesity associated) was the first gene identified through a genome-wide association study (GWAS) associated with obesity in humans. Subsequently, a cluster of single nucleotide polymorphisms (SNPs) in the first intron of the FTO gene was discovered to be associated with BMI and body composition. Various studies have explored the mechanistic basis behind this association. Thus, emerging evidence showed that FTO plays a key role regulating adipose tissue development and functions in body size and composition. Recent prevalent research topic concentrated in the three neighboring genes of FTO: RPGRIP1L, IRX3 and IRX5, as having a functional link between obesity-associated common variants within FTO and the observed human phenotypes. The purpose of this review is to present a comprehensive picture of the impact of FTO on obesity susceptibility and to illuminate these new studies of FTO function in adipose tissue.
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Affiliation(s)
- Qingyun Yang
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Tiancun Xiao
- Inorganic Chemistry Laboratory, Oxford University, South Parks Road, OX1 3QR, United Kingdom.,Guangzhou Boxabio Technology Ltd, Guangzhou Science City, P R China
| | - Jiao Guo
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zhengquan Su
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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Nordang GBN, Busk ØL, Tveten K, Hanevik HI, Fell AKM, Hjelmesæth J, Holla ØL, Hertel JK. Next-generation sequencing of the monogenic obesity genes LEP, LEPR, MC4R, PCSK1 and POMC in a Norwegian cohort of patients with morbid obesity and normal weight controls. Mol Genet Metab 2017; 121:51-56. [PMID: 28377240 DOI: 10.1016/j.ymgme.2017.03.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Rare sequence variants in at least five genes are known to cause monogenic obesity. In this study we aimed to investigate the prevalence of, and characterize, rare coding and splice site variants in LEP, LEPR, MC4R, PCSK1 and POMC in patients with morbid obesity and normal weight controls. METHOD Targeted next-generation sequencing of all exons in LEP, LEPR, MC4R, PCSK1 and POMC was performed in 485 patients with morbid obesity and 327 normal weight population-based controls from Norway. RESULTS In total 151 variants were detected. Twenty-eight (18.5%) of these were rare, coding or splice variants and five (3.3%) were novel. All individuals, except one control, were heterozygous for the 28 variants, and the distribution of the rare variants showed a significantly higher carrier frequency among cases than controls (9.9% vs. 4.9%, p=0.011). Four variants in MC4R were classified as pathogenic or likely pathogenic. CONCLUSION Four cases (0.8%) of monogenic obesity were detected, all due to MC4R variants previously linked to monogenic obesity. Significant differences in carrier frequencies among patients with morbid obesity and normal weight controls suggest an association between heterozygous rare coding variants in these five genes and morbid obesity. However, additional studies in larger cohorts and functional testing of the novel variants identified are required to confirm the findings.
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Affiliation(s)
- Gry B N Nordang
- Morbid Obesity Centre, Vestfold Hospital Trust, Tønsberg, Norway; Department of Occupational and Environmental Medicine, Telemark Hospital, Skien, Norway; Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, Skien, Norway.
| | - Øyvind L Busk
- Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, Skien, Norway
| | - Kristian Tveten
- Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, Skien, Norway
| | | | - Anne Kristin M Fell
- Department of Occupational and Environmental Medicine, Telemark Hospital, Skien, Norway
| | - Jøran Hjelmesæth
- Morbid Obesity Centre, Vestfold Hospital Trust, Tønsberg, Norway; Department of Endocrinology, Morbid Obesity and Preventive Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Øystein L Holla
- Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, Skien, Norway
| | - Jens K Hertel
- Morbid Obesity Centre, Vestfold Hospital Trust, Tønsberg, Norway
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20
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Mizuno TM, Lew PS, Luo Y, Leckstrom A. Negative regulation of hepatic fat mass and obesity associated (Fto) gene expression by insulin. Life Sci 2017; 170:50-55. [DOI: 10.1016/j.lfs.2016.11.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
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21
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Andraweera PH, Dekker GA, Leemaqz S, McCowan L, Roberts CT. The obesity associated FTO gene variant and the risk of adverse pregnancy outcomes: Evidence from the SCOPE study. Obesity (Silver Spring) 2016; 24:2600-2607. [PMID: 27768255 DOI: 10.1002/oby.21662] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/19/2016] [Accepted: 08/02/2016] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To investigate whether the FTO rs9939609 single nucleotide polymorphism (SNP), which is a risk factor for obesity and vascular diseases, is also associated with pregnancy complications including pre-eclampsia, gestational hypertension, small for gestational age pregnancy (SGA), and spontaneous preterm birth (sPTB). METHODS A case-control study of 1,741 nulliparous Caucasian women, their partners, and infants was conducted. DNA was extracted from peripheral blood or saliva from parents and cord blood from infants and genotyped using the Sequenom MassARRAY system. RESULTS The prevalence of maternal and infant AA genotype of FTO rs9939609 was increased in the SGA group compared with the uncomplicated pregnancy group (19.2% vs. 13.4%, OR = 1.7, 95% CI = 1.1-2.6, P = 0.02 and 24.6% vs. 12.5%, OR = 2.7, 95% CI = 1.6-4.6, P = 0.0002). The prevalence of maternal and infant AA genotype of FTO rs9939609 was also increased in the sPTB group compared with the uncomplicated pregnancy group (20.8% vs. 13.4%, OR = 2.1, 95% CI = 1.2-3.8, P = 0.009 and 20.0% vs. 12.5%, OR = 2.4, 95% CI = 1.0-5.3, P = 0.03). CONCLUSIONS The maternal and infant AA genotype of the obesity associated FTO rs9939609 SNP associates with increased risk for SGA and sPTB. This SNP may be important in predicting the risk of these pregnancy complications and subsequent vascular diseases.
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Affiliation(s)
- Prabha H Andraweera
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Gustaaf A Dekker
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, Australia
- Women's and Children's Division, Lyell McEwin Hospital, Adelaide, South Australia
| | - Shalem Leemaqz
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Lesley McCowan
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Claire T Roberts
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, The University of Adelaide, Adelaide, Australia
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22
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Sequencing of FTO and ALKBH5 in men undergoing infertility work-up identifies an infertility-associated variant and two missense mutations. Fertil Steril 2016; 105:1170-1179.e5. [DOI: 10.1016/j.fertnstert.2016.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/10/2015] [Accepted: 01/06/2016] [Indexed: 11/18/2022]
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23
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Stratigopoulos G, Burnett LC, Rausch R, Gill R, Penn DB, Skowronski AA, LeDuc CA, Lanzano AJ, Zhang P, Storm DR, Egli D, Leibel RL. Hypomorphism of Fto and Rpgrip1l causes obesity in mice. J Clin Invest 2016; 126:1897-910. [PMID: 27064284 DOI: 10.1172/jci85526] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/25/2016] [Indexed: 01/19/2023] Open
Abstract
Noncoding polymorphisms in the fat mass and obesity-associated (FTO) gene represent common alleles that are strongly associated with effects on food intake and adiposity in humans. Previous studies have suggested that the obesity-risk allele rs8050136 in the first intron of FTO alters a regulatory element recognized by the transcription factor CUX1, thereby leading to decreased expression of FTO and retinitis pigmentosa GTPase regulator-interacting protein-1 like (RPGRIP1L). Here, we evaluated the effects of rs8050136 and another potential CUX1 element in rs1421085 on expression of nearby genes in human induced pluripotent stem cell-derived (iPSC-derived) neurons. There were allele-dosage effects on FTO, RPGRIP1L, and AKT-interacting protein (AKTIP) expression, but expression of other vicinal genes, including IRX3, IRX5, and RBL2, which have been implicated in mediating functional effects, was not altered. In vivo manipulation of CUX1, Fto, and/or Rpgrip1l expression in mice affected adiposity in a manner that was consistent with CUX1 influence on adiposity via remote effects on Fto and Rpgrip1l expression. In support of a mechanism, mice hypomorphic for Rpgrip1l exhibited hyperphagic obesity, as the result of diminished leptin sensitivity in Leprb-expressing neurons. Together, the results of this study indicate that the effects of FTO-associated SNPs on energy homeostasis are due in part to the effects of these genetic variations on hypothalamic FTO, RPGRIP1L, and possibly other genes.
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Butler MG. Single Gene and Syndromic Causes of Obesity: Illustrative Examples. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 140:1-45. [PMID: 27288824 DOI: 10.1016/bs.pmbts.2015.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Obesity is a significant health problem in westernized societies, particularly in the United States where it has reached epidemic proportions in both adults and children. The prevalence of childhood obesity has doubled in the past 30 years. The causation is complex with multiple sources, including an obesity promoting environment with plentiful highly dense food sources and overall decreased physical activity noted for much of the general population, but genetic factors clearly play a role. Advances in genetic technology using candidate gene approaches, genome-wide association studies, structural and expression microarrays, and next generation sequencing have led to the discovery of hundreds of genes recognized as contributing to obesity. Polygenic and monogenic causes of obesity are now recognized including dozens of examples of syndromic obesity with Prader-Willi syndrome, as a classical example and recognized as the most common known cause of life-threatening obesity. Genetic factors playing a role in the causation of obesity will be discussed along with the growing evidence of single genes and the continuum between monogenic and polygenic obesity. The clinical and genetic aspects of four classical but rare obesity-related syndromes (ie, Prader-Willi, Alström, fragile X, and Albright hereditary osteodystrophy) will be described and illustrated in this review of single gene and syndromic causes of obesity.
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Affiliation(s)
- Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, United States of America.
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Analysis of Genes Involved in Body Weight Regulation by Targeted Re-Sequencing. PLoS One 2016; 11:e0147904. [PMID: 26828654 PMCID: PMC4734691 DOI: 10.1371/journal.pone.0147904] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/11/2016] [Indexed: 12/16/2022] Open
Abstract
Introduction Genes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing. Methods We enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) ≥ 99th percentile and 176 lean adults (BMI ≤ 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults. Results and Conclusion We detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (pTDT = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.
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A patient with a novel homozygous missense mutation in FTO and concomitant nonsense mutation in CETP. J Hum Genet 2016; 61:395-403. [PMID: 26740239 PMCID: PMC4880488 DOI: 10.1038/jhg.2015.160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/30/2015] [Accepted: 11/30/2015] [Indexed: 12/19/2022]
Abstract
The fat mass and obesity associated gene (FTO) has previously been associated with a variety of diseases and conditions, notably obesity, acute coronary syndrome and metabolic syndrome. Reports describing mutations in FTO as well as FTO animal models have further demonstrated a role for FTO in the development of the brain and other organs. Here, we describe a patient born of consanguineous union who presented with microcephaly, developmental delay, behavioral abnormalities, dysmorphic facial features, hypotonia, and other various phenotypic abnormalities. Whole exome sequencing revealed a novel homozygous missense mutation in FTO and a nonsense mutation in the cholesteryl ester transfer protein (CETP). Exome CNV analysis revealed no disease causing large duplications or deletions within coding regions. Patient’s, her parents’ and non-related control’ fibroblasts were analyzed for morphologic defects, abnormal proliferation, apoptosis and transcriptome profile. We have shown that FTO is located in nucleus of cells from each tested samples. Western blot analysis demonstrated no changes in patient FTO. Q-PCR analysis revealed slightly decreased levels of FTO expression in patient cells compared to controls. No morphological or proliferation differences between the patient and control fibroblasts were observed. There is still much to be learned about the molecular mechanisms by which mutations in FTO contribute to such severe phenotypes.
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Rohena L, Lawson M, Guzman E, Ganapathi M, Cho MT, Haverfield E, Anyane-Yeboa K. FTO variant associated with malformation syndrome. Am J Med Genet A 2015; 170A:1023-8. [PMID: 26697951 DOI: 10.1002/ajmg.a.37515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 12/06/2015] [Indexed: 11/07/2022]
Abstract
Common FTO variants are associated with obesity. However, it has recently been shown that homozygous FTO c.947G>A variant, which predicts p.R316Q, and c.956C>T, which predicts p.S319F, are associated with a malformation syndrome inherited in an autosomal recessive pattern. We present a similar homozygous FTO c.965G>A variant that predicts p.R322Q, associated with a lethal malformation syndrome in a consanguineous Yemeni family. Functional studies showed that the p.R316Q, p.S219F, and p.R322Q variants render the FTO protein inactive. We further expand on the phenotype of homozygous FTO loss-of-function mutations to include eye abnormalities, gingival overgrowth, craniosynostosis, and cutaneous photosensitivity.
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Affiliation(s)
- Luis Rohena
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas
| | - Michelle Lawson
- Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas
| | - Edwin Guzman
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | | | | | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York
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Chesi A, Grant SFA. The Genetics of Pediatric Obesity. Trends Endocrinol Metab 2015; 26:711-721. [PMID: 26439977 PMCID: PMC4673034 DOI: 10.1016/j.tem.2015.08.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/24/2023]
Abstract
Obesity among children and adults has notably escalated over recent decades and represents a global major health problem. We now know that both genetic and environmental factors contribute to its complex etiology. Genome-wide association studies (GWAS) have revealed compelling genetic signals influencing obesity risk in adults. Recent reports for childhood obesity revealed that many adult loci also play a role in the pediatric setting. Childhood GWAS have uncovered novel loci below the detection range in adult studies, suggesting that obesity genes may be more easily uncovered in the pediatric setting. Shedding light on the genetic architecture of childhood obesity will facilitate the prevention and treatment of pediatric cases, and will have fundamental implications for diseases that present later in life.
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Affiliation(s)
- Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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Daoud H, Zhang D, McMurray F, Yu A, Luco SM, Vanstone J, Jarinova O, Carson N, Wickens J, Shishodia S, Choi H, McDonough MA, Schofield CJ, Harper ME, Dyment DA, Armour CM. Identification of a pathogenicFTOmutation by next-generation sequencing in a newborn with growth retardation and developmental delay. J Med Genet 2015; 53:200-7. [DOI: 10.1136/jmedgenet-2015-103399] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/28/2015] [Indexed: 11/04/2022]
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30
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Jeong HS, Hayashi G, Okamoto A. Diazirine photocrosslinking recruits activated FTO demethylase complexes for specific N(6)-methyladenosine recognition. ACS Chem Biol 2015; 10:1450-5. [PMID: 25751089 DOI: 10.1021/cb5010096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
N(6)-methyladenosine (m(6)A) is a prevalent modification of RNAs. m(6)A exists in mRNA and plays an important role in RNA biological pathways and in RNA epigenetic regulation. We applied diazirine photocrosslinking to the event of m(6)A recognition mediated by the fat mass and obesity associated (FTO) demethylase. A highly photoreactive diazirine adjacent to m(6)A on the RNA successfully recruited activated FTO complexes with an m(6)A preference. The process of recognition of m(6)A via FTO using diazirine photocrosslinking was controlled by the α-ketoglutarate (α-KG) cosubstrate and the Fe(II) cofactor, which are involved in m(6)A oxidative demethylation. In addition, FTO bound to ssRNAs prior to the m(6)A recognition process. Diazirine photocrosslinking contributes to increasing the chances of capturing activated FTO complexes with specific m(6)A recognition and provides new insights into the dynamic FTO oxidative demethylation process.
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Affiliation(s)
- Hyun Seok Jeong
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Gosuke Hayashi
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department
of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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31
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Apalasamy YD, Mohamed Z. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity. Hum Genet 2015; 134:361-74. [PMID: 25687726 DOI: 10.1007/s00439-015-1533-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023]
Abstract
Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.
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Affiliation(s)
- Yamunah Devi Apalasamy
- Department of Pharmacology, Pharmacogenomics Laboratory, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia,
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Guo F, Zhang Y, Zhang C, Wang S, Ni Y, Zhao R. Fat mass and obesity associated (FTO) gene regulates gluconeogenesis in chicken embryo fibroblast cells. Comp Biochem Physiol A Mol Integr Physiol 2015; 179:149-56. [DOI: 10.1016/j.cbpa.2014.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/02/2014] [Accepted: 10/13/2014] [Indexed: 02/01/2023]
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Single nucleotide polymorphisms of the FTO gene and cancer risk: an overview. Mol Biol Rep 2014; 42:699-704. [PMID: 25387436 DOI: 10.1007/s11033-014-3817-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 11/05/2014] [Indexed: 12/19/2022]
Abstract
The FTO (fat mass and obesity-associated) gene has a strong linkage disequilibrium block, within which SNPs have been identified that are involved in the development of obesity. Recently some of these variants have also been associated with cancer. However, identification of the possible mechanisms that could explain these associations has proven to be elusive. It has been found that FTO polymorphisms can regulate the expression of genes at large kilobases of distance as well as the expression of the FTO gene itself, and regions for transcription factor binding. To date it has been observed that variants rs9939609, rs17817449, rs8050136, rs1477196, rs6499640, rs16953002, rs11075995 and rs1121980 are associated with the risk of developing cancer. Some studies have produced negative results when comparing the same polymorphisms, but make a simple association between polymorphic variants and cancer, have proved difficult because this relation is by nature multifactorial. A certain degree of variation resulting from the improper design of studies or processing of data can lead to erroneous conclusions. However, it is now unquestionable that certain FTO polymorphisms regulate genetic expression related to cancer susceptibility, although this field is just beginning to be understood.
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Abstract
The fat mass and obesity-associated (FTO) gene was placed center stage when common intronic variants within the gene were robustly associated with human obesity. Murine models of perturbed Fto expression have shown effects on body weight and composition. However, a clear understanding of the link between FTO intronic variants and FTO activity has remained elusive. Two recent reports now indicate that obesity-associated SNPs appear functionally connected not with FTO but with two neighboring genes: IRX3 and RPGRIP1L. Here, we review these new findings and consider the implications for future analysis of GWAS hits.
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Affiliation(s)
- Y C Loraine Tung
- Medical Research Council Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Giles S H Yeo
- Medical Research Council Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Stephen O'Rahilly
- Medical Research Council Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Anthony P Coll
- Medical Research Council Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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35
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Yeo GSH. The role of the FTO (Fat Mass and Obesity Related) locus in regulating body size and composition. Mol Cell Endocrinol 2014; 397:34-41. [PMID: 25224490 DOI: 10.1016/j.mce.2014.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/10/2014] [Accepted: 09/10/2014] [Indexed: 01/23/2023]
Abstract
Genomewide association studies (GWAS) have indicated that SNPs on a chromosome 16 locus encompassing FTO, as well as IRX3, 5, 6, FTM and FTL are robustly associated with human obesity. GWAS, however, are by nature gene agnostic, and SNPs reaching the appropriate statistical threshold for a given phenotype can appear anywhere in the genome, within, near or far away from any coding sequence. Thus a major challenge in the field has been to translate these statistical hits into real biological insight. The key question is which of these genes are responsible for the association with obesity, and what is the underlying mechanism? With loss of function FTO mutations in both mice and humans resulting in severe growth retardation and mice globally over-expressing FTO being obese, the initial attention was focussed on this gene. We and others have shown that in vitro, recombinant FTO is able to catalyse the Fe(II)- and 2OG-dependent demethylation of single stranded nucleic-acids, with a preference for RNA. We have shown that FTO expression is regulated by essential amino acids (AAs) and that it couples amino acid levels to mammalian Target of Rapamycin Complex 1 (mTORC1) signalling, through a mechanism dependent on its ability to demethylate. Thus FTO is an AA sensor and plays a key role regulating appropriate growth and translation. However, recent data focussing on obesity associated variants within FTO have implicated two neighbouring genes, RPGRIP1L and IRX3, as having a functional link between the SNP and the observed human phenotypes. As with Fto, perturbing the expression of these genes in mice results in a bodyweight phenotype, with homozygous deletion of Irx3 resulting in a smaller mouse and heterozygous deletion of Rpgrip1l leading to a mild obesity phenotype. Thus it may be that a number of genes in this region play an important role in determining body composition.
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Affiliation(s)
- Giles S H Yeo
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
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36
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Abstract
SNPs (single nucleotide polymorphisms) on a chromosome 16 locus encompassing FTO, as well as IRX3, 5, 6, FTM and FTL are robustly associated with human obesity. FTO catalyses the Fe(II)- and 2OG-dependent demethylation of RNA and is an AA (amino acid) sensor that couples AA levels to mTORC1 (mammalian target of rapamycin complex 1) signalling, thereby playing a key role in regulating growth and translation. However, the cellular compartment in which FTO primarily resides to perform its biochemical role is unclear. Here, we undertake live cell imaging of GFP (green fluorescent protein)-FTO, and demonstrate that FTO resides in both the nucleus and cytoplasm. We show using ‘FLIP’ (fluorescence loss in photobleaching) that a mobile FTO fraction shuttles between both compartments. We performed a proteomic study and identified XPO2 (Exportin 2), one of a family of proteins that mediates the shuttling of proteins between the nucleus and the cytoplasm, as a binding partner of FTO. Finally, using deletion studies, we show that the N-terminus of FTO is required for its ability to shuttle between the nucleus and cytoplasm. In conclusion, FTO is present in both the nucleus and cytoplasm, with a mobile fraction that shuttles between both cellular compartments, possibly by interaction with XPO2. Exportin interacts with FTO and this interaction might be involved in the nucelocytoplasmic shuttling of FTO in the cell.
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37
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Abstract
Heritability of obesity and body weight variation is high. Molecular genetic studies have led to the identification of mutations in a few genes, with a major effect on obesity (major genes and monogenic forms). Analyses of these genes have helped to unravel important pathways and have created a more profound understanding of body weight regulation. For most individuals, a polygenic basis is relevant for the genetic predisposition to obesity. Small effect sizes are conveyed by the polygenic variants. Hence, only if a number of these variants is harboured, a sizeable phenotypic effect is detectable. Most, if not all, of the genes relevant to weight regulation are expressed in the hypothalamus. This underscores the major role of this region of the brain in body weight regulation.
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Affiliation(s)
- Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
| | - Anna-Lena Volckmar
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
| | - Jochen Antel
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
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38
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Stratigopoulos G, Martin Carli JF, O'Day DR, Wang L, Leduc CA, Lanzano P, Chung WK, Rosenbaum M, Egli D, Doherty DA, Leibel RL. Hypomorphism for RPGRIP1L, a ciliary gene vicinal to the FTO locus, causes increased adiposity in mice. Cell Metab 2014; 19:767-79. [PMID: 24807221 PMCID: PMC4131684 DOI: 10.1016/j.cmet.2014.04.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 11/11/2013] [Accepted: 04/18/2014] [Indexed: 12/31/2022]
Abstract
Common polymorphisms in the first intron of FTO are associated with increased body weight in adults. Previous studies have suggested that a CUX1-regulatory element within the implicated FTO region controls expression of FTO and the nearby ciliary gene, RPGRIP1L. Given the role of ciliary genes in energy homeostasis, we hypothesized that mice hypomorphic for Rpgrip1l would display increased adiposity. We find that Rpgrip1l⁺/⁻ mice are hyperphagic and fatter, and display diminished suppression of food intake in response to leptin administration. In the hypothalamus of Rpgrip1l⁺/⁻ mice, and in human fibroblasts with hypomorphic mutations in RPGRIP1L, the number of AcIII-positive cilia is diminished, accompanied by impaired convening of the leptin receptor to the vicinity of the cilium, and diminished pStat3 in response to leptin. These findings suggest that RPGRIP1L may be partly or exclusively responsible for the obesity susceptibility signal at the FTO locus.
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Affiliation(s)
- George Stratigopoulos
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA.
| | - Jayne F Martin Carli
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Diana R O'Day
- Divisions of Developmental Medicine and Genetic Medicine, Department of Pediatrics, Seattle Children's Research Institute and University of Washington 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Liheng Wang
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Charles A Leduc
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Patricia Lanzano
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Michael Rosenbaum
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA
| | - Daniel A Doherty
- Divisions of Developmental Medicine and Genetic Medicine, Department of Pediatrics, Seattle Children's Research Institute and University of Washington 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA.
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Chen W, Zhang L, Zheng G, Fu Y, Ji Q, Liu F, Chen H, He C. Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett 2014; 588:892-8. [PMID: 24561204 DOI: 10.1016/j.febslet.2014.02.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 02/08/2014] [Indexed: 12/22/2022]
Abstract
ALKBH5, a member of AlkB family proteins, has been reported as a mammalian N(6)-methyladenosine (m(6)A) RNA demethylase. Here we report the crystal structure of zebrafish ALKBH5 (fALKBH5) with the resolution of 1.65Å. Structural superimposition shows that fALKBH5 is comprised of a conserved jelly-roll motif. However, it possesses a loop that interferes potential binding of a duplex nucleic acid substrate, suggesting an important role in substrate selection. In addition, several active site residues are different between the two known m(6)A RNA demethylases, ALKBH5 and FTO, which may result in their slightly different pathways of m(6)A demethylation.
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Affiliation(s)
- Weizhong Chen
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA; Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Liang Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Quanjiang Ji
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Fange Liu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA
| | - Hao Chen
- Coordination Chemistry Institute and the State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
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Abstract
Single nucleotide polymorphisms (SNPs) that cluster in the first intron of fat mass and obesity associated (FTO) gene are associated obesity traits in genome-wide association studies. The minor allele increases BMI by 0.39 kg/m(2) (or 1,130 g in body weight) and risk of obesity by 1.20-fold. This association has been confirmed across age groups and populations of diverse ancestry; the largest effect is seen in young adulthood. The effect of FTO SNPs on obesity traits in populations of African and Asian ancestry is similar or somewhat smaller than in European ancestry populations. However, the BMI-increasing allele in FTO is substantially less prevalent in populations with non-European ancestry. FTO SNPs do not influence physical activity levels; yet, in physically active individuals, FTO's effect on obesity susceptibility is attenuated by approximately 30%. Evidence from epidemiological and functional studies suggests that FTO confers an increased risk of obesity by subtly changing food intake and preference. Moreover, emerging data suggest a role for FTO in nutrient sensing, regulation of mRNA translation and general growth. In this Review, we discuss the genetic epidemiology of FTO and discuss how its complex biology might link to the regulation of body weight.
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Affiliation(s)
- Ruth J F Loos
- The Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1003, New York, NY 10029-6574, USA
| | - Giles S H Yeo
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
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41
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Zhang GW, Gao L, Chen SY, Zhao XB, Tian YF, Wang X, Deng XS, Lai SJ. Single nucleotide polymorphisms in the FTO gene and their association with growth and meat quality traits in rabbits. Gene 2013; 527:553-7. [DOI: 10.1016/j.gene.2013.06.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 06/09/2013] [Accepted: 06/10/2013] [Indexed: 12/26/2022]
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Zheng Z, Hong L, Huang X, Yang P, Li J, Ding Y, Yao RE, Geng J, Shen Y, Shen Y, Fu Q, Yu Y. Screening for coding variants in FTO and SH2B1 genes in Chinese patients with obesity. PLoS One 2013; 8:e67039. [PMID: 23825611 PMCID: PMC3692548 DOI: 10.1371/journal.pone.0067039] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 05/14/2013] [Indexed: 01/08/2023] Open
Abstract
Objective To investigate potential functional variants in FTO and SH2B1 genes among Chinese children with obesity. Methods Sanger sequencing of PCR products of all FTO and SH2B1 exons and their flanking regions were performed in 338 Chinese Han children with obesity and 221 age- and sex-matched lean controls. Results A total of seven and five rare non-synonymous variants were identified in FTO and SH2B1, respectively. The overall frequencies of FTO and SH2B1 rare non-synonymous variants were similar in obese and lean children (2.37% and 0.90% vs. 1.81% and 1.36%, P>0.05). However, four out of the seven variants in FTO were novel and all were unique to obese children (p>0.05). None of the novel variants was consistently being predicted to be deleterious. Four out of five variants in SH2B1 were novel and one was unique to obese children (p>0.05). One variant (L293R) that was consistently being predicted as deleterious in SH2B1 gene was unique to lean control. While rare missense mutations were more frequently detected in girls from obesity as well as lean control than boys, the difference was not statistically significant. In addition, it's shown that the prevalence of rare missense mutations of FTO as well as SH2B1 was similar across different ethnic groups. Conclusion The rare missense mutations of FTO and SH2B1 did not confer risks of obesity in Chinese Han children in our cohort.
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Affiliation(s)
- Zhaojing Zheng
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Li Hong
- Department of Nutrition, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Xiaodong Huang
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Peirong Yang
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Juan Li
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yu Ding
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Ru-en Yao
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Juan Geng
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yongnian Shen
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
| | - Yiping Shen
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
- Department of Laboratory Medicine, Children’s Hospital Boston, Boston, Massachusetts, United States of America
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
- * E-mail: (QHF); (YGY)
| | - Yongguo Yu
- Department of Internal Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China
- * E-mail: (QHF); (YGY)
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Davies RW, Lau P, Naing T, Nikpay M, Doelle H, Harper ME, Dent R, McPherson R. A 680 kb duplication at the FTO locus in a kindred with obesity and a distinct body fat distribution. Eur J Hum Genet 2013; 21:1417-22. [PMID: 23591406 DOI: 10.1038/ejhg.2013.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 03/03/2013] [Accepted: 03/07/2013] [Indexed: 11/09/2022] Open
Abstract
Common intronic SNPs in the human fat mass and obesity associated (FTO) gene are strongly associated with body mass index (BMI). In mouse models, inactivation of the Fto gene results in a lean phenotype, whereas overexpression of Fto leads to increased food intake and obesity. The latter finding suggests that copy number variants at the FTO locus might be associated with extremes of adiposity. To address this question, we searched for rare, private or de novo copy number variation in a cohort of 985 obese and 869 lean subjects of European ancestry drawn from the extremes of the BMI distribution, genotyped on Affymetrix 6.0 arrays. A ∼680 kb duplication, confirmed by real-time PCR and G-to-FISH analyses, was observed between ∼rs11859825 and rs9932411 in a 68-year-old male with severe obesity. The duplicated region on chromosome 16 spans the entire genome-wide association studies risk locus for obesity, and further encompasses RBL2, AKTIP, RPGRIP1L and all but the last exon of the FTO gene. Affected family members exhibit a unique obesity phenotype, characterized by increased fat distribution in the shoulders and neck with a significantly increased neck circumference. This phenotype was accompanied by increased peripheral blood expression of RBL2 with no alteration in expression of FTO or other genes in the region. No other duplications or deletions in this region were identified in the cohort of obese and lean individuals or in a further survey of 4778 individuals, suggesting that large rare copy number variants surrounding the FTO gene are not a frequent cause of obesity.
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Affiliation(s)
- Robert W Davies
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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Abstract
It has long been known that there is a genetic component to obesity, and that characterizing this underlying factor would likely offer the possibility of better intervention in the future. Monogenic obesity has proved to be relatively straightforward, with a combination of linkage analysis and mouse models facilitating the identification of multiple genes. In contrast, genome-wide association studies have successfully revealed a variety of genetic loci associated with the more common form of obesity, allowing for very strong consensus on the underlying genetic architecture of the phenotype for the first time. Although a number of significant findings have been made, it appears that very little of the apparent heritability of body mass index has actually been explained to date. New approaches for data analyses and advances in technology will be required to uncover the elusive missing heritability, and to aid in the identification of the key causative genetic underpinnings of obesity.
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Affiliation(s)
- Qianghua Xia
- Division of Human Genetics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
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45
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McMurray F, Church CD, Larder R, Nicholson G, Wells S, Teboul L, Tung YCL, Rimmington D, Bosch F, Jimenez V, Yeo GSH, O'Rahilly S, Ashcroft FM, Coll AP, Cox RD. Adult onset global loss of the fto gene alters body composition and metabolism in the mouse. PLoS Genet 2013; 9:e1003166. [PMID: 23300482 PMCID: PMC3536712 DOI: 10.1371/journal.pgen.1003166] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/26/2012] [Indexed: 01/27/2023] Open
Abstract
The strongest BMI–associated GWAS locus in humans is the FTO gene. Rodent studies demonstrate a role for FTO in energy homeostasis and body composition. The phenotypes observed in loss of expression studies are complex with perinatal lethality, stunted growth from weaning, and significant alterations in body composition. Thus understanding how and where Fto regulates food intake, energy expenditure, and body composition is a challenge. To address this we generated a series of mice with distinct temporal and spatial loss of Fto expression. Global germline loss of Fto resulted in high perinatal lethality and a reduction in body length, fat mass, and lean mass. When ratio corrected for lean mass, mice had a significant increase in energy expenditure, but more appropriate multiple linear regression normalisation showed no difference in energy expenditure. Global deletion of Fto after the in utero and perinatal period, at 6 weeks of age, removed the high lethality of germline loss. However, there was a reduction in weight by 9 weeks, primarily as loss of lean mass. Over the subsequent 10 weeks, weight converged, driven by an increase in fat mass. There was a switch to a lower RER with no overall change in food intake or energy expenditure. To test if the phenotype can be explained by loss of Fto in the mediobasal hypothalamus, we sterotactically injected adeno-associated viral vectors encoding Cre recombinase to cause regional deletion. We observed a small reduction in food intake and weight gain with no effect on energy expenditure or body composition. Thus, although hypothalamic Fto can impact feeding, the effect of loss of Fto on body composition is brought about by its actions at sites elsewhere. Our data suggest that Fto may have a critical role in the control of lean mass, independent of its effect on food intake. The fat mass and obesity (FTO) gene has one of the strongest links with body mass index (BMI) in the human population. One in six people have the “risk” alteration and weigh 3 kg more than those with the unaltered gene, but it is not understood how this gene influences BMI and obesity. We set out to understand how and where in the body FTO affects food intake, energy expenditure, and body composition using a mouse model that can be manipulated to lack FTO at particular times and/or places. Removing FTO everywhere from conception had a dramatic effect on body composition and resulted in stunted growth and some lethality. Removing FTO everywhere but only in adult animals resulted in better viability and normal growth but, surprisingly, reduced lean mass and increased fat mass with a change in the type of metabolic fuel being used. Finally, we removed FTO from the hypothalamus of adult animals, an important brain region involved in energy metabolism. These animals showed a mild reduction in food intake and weight gain. Our experiments show that FTO has an important role in body composition and that other brain areas outside of the hypothalamus are also important in determining its effects.
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Affiliation(s)
- Fiona McMurray
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Chris D. Church
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Rachel Larder
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - George Nicholson
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Sara Wells
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Lydia Teboul
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
| | - Y. C. Loraine Tung
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Debra Rimmington
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Fatima Bosch
- Center of Animal Biotechnology and Gene Therapy and Department of Biochemistry and Molecular Biology, School of Veterinary Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Veronica Jimenez
- Center of Animal Biotechnology and Gene Therapy and Department of Biochemistry and Molecular Biology, School of Veterinary Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Giles S. H. Yeo
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Stephen O'Rahilly
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Frances M. Ashcroft
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
| | - Anthony P. Coll
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Roger D. Cox
- MRC Harwell, Harwell Science and Innovation Campus, Harwell, United Kingdom
- * E-mail:
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Abstract
Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.
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Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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47
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Deliard S, Panossian S, Mentch FD, Kim CE, Hou C, Frackelton EC, Bradfield JP, Glessner JT, Zhang H, Wang K, Sleiman PM, Chiavacci RM, Berkowitz RI, Hakonarson H, Zhao J, Grant SF. The missense variation landscape of FTO, MC4R, and TMEM18 in obese children of African Ancestry. Obesity (Silver Spring) 2013; 21:159-63. [PMID: 23505181 PMCID: PMC3605748 DOI: 10.1002/oby.20147] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 10/18/2012] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Common variation at the loci harboring fat mass and obesity (FTO), melanocortin receptor 4 (MC4R), and transmembrane protein 18 (TMEM18) is consistently reported as being statistically most strongly associated with obesity. Investigations if these loci also harbor rarer missense variants that confer substantially higher risk of common childhood obesity in African American (AA) children were conducted. DESIGN AND METHODS The exons of FTO, MC4R, and TMEM18 in an initial subset of our cohort were sequenced, that is, 200 obese (BMI ≥ 95 th percentile) and 200 lean AA children (BMI ≤ 5 th percentile). Any missense exonic variants that were uncovered went on to be further genotyped in a further 768 obese and 768 lean (BMI≤50th percentile) children of the same ethnicity. RESULTS A number of exonic variants were observed from our sequencing effort: seven in FTO, of which four were non-synonymous (A163T, G182A, M400V, and A405V), thirteen in MC4R, of which six were non-synonymous (V103I, N123S, S136A, F202L, N240S, and I251L), and four in TMEM18, of which two were non-synonymous (P2S and V113L). Follow-up genotyping of these missense variants revealed only one significant difference in allele frequency between cases and controls, namely with N240S in MC4R (Fisher's exact P = 0.0001). CONCLUSION In summary, moderately rare missense variants within the FTO, MC4R, and TMEM18 genes observed in our study did not confer risk of common childhood obesity in African Americans except for a degree of evidence for one known loss-of-function variant in MC4R.
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Affiliation(s)
- Sandra Deliard
- Division of Human Genetics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Saarene Panossian
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Frank D. Mentch
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Cecilia E. Kim
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Cuiping Hou
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Edward C. Frackelton
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Joseph T. Glessner
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Haitao Zhang
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Kai Wang
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Patrick M.A. Sleiman
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Robert I. Berkowitz
- Behavioral Health Center and Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
- Center for Weight and Eating Disorders, Department of Psychiatry, University of Pennsylvania
| | - Hakon Hakonarson
- Division of Human Genetics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
- Department of Pediatrics, University of Pennsylvania School of Medicine
| | - Jianhua Zhao
- Division of Human Genetics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
| | - Struan F.A. Grant
- Division of Human Genetics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
- Center for Applied Genomics, Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia
- Department of Pediatrics, University of Pennsylvania School of Medicine
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48
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Lupo PJ, Canfield MA, Chapa C, Lu W, Agopian AJ, Mitchell LE, Shaw GM, Waller DK, Olshan AF, Finnell RH, Zhu H. Diabetes and obesity-related genes and the risk of neural tube defects in the national birth defects prevention study. Am J Epidemiol 2012; 176:1101-9. [PMID: 23132673 DOI: 10.1093/aje/kws190] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Few studies have evaluated genetic susceptibility related to diabetes and obesity as a risk factor for neural tube defects (NTDs). The authors investigated 23 single nucleotide polymorphisms among 9 genes (ADRB3, ENPP1, FTO, LEP, PPARG, PPARGC1A, SLC2A2, TCF7L2, and UCP2) associated with type 2 diabetes or obesity. Samples were obtained from 737 NTD case-parent triads included in the National Birth Defects Prevention Study during 1999-2007. Log-linear models were used to evaluate maternal and offspring genetic effects. After application of the false discovery rate, there were 5 significant maternal genetic effects. The less common alleles at the 4 FTO single nucleotide polymorphisms showed a reduction of NTD risk (for rs1421085, relative risk (RR) = 0.73 (95% confidence interval (CI): 0.62, 0.87); for rs8050136, RR = 0.79 (95% CI: 0.67, 0.93); for rs9939609, RR = 0.79 (95% CI: 0.67, 0.94); and for rs17187449, RR = 0.80 (95% CI: 0.68, 0.95)). Additionally, maternal LEP rs2071045 (RR = 1.31, 95% CI: 1.08, 1.60) and offspring UCP2 rs660339 (RR = 1.32, 95% CI: 1.06, 1.64) were associated with NTD risk. Furthermore, the maternal genotype for TCF7L2 rs3814573 suggested an increased NTD risk among obese women. These findings indicate that maternal genetic variants associated with glucose homeostasis may modify the risk of having an NTD-affected pregnancy.
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Affiliation(s)
- Philip J Lupo
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas, Houston, TX, USA
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Yeo GS, O'Rahilly S. Uncovering the biology of FTO. Mol Metab 2012; 1:32-6. [PMID: 24024116 PMCID: PMC3757649 DOI: 10.1016/j.molmet.2012.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/21/2012] [Accepted: 06/21/2012] [Indexed: 11/22/2022] Open
Abstract
Genome-wide association studies have revealed that SNPs in the first intron of FTO (Fat mass and Obesity related) are robustly associated with body mass index and obesity. Subsequently, it has become clear that this association with body weight, and increasingly food intake, is replicable across multiple populations and different age groups. However, to date, no conclusive link has been made between the risk alleles and FTO expression or its physiological role. FTO deficiency leads to a complex phenotype including postnatal mortality and growth retardation, pointing to some fundamental developmental role. Yet, the weight of evidence from a number of animal models where FTO expression has been perturbed indicates some role for FTO in energy homoeostasis. In addition, emerging data points to a role for FTO in the sensing of nutrients. In this review, we explore the in vivo and in vitro evidence detailing FTO's different faces and discuss how these might link to the regulation of body weight.
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Affiliation(s)
- Giles S.H. Yeo
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Stephen O'Rahilly
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
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50
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Kinetic analysis of FTO (fat mass and obesity-associated) reveals that it is unlikely to function as a sensor for 2-oxoglutarate. Biochem J 2012; 444:183-7. [PMID: 22435707 DOI: 10.1042/bj20120065] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Genomewide-association studies have revealed that SNPs (single nucleotide polymorphisms) in FTO (fat mass and obesity-associated) are robustly associated with BMI (body mass index) and obesity. FTO is an Fe(II) 2-OG (2-oxoglutarate)-dependent dioxygenase that can demethylate 3-meT (3-methylthymine) in single-stranded DNA, as well as 3-meU (3-methyluracil) and N6-methyl adenosine in RNA. In the present paper we describe the development of an RNase-cleavage assay measuring the demethylation activity of FTO on 3-meU. RNase A cleaves at the 3'-end of pyrimidines, including uracil, and a methyl group at position three of uracil inhibits cleavage. An oligonucleotide probe was designed consisting of a DNA stem, an RNA loop containing a single 3-meU as the only RNase A-cleavage site, a fluorescent reporter on one end and a quencher at the other end. FTO demethylation of the unique 3-meU enables RNase A cleavage, releasing the quencher and enabling a fluorescent signal. In the presence of excess RNase A, FTO activity is limiting to the development of fluorescent signal, which can be read continuously and is able to discriminate between wild-type and the catalytically dead R316Q FTO. 2-OG is a co-substrate of FTO and, as a metabolite in the citric acid cycle, is a marker of intracellular nutritional status. The assay described in the present paper was used to measure, for the first time, the K(m) of FTO for 2-OG. The K(m) of 2.88 μM is up to 10-fold lower than the estimated intracellular concentrations of 2-OG, rendering it unlikely that FTO functions as a sensor for 2-OG levels.
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