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Chanarat S. UBL5/Hub1: An Atypical Ubiquitin-Like Protein with a Typical Role as a Stress-Responsive Regulator. Int J Mol Sci 2021; 22:ijms22179384. [PMID: 34502293 PMCID: PMC8431670 DOI: 10.3390/ijms22179384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 11/23/2022] Open
Abstract
Members of the ubiquitin-like protein family are known for their ability to modify substrates by covalent conjugation. The highly conserved ubiquitin relative UBL5/Hub1, however, is atypical because it lacks a carboxy-terminal di-glycine motif required for conjugation, and the whole E1-E2-E3 enzyme cascade is likely absent. Though the conjugation-mediated role of UBL5/Hub1 is controversial, it undoubtedly functions by interacting non-covalently with its partners. Several interactors of UBL5/Hub1 identified to date have suggested broad stress-responsive functions of the protein, for example, stress-induced control of pre-mRNA splicing, Fanconi anemia pathway of DNA damage repair, and mitochondrial unfolded protein response. While having an atypical mode of function, UBL5/Hub1 is still a stress protein that regulates feedback to various stimuli in a similar manner to other ubiquitin-like proteins. In this review, I discuss recent progress in understanding the functions of UBL5/Hub1 and the fundamental questions which remain to be answered.
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Affiliation(s)
- Sittinan Chanarat
- Laboratory of Molecular Cell Biology, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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2
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DNA methylation regulates hypothalamic gene expression linking parental diet during pregnancy to the offspring's risk of obesity in Psammomys obesus. Int J Obes (Lond) 2016; 40:1079-88. [PMID: 27108813 DOI: 10.1038/ijo.2016.64] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/18/2016] [Accepted: 03/22/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND/OBJECTIVE The rising incidence of obesity is a major public health issue worldwide. Recent human and animal studies suggest that parental diet can influence fetal development and is implicated with risk of obesity and type 2 diabetes in offspring. The hypothalamus is central to body energy homoeostasis and appetite by controlling endocrine signals. We hypothesise that offspring susceptibility to obesity is programmed in the hypothalamus in utero and mediated by changes to DNA methylation, which persist to adulthood. We investigated hypothalamic genome-wide DNA methylation in Psammomys obesus diet during pregnancy to the offspring's risk of obesity. METHODS Using methyl-CpG binding domain capture and deep sequencing (MBD-seq), we examined the hypothalamus of offspring exposed to a low-fat diet and standard chow diet during the gestation and lactation period. RESULTS Offspring exposed to a low-fat parental diet were more obese and had increased circulating insulin and glucose levels. Methylome profiling identified 1447 genomic regions of differential methylation between offspring of parents fed a low-fat diet compared with parents on standard chow diet. Pathway analysis shows novel DNA methylation changes of hypothalamic genes associated with neurological function, nutrient sensing, appetite and energy balance. Differential DNA methylation corresponded to changes in hypothalamic gene expression of Tas1r1 and Abcc8 in the offspring exposed to low-fat parental diet. CONCLUSION Subject to parental low-fat diet, we observe DNA methylation changes of genes associated with obesity in offspring.
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Kaspi A, Ziemann M, Keating ST, Khurana I, Connor T, Spolding B, Cooper A, Lazarus R, Walder K, Zimmet P, El-Osta A. Non-referenced genome assembly from epigenomic short-read data. Epigenetics 2015; 9:1329-38. [PMID: 25437048 DOI: 10.4161/15592294.2014.969610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
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Affiliation(s)
- Antony Kaspi
- a Epigenetics in Human Health and Disease Laboratory ; Baker IDI Heart and Diabetes Institute ; The Alfred Medical Research and Education Precinct ; Melbourne , Victoria , Australia
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4
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Cesar ASM, Regitano LCA, Koltes JE, Fritz-Waters ER, Lanna DPD, Gasparin G, Mourão GB, Oliveira PSN, Reecy JM, Coutinho LL. Putative regulatory factors associated with intramuscular fat content. PLoS One 2015; 10:e0128350. [PMID: 26042666 PMCID: PMC4456163 DOI: 10.1371/journal.pone.0128350] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 04/26/2015] [Indexed: 01/12/2023] Open
Abstract
Intramuscular fat (IMF) content is related to insulin resistance, which is an important prediction factor for disorders, such as cardiovascular disease, obesity and type 2 diabetes in human. At the same time, it is an economically important trait, which influences the sensorial and nutritional value of meat. The deposition of IMF is influenced by many factors such as sex, age, nutrition, and genetics. In this study Nellore steers (Bos taurus indicus subspecies) were used to better understand the molecular mechanisms involved in IMF content. This was accomplished by identifying differentially expressed genes (DEG), biological pathways and putative regulatory factors. Animals included in this study had extreme genomic estimated breeding value (GEBV) for IMF. RNA-seq analysis, gene set enrichment analysis (GSEA) and co-expression network methods, such as partial correlation coefficient with information theory (PCIT), regulatory impact factor (RIF) and phenotypic impact factor (PIF) were utilized to better understand intramuscular adipogenesis. A total of 16,101 genes were analyzed in both groups (high (H) and low (L) GEBV) and 77 DEG (FDR 10%) were identified between the two groups. Pathway Studio software identified 13 significantly over-represented pathways, functional classes and small molecule signaling pathways within the DEG list. PCIT analyses identified genes with a difference in the number of gene-gene correlations between H and L group and detected putative regulatory factors involved in IMF content. Candidate genes identified by PCIT include: ANKRD26, HOXC5 and PPAPDC2. RIF and PIF analyses identified several candidate genes: GLI2 and IGF2 (RIF1), MPC1 and UBL5 (RIF2) and a host of small RNAs, including miR-1281 (PIF). These findings contribute to a better understanding of the molecular mechanisms that underlie fat content and energy balance in muscle and provide important information for the production of healthier beef for human consumption.
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Affiliation(s)
- Aline S. M. Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | | | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Eric R. Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Dante P. D. Lanna
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Gustavo Gasparin
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Gerson B. Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Priscila S. N. Oliveira
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565–905, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Luiz L. Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
- * E-mail:
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5
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Yako YY, Echouffo-Tcheugui JB, Balti EV, Matsha TE, Sobngwi E, Erasmus RT, Kengne AP. Genetic association studies of obesity in Africa: a systematic review. Obes Rev 2015; 16:259-72. [PMID: 25641693 DOI: 10.1111/obr.12260] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 12/31/2022]
Abstract
Obesity is increasing in Africa, but the underlying genetic background largely remains unknown. We assessed existing evidence on genetic determinants of obesity among populations within Africa. MEDLINE and EMBASE were searched and the bibliographies of retrieved articles were examined. Included studies had to report on the association of a genetic marker with obesity indices and the presence/occurrence of obesity/obesity trait. Data were extracted on study design and characteristics, genetic determinants and effect estimates of associations with obesity indices. According to this data, over 300 polymorphisms in 42 genes have been studied in various population groups within Africa mostly through the candidate gene approach. Polymorphisms in genes such as ACE, ADIPOQ, ADRB2, AGRP, AR, CAPN10, CD36, C7orf31, DRD4, FTO, MC3R, MC4R, SGIP1 and LEP were found to be associated with various measures of obesity. Of the 36 polymorphisms previously validated by genome-wide association studies (GWAS) elsewhere, only FTO and MC4R polymorphisms showed significant associations with obesity in black South Africans, Nigerians and Ghanaians. However, these data are insufficient to establish the true nature of genetic susceptibility to obesity in populations within Africa. There has been recent progress in describing the genetic architecture of obesity among populations within Africa. This effort needs to be sustained via GWAS studies.
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Affiliation(s)
- Y Y Yako
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa; Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
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6
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Masopust M, Weisz F, Bartenschlager H, Knoll A, Vykoukalová Z, Geldermann H, Cepica S. Porcine ubiquitin-like 5 (UBL5) gene: genomic organization, polymorphisms, mRNA cloning, splicing variants and association study. Mol Biol Rep 2014; 41:2353-62. [PMID: 24458823 DOI: 10.1007/s11033-014-3089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
Ubiquitin-like 5 (UBL5), which is supposed to be involved in regulation of feed intake, energy metabolism, obesity and type 2 diabetes, is located at position 62.1 cM on the pig chromosome 2 region harbouring quantitative trait loci for carcass and meat quality. The 4,354 bp genomic sequence (FR798948) of the porcine gene encompassing the promoter and entire gene was cloned by polymerase chain reaction. Comparative sequencing revealed 13 polymorphisms in noncoding regions. Synthesis of full-length cDNA sequences using rapid amplification of 5' and 3' ends showed three splice variants. Variants 1 and 2 differ in transcription length for the untranslated part of exon 1 with deduced protein of 73 amino acid (aa) residues and 100 % identities between human, mouse and other species. Variant 3, with 4 bp deletion at the 3' end of exon 2, encodes a truncated protein with 28 aa residues. In a Wild boar×Meishan F2 population (n = 334) with 47 recorded traits, loci FR798948:g.2788G>A and FR798948:g.2141T>C were associated at nominal P < 0.05 with fat deposition, growth and fattening and muscling but after adjustment for multiple testing (Benjamini and Hochberg, J R Stat Soc B 57:289-300, 1995) only eight fat deposition traits showed suggestive association with FR798948:g.2788G>A at adjusted P < 0.10. In a Meishan×Large White (MLW) cross (n = 562) with six trait records available, FR798948:g.2141T>C showed suggestive association with growth (adjusted P = 0.0690). As association mapping conducted in the outbred MLW population is more precise than in the three generation F2 population the UBL5 gene tends to be associated with growth rather than with fat accretion.
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Affiliation(s)
- Martin Masopust
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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7
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Cepica S, Zambonelli P, Weisz F, Bigi M, Knoll A, Vykoukalová Z, Masopust M, Gallo M, Buttazzoni L, Davoli R. Association mapping of quantitative trait loci for carcass and meat quality traits at the central part of chromosome 2 in Italian Large White pigs. Meat Sci 2013; 95:368-75. [PMID: 23747631 DOI: 10.1016/j.meatsci.2013.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/24/2013] [Accepted: 05/01/2013] [Indexed: 01/13/2023]
Abstract
Association mapping of the central part of porcine chromosome 2 harboring QTLs for carcass and meat quality traits was performed with 17 gene-tagged SNPs located between 44.0 and 77.5 Mb on a physical map (Sscrofa10.2) in Italian Large White pigs. For the analyzed animals records of estimated breeding values for average daily gain, back fat thickness, lean cuts, ham weight, feed conversion ratio, pH1, pHu, CIE L*, CIE a*, CIE b* and drip loss were available. A significant QTL for fat deposition (adjusted P=0.0081) and pH1 (adjusted P=0.0972) to MYOD1 at position 44.4 Mb and a QTL for growth and meatiness (adjusted P=0.0238-0.0601) to UBL5 at position 68.9 Mb were mapped. These results from association mapping are much more accurate than those from linkage mapping and facilitate further search for position candidate genes and causative mutations needed for application of markers through marker assisted selection.
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Affiliation(s)
- S Cepica
- Institute of Animal Physiology and Genetics, The Academy of Sciences of the Czech Republic, Liběchov, Czech Republic.
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Del-Aguila JL, Beitelshees AL, Cooper-Dehoff RM, Chapman AB, Gums JG, Bailey K, Gong Y, Turner ST, Johnson JA, Boerwinkle E. Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. THE PHARMACOGENOMICS JOURNAL 2013; 14:35-40. [PMID: 23400010 PMCID: PMC3812324 DOI: 10.1038/tpj.2013.3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/13/2012] [Accepted: 01/03/2013] [Indexed: 12/02/2022]
Abstract
Hydrochlorothiazide (HCTZ) is one of the most widely prescribed antihypertensive medications. Although it is well known that HCTZ is associated with hyperglycemia and hypertriglyceridemia, the mechanisms underlying these adverse effects are not well understood. We performed a genome-wide association study and meta-analysis of the change in fasting plasma glucose and triglycerides in response to HCTZ from two different clinical trials: the Pharmacogenomic Evaluation of Antihypertensive Responses and the Genetic Epidemiology of Responses to Antihypertensive studies. Two single-nucleotide polymorphisms (rs12279250 and rs4319515 (r2=0.73)), located at 11p15.1 in the NELL1 gene, achieved genome-wide significance for association with change in fasting plasma triglycerides in African Americans, whereby each variant allele was associated with a 28 mg dl−1 increase in the change in triglycerides. NELL1 encodes a cytoplasmic protein that contains epidermal growth factor-like repeats and has been shown to represses adipogenic differentiation. These findings may represent a novel mechanism underlying HCTZ-induced adverse metabolic effects.
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Affiliation(s)
- J L Del-Aguila
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - A L Beitelshees
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD, USA
| | - R M Cooper-Dehoff
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - A B Chapman
- Renal Division, Emory University School of Medicine, Atlanta, GA, USA
| | - J G Gums
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - K Bailey
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Y Gong
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - S T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - J A Johnson
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - E Boerwinkle
- 1] Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA [2] Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX, USA
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9
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Arnaiz-Villena A, Fernández-Honrado M, Areces C, Enríquez-de-Salamanca M, Abd-El-Fatah-Khalil S, Coca C, Arribas I, Algora M, Rey D. Amerindians show no association of PPAR-γ2 gene Ala12 allele and obesity: an “unthrifty” variant population genetics. Mol Biol Rep 2012; 40:1767-74. [DOI: 10.1007/s11033-012-2230-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/10/2012] [Indexed: 01/22/2023]
Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, The Madrid Regional Blood Center, University Complutense, Pabellón 5, Planta 4. Avda. Complutense s/n, 28040, Madrid, Spain.
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10
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Pérusse L, Rankinen T, Zuberi A, Chagnon YC, Weisnagel SJ, Argyropoulos G, Walts B, Snyder EE, Bouchard C. The Human Obesity Gene Map: The 2004 Update. ACTA ACUST UNITED AC 2012; 13:381-490. [PMID: 15833932 DOI: 10.1038/oby.2005.50] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This paper presents the eleventh update of the human obesity gene map, which incorporates published results up to the end of October 2004. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTLs) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2004, 173 human obesity cases due to single-gene mutations in 10 different genes have been reported, and 49 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 166 genes which, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 221. The number of human obesity QTLs derived from genome scans continues to grow, and we have now 204 QTLs for obesity-related phenotypes from 50 genome-wide scans. A total of 38 genomic regions harbor QTLs replicated among two to four studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably with 358 findings of positive associations with 113 candidate genes. Among them, 18 genes are supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. Overall, >600 genes, markers, and chromosomal regions have been associated or linked with human obesity phenotypes. The electronic version of the map with links to useful publications and genomic and other relevant sites can be found at http://obesitygene.pbrc.edu.
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Affiliation(s)
- Louis Pérusse
- Division of Kinesiology, Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Sainte-Foy, Québec, Canada
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Rey D, Fernandez-Honrado M, Areces C, Algora M, Abd-El-Fatah-Khalil S, Enriquez-de-Salamanca M, Coca C, Arribas I, Arnaiz-Villena A. Amerindians show no association of PC-1 gene Gln121 allele and obesity: a thrifty gene population genetics. Mol Biol Rep 2012; 39:7687-93. [PMID: 22327785 DOI: 10.1007/s11033-012-1604-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 02/02/2012] [Indexed: 01/06/2023]
Abstract
PC-1 Gln121 gene is a risk factor for type 2 diabetes, obesity and insulin resistance in European/American Caucasoids and Orientals. We have aimed to correlate for the first time this gene in Amerindians with obesity and their corresponding individuals genotypes with obesity in order to establish preventive medicine programs for this population and also studying the evolution of gene frequencies in world populations. Central obesity was diagnosed by waist circumference perimeter and food intake independent HDL-cholesterol plasma levels were measured. HLA genes were determined in order to more objectively ascertain participants Amerindians origin. 321 Amerindian blood donors who were healthy according to the blood doning parameters were studied. No association was found between PC-1 Gln121 variant and obesity. Significant HDL-cholesterol lower values were found in the PC-1 Lys121 bearing gene individuals versus PC-1 Gln121 bearing gene ones (45.1 ± 12.7 vs. 48.7 ± 15.2 mg/dl, p < 0.05). Population analyses showed a world geographical gradient in the PC-1 Gln121 allele frequency: around 9% in Orientals, 15% in European Caucasoids and 76% in Negroids. The conclusions are: (1) No association of PC-1 Gln121 gene is found with obesity in Amerindians when association is well established in Europeans. (2) PC-1 Gln121 gene is associated to higher levels of HDL-cholesterol than the alternative PC-1 Lys121 allele. This may be specific for Amerindians. (3) Amerindians have an intermediate frequency of this possible PC-1 Gln121 thrifty gene when compared with Negroid African Americans (78.5%) or Han Chinese (7.5%, p < 0.0001). Historical details of African and other groups may support the hypothesis that PC-1 Gln121 is indeed a thrifty gene.
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Affiliation(s)
- Diego Rey
- Departamento de Inmunología, Facultad de Medicina, The Madrid Regional Blood Center, University Complutense, Pabellón 5, planta 4 Avda Complutense, 28040 Madrid, Spain
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12
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Cummings N, Shields KA, Curran JE, Bozaoglu K, Trevaskis J, Gluschenko K, Cai G, Comuzzie AG, Dyer TD, Walder KR, Zimmet P, Collier GR, Blangero J, Jowett JBM. Genetic variation in SH3-domain GRB2-like (endophilin)-interacting protein 1 has a major impact on fat mass. Int J Obes (Lond) 2011; 36:201-6. [PMID: 21407171 DOI: 10.1038/ijo.2011.67] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The SH3-domain GRB2-like (endophilin)-interacting protein 1 (SGIP1) gene has been shown to be differentially expressed in the hypothalamus of lean versus obese Israeli sand rats (Psammomys obesus), and is suspected of having a role in regulating food intake. The purpose of this study was to assess the role of genetic variation in SGIP1 in human disease. SUBJECTS We performed single-nucleotide polymorphism (SNP) genotyping in a large family pedigree cohort from the island of Mauritius. The Mauritius Family Study (MFS) consists of 400 individuals from 24 Indo-Mauritian families recruited from the genetically homogeneous population of Mauritius. We measured markers of the metabolic syndrome, including diabetes and obesity-related phenotypes such as fasting plasma glucose, waist:hip ratio, body mass index and fat mass. RESULTS Statistical genetic analysis revealed associations between SGIP1 polymorphisms and fat mass (in kilograms) as measured by bioimpedance. SNP genotyping identified associations between several genetic variants and fat mass, with the strongest association for rs2146905 (P=4.7 × 10(-5)). A strong allelic effect was noted for several SNPs where fat mass was reduced by up to 9.4% for individuals homozygous for the minor allele. CONCLUSIONS Our results show association between genetic variants in SGIP1 and fat mass. We provide evidence that variation in SGIP1 is a potentially important determinant of obesity-related traits in humans.
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Affiliation(s)
- N Cummings
- Genomics and Systems Biology, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
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Ma SL, Tang NLS, Tam CWC, Lui VWC, Lam LCW, Chiu HFK, Driver JA, Pastorino L, Lu KP. A PIN1 polymorphism that prevents its suppression by AP4 associates with delayed onset of Alzheimer's disease. Neurobiol Aging 2010; 33:804-13. [PMID: 20580132 DOI: 10.1016/j.neurobiolaging.2010.05.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/12/2010] [Accepted: 05/16/2010] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD), the most common form of dementia, is characterized by the presence of neurofibrillary tangles composed of tau and senile plaques of amyloid-beta peptides (Aβ) derived from amyloid precursor protein (APP). Pin1 is a unique prolyl isomerase that has been shown to protect against age-dependent neurodegeneration by acting on phosphorylated tau and APP to suppress tangle formation and amyloidogenic APP processing. Here we report a functional polymorphism, rs2287839, in the Pin1 promoter that is significantly associated with a 3-year delay in the average age at onset (AAO) of late-onset AD in a Chinese population. More significantly, the Pin1 polymorphism rs2287839 is located within the consensus binding motif for the brain-selective transcription factor, AP4 (CAGCTG) and almost completely abolishes the ability of AP4 to bind and suppress the Pin1 promoter, as shown by chromatin immunoprecipitation, electrophoretic mobility shift assay, and promoter luciferase assay. Moreover, overexpression or knockdown of AP4 resulted in an 80% reduction or 2-fold increase in endogenous Pin1 levels, respectively. Thus, AP4 is a novel transcriptional repressor of Pin1 expression and the Pin1 promoter single nucleotide polymorphism (SNP) identified in this study that prevents such suppression is associated with delayed onset of AD. These results indicate that regulation of Pin1 by AP4 plays a critical role in determining age at onset of AD and might be a novel therapeutic target to delay the onset of AD.
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Affiliation(s)
- Suk Ling Ma
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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14
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Bernstein HG, Lendeckel U, Dobrowolny H, Stauch R, Steiner J, Grecksch G, Becker A, Jirikowski GF, Bogerts B. Beacon-like/ubiquitin-5-like immunoreactivity is highly expressed in human hypothalamus and increased in haloperidol-treated schizophrenics and a rat model of schizophrenia. Psychoneuroendocrinology 2008; 33:340-51. [PMID: 18191906 DOI: 10.1016/j.psyneuen.2007.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 11/30/2007] [Accepted: 12/01/2007] [Indexed: 10/22/2022]
Abstract
The beacon gene is involved in the regulation of energy metabolism, food intake, and obesity. We localized its gene product, beacon-/ubiquitin 5-like immunoreactivity in brains of normal-weight, non-psychotic individuals, adipose (BMI over 32), non-psychotic individuals, and haloperidol-treated schizophrenics. The protein was found to be highly expressed in many neurons of the paraventricular and supraoptic hypothalamic nuclei. Besides, it was detected in neurons of other hypothalamic areas (suprachiasmatic, arcuate, and ventromedial nuclei) as well as outside the hypothalamus (Nuc. basalis Meynert, thalamus, hippocampus, and some neocortical areas). A morphometric analysis of beacon-immunoreactive hypothalamic and neocortical neurons revealed that compared to normal-weight controls in haloperidol-treated schizophrenics, there was a significant increase of protein-expressing supraoptic, paraventricular, and orbitofrontal neurons. However, a significant increase in beacon-expressing supraoptic neurons was also seen in adipose, non-psychotic individuals in comparison with normal-weight controls. Haloperidol at different doses has no effect on beacon expression in SHSY5Y neuroblastoma cells, which makes the assumption unlikely that haloperidol per se is responsible for the increased neuronal expression of the peptide in schizophrenics. In rats with a neonatal lesion of the ventral hippocampus (a widely used animal model of schizophrenia), we found an increased neuronal expression of beacon in the paraventricular and supraoptic nuclei. We suppose that elevated hypothalamic expression of beacon-like protein in non-obese schizophrenics is not primarily related to metabolic alterations, but to a certain role in schizophrenia, which is possibly unrelated to aspects of weight gain and obesity. The latter assumption finds some support by data obtained in rats with ventral hippocampus lesion.
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Affiliation(s)
- Hans-Gert Bernstein
- Department of Psychiatry, University of Magdeburg, Leipziger Str. 44, D-39120 Magdeburg, Germany.
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Riha RL, Diefenbach K, Jennum P, McNicholas WT. Genetic aspects of hypertension and metabolic disease in the obstructive sleep apnoea–hypopnoea syndrome. Sleep Med Rev 2008; 12:49-63. [DOI: 10.1016/j.smrv.2007.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Aston-Mourney K, Wong N, Kebede M, Zraika S, Balmer L, McMahon JM, Fam BC, Favaloro J, Proietto J, Morahan G, Andrikopoulos S. Increased nicotinamide nucleotide transhydrogenase levels predispose to insulin hypersecretion in a mouse strain susceptible to diabetes. Diabetologia 2007; 50:2476-85. [PMID: 17922105 DOI: 10.1007/s00125-007-0814-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 07/17/2007] [Indexed: 01/02/2023]
Abstract
AIMS/HYPOTHESIS Insulin hypersecretion may be an independent predictor of progression to type 2 diabetes. Identifying genes affecting insulin hypersecretion are important in understanding disease progression. We have previously shown that diabetes-susceptible DBA/2 mice congenitally display high insulin secretion. We studied this model to map and identify the gene(s) responsible for this trait. METHODS Intravenous glucose tolerance tests followed by a genome-wide scan were performed on 171 (C57BL/6 x DBA/2) x C57BL/6 backcross mice. RESULTS A quantitative trait locus, designated hyperinsulin production-1 (Hip1), was mapped with a logarithm of odds score of 7.7 to a region on chromosome 13. Production of congenic mice confirmed that Hip1 influenced the insulin hypersecretion trait. By studying appropriate recombinant inbred mouse strains, the Hip1 locus was further localised to a 2 Mb interval, which contained only nine genes. Expression analysis showed that the only gene differentially expressed in islets isolated from the parental strains was Nnt, which encodes the mitochondrial proton pump, nicotinamide nucleotide transhydrogenase (NNT). We also found in five mouse strains a positive correlation (r2 = 0.90, p < 0.01) between NNT activity and first-phase insulin secretion, emphasising the importance of this enzyme in beta cell function. Furthermore, of these five strains, only those with high NNT activity are known to exhibit severe diabetes after becoming obese. CONCLUSIONS/INTERPRETATION Insulin hypersecretion is associated with increased Nnt expression. We suggest that NNT must play an important role in beta cell function and that its effect on the high insulin secretory capacity of the DBA/2 mouse may predispose beta cells of these mice to failure.
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Affiliation(s)
- K Aston-Mourney
- The University of Melbourne Department of Medicine (AH/NH), Heidelberg Repatriation Hospital, Heidelberg Heights, Melbourne, VIC, Australia
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Benyamin B, Sørensen TIA, Schousboe K, Fenger M, Visscher PM, Kyvik KO. Are there common genetic and environmental factors behind the endophenotypes associated with the metabolic syndrome? Diabetologia 2007; 50:1880-1888. [PMID: 17624514 DOI: 10.1007/s00125-007-0758-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 06/05/2007] [Indexed: 01/01/2023]
Abstract
AIMS/HYPOTHESIS The cluster of obesity, insulin resistance, dyslipidaemia and hypertension, called the metabolic syndrome, has been suggested as a risk factor for cardiovascular disease and type 2 diabetes. The aim of the present study was to evaluate whether there are common genetic and environmental factors influencing this cluster in a general population of twin pairs. MATERIALS AND METHODS A multivariate genetic analysis was performed on nine endophenotypes associated with the metabolic syndrome from 625 adult twin pairs of the GEMINAKAR study of the Danish Twin Registry. RESULTS All endophenotypes showed moderate to high heritability (0.31-0.69) and small common environmental variance (0.05-0.21). In general, genetic and phenotypic correlations between the endophenotypes were strong only within sets of physiologically similar endophenotypes, but weak to moderate for other pairs of endophenotypes. However, moderate correlations between insulin resistance indices and either obesity-related endophenotypes or triacylglycerol levels indicated that some common genetic backgrounds are shared between those components. CONCLUSIONS/INTERPRETATION We demonstrated that, in a general population, the endophenotypes associated with the metabolic syndrome apparently do not share a substantial common genetic or familial environmental background.
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Affiliation(s)
- B Benyamin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - T I A Sørensen
- Danish Epidemiology Science Centre, Institute of Preventive Medicine, Copenhagen University Hospitals, Centre for Health and Society, Copenhagen, Denmark
| | - K Schousboe
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Sdr. Boulevard 23A, 5000, Odense C, Denmark
| | - M Fenger
- Department of Clinical Biochemistry, University Hospital of Copenhagen, Hvidovre, Denmark
| | - P M Visscher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - K O Kyvik
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Sdr. Boulevard 23A, 5000, Odense C, Denmark.
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18
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Oikawa S. [Metabolic syndrome and aging]. Nihon Ronen Igakkai Zasshi 2007; 44:168-70. [PMID: 17527009 DOI: 10.3143/geriatrics.44.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
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Kent JW, Mahaney MC, Comuzzie AG, Göring HHH, Almasy L, Dyer TD, Cole SA, MacCluer JW, Blangero J. Quantitative trait locus on Chromosome 19 for circulating levels of intercellular adhesion molecule-1 in Mexican Americans. Atherosclerosis 2006; 195:367-73. [PMID: 17112530 PMCID: PMC2719976 DOI: 10.1016/j.atherosclerosis.2006.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 09/22/2006] [Accepted: 10/06/2006] [Indexed: 10/23/2022]
Abstract
Circulating soluble intercellular adhesion molecule-1 (sICAM-1) is a biochemical marker of inflammation. We performed variance-components-based quantitative genetic analyses in SOLAR of sICAM-1 in 1170 individuals from Mexican American families in the San Antonio Family Heart Study. The trait is heritable (h(2)=0.50+/-0.06, P<10(-6)). Multipoint linkage analysis using a approximately 10-cM microsatellite map revealed a region on Chromosome 19p near marker D19S586 showing strong evidence of linkage for sICAM-1 (empirically adjusted univariate-equivalent LOD=4.95), coincident with the structural gene ICAM1. This region has been identified previously as a QTL for inflammatory, autoimmune, and metabolic syndrome traits. There is significant evidence (P=0.0023) of locus heterogeneity for sICAM-1 in this sample: a subset of pedigrees contributes most of the linkage signal for sICAM-1 on Chromosome 19, suggesting a logical focus for future genetic dissection of the trait.
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Affiliation(s)
- Jack W Kent
- Department of Genetics, Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, TX 78245-0549, USA.
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Abstract
Complex interactions between inherited factors and the environment determine an individual's susceptibility to type 2 diabetes mellitus and related syndromes. Insulin resistance, obesity, hypertension, and hyperlipidemia frequently precede the development of frank diabetes and aggregate in families. Several genome-wide scans have recently been performed in families with this constellation of findings, called the "metabolic syndrome." These analyses strongly support an inherited component to the syndrome. In this review, we provide an overview of the evidence in support of an inherited contribution to the metabolic syndrome and the search for causative genomic regions. When multiple genome scans involving different patient cohorts implicate a common genomic region as susceptible to the metabolic syndrome, it is highly likely that causative genes reside in that area. Identification of these genes will dramatically improve our understanding of the mechanisms that underlie the metabolic syndrome, and could lead to novel treatment strategies. It is hoped that these therapies will also prevent the future development of type 2 diabetes mellitus and atherosclerotic complications, both common among individuals affected by the metabolic syndrome.
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Affiliation(s)
- Michèle M Sale
- Department of Internal Medicine, Section on Nephrology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1053, USA
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21
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Benedetti C, Haynes CM, Yang Y, Harding HP, Ron D. Ubiquitin-like protein 5 positively regulates chaperone gene expression in the mitochondrial unfolded protein response. Genetics 2006; 174:229-39. [PMID: 16816413 PMCID: PMC1569816 DOI: 10.1534/genetics.106.061580] [Citation(s) in RCA: 284] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Perturbation of the protein-folding environment in the mitochondrial matrix selectively upregulates the expression of nuclear genes encoding mitochondrial chaperones. To identify components of the signal transduction pathway(s) mediating this mitochondrial unfolded protein response (UPR(mt)), we first isolated a temperature-sensitive mutation (zc32) that conditionally activates the UPR(mt) in C. elegans and subsequently searched for suppressors by systematic inactivation of genes. RNAi of ubl-5, a gene encoding a ubiquitin-like protein, suppresses activation of the UPR(mt) markers hsp-60::gfp and hsp-6::gfp by the zc32 mutation and by other manipulations that promote mitochondrial protein misfolding. ubl-5 (RNAi) inhibits the induction of endogenous mitochondrial chaperone encoding genes hsp-60 and hsp-6 and compromises the ability of animals to cope with mitochondrial stress. Mitochondrial morphology and assembly of multi-subunit mitochondrial complexes of biotinylated proteins are also perturbed in ubl-5(RNAi) worms, indicating that UBL-5 also counteracts physiological levels of mitochondrial stress. Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms, suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding.
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Affiliation(s)
- Cristina Benedetti
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York 10016, USA
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22
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Siani A, Strazzullo P. Tackling the genetic bases of metabolic syndrome: a realistic objective? Nutr Metab Cardiovasc Dis 2006; 16:309-312. [PMID: 16829338 DOI: 10.1016/j.numecd.2005.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 12/30/2005] [Indexed: 11/20/2022]
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Rankinen T, Zuberi A, Chagnon YC, Weisnagel SJ, Argyropoulos G, Walts B, Pérusse L, Bouchard C. The human obesity gene map: the 2005 update. Obesity (Silver Spring) 2006; 14:529-644. [PMID: 16741264 DOI: 10.1038/oby.2006.71] [Citation(s) in RCA: 685] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper presents the 12th update of the human obesity gene map, which incorporates published results up to the end of October 2005. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTL) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2005, 176 human obesity cases due to single-gene mutations in 11 different genes have been reported, 50 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 244 genes that, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 408. The number of human obesity QTLs derived from genome scans continues to grow, and we now have 253 QTLs for obesity-related phenotypes from 61 genome-wide scans. A total of 52 genomic regions harbor QTLs supported by two or more studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably, with 426 findings of positive associations with 127 candidate genes. A promising observation is that 22 genes are each supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. The electronic version of the map with links to useful publications and relevant sites can be found at http://obesitygene.pbrc.edu.
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Affiliation(s)
- Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA 70808-4124, USA
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Affiliation(s)
- Ambika Babu
- Division of Endocrinology, John H. Stroger Hospital and Rush University Medical Center, Chicago, IL, USA
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Ng YK, Brailoiu GC, Dun SL, Ling EA, Yang J, Chang JK, Dun NJ. Beacon immunoreactivity in the rat hypothalamus. J Neurosci Res 2006; 83:1106-17. [PMID: 16511859 DOI: 10.1002/jnr.20808] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beacon (BC) is a peptide of 73 amino acids, whose gene expression was first reported in the hypothalamus of Psammomys obesus (or Israeli sand rat). To appreciate better the functional role of BC in normal rats and sand rats, the distribution of BC immunoreactivity (irBC) and its subcellular localization were studied in the brain of Sprague-Dawley rats. In the hypothalamus, intense staining was present in neurons of the supraoptic (SO), paraventricular (PVH), and accessory neurosecretory nuclei and in cell processes of median eminence. Double labeling of the hypothalamic sections with mouse monoclonal oxytocin (OT) antibody and rabbit polyclonal BC antiserum revealed that nearly all OT-immunoreactive cells from SO, PVH, and accessory neurosecretory nuclei were irBC. Double labeling of the sections with guinea pig vasopressin (VP) antiserum and BC antiserum showed that a population of VP-immunoreactive neurons was irBC. By immunoelectron microscopy, immunoreactive product was associated with mitochondrial membranes or appeared as electron-dense bodies in many PVH and SO neurons. Most of the neurosecretory granules were unstained for BC. Taken together, our results indicate the presence of beacon in the OT-containing neurons and a population of VP-containing neurons, mostly associated with mitochondrial membrane. Insofar as the amino acids sequence of beacon is identical to that of ubiquitin-like 5, it is possible that the distribution of BC immunoreactivity noted in our study is that of ubiquitin-like 5 peptide in the rat hypothalamus.
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Affiliation(s)
- Y K Ng
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Seda O, Liska F, Krenova D, Kazdova L, Sedova L, Zima T, Peng J, Pelinkova K, Tremblay J, Hamet P, Kren V. Dynamic genetic architecture of metabolic syndrome attributes in the rat. Physiol Genomics 2005; 21:243-52. [PMID: 15728334 DOI: 10.1152/physiolgenomics.00230.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The polydactylous rat strain (PD/Cub) is a highly inbred (F > 90) genetic model of metabolic syndrome. The aim of this study was to analyze the genetic architecture of the metabolic derangements found in the PD/Cub strain and to assess its dynamics in time and in response to diet and medication. We derived a PD/Cub × BN/Cub (Brown Norway) F2 intercross population of 149 male rats and performed metabolic profiling and genotyping and multiple levels of genetic linkage and statistical analyses at five different stages of ontogenesis and after high-sucrose diet feeding and dexamethasone administration challenges. The interval mapping analysis of 83 metabolic and morphometric traits revealed over 50 regions genomewide with significant or suggestive linkage to one or more of the traits in the segregating PD/Cub × BN/Cub population. The multiple interval mapping showed that, in addition to “single” quantitative train loci, there are more than 30 pairs of loci across the whole genome significantly influencing the variation of particular traits in an epistatic fashion. This study represents the first whole genome analysis of metabolic syndrome in the PD/Cub model and reveals several new loci previously not connected to the genetics of insulin resistance and dyslipidemia. In addition, it attempts to present the concept of “dynamic genetic architecture” of metabolic syndrome attributes, evidenced by shifts in the genetic determination of syndrome features during ontogenesis and during adaptation to the dietary and pharmacological influences.
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Affiliation(s)
- Ondrej Seda
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal, Montreal, Canada
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