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Fu Y, Wang L, Tang Z, Yin D, Xu J, Fan Y, Li X, Zhao S, Liu X. An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat-related traits in pigs. Anim Genet 2020; 51:683-693. [PMID: 32557818 DOI: 10.1111/age.12971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/27/2022]
Abstract
Meat quality improvement is of great interest to researchers in pig breeding and many researchers have identified abundant associated quantitative trait loci, genes and polymorphisms (QTXs) for fat-related traits. However, it is challenging to determine credible candidate genes from a mass of associations. The efficiency of identification of credible candidate genes in these QTXs is restricted by limited integration analyses of data from multiple omics. In this study, we constructed a 'candidate gene map' of fat-related traits in pigs based on published literature and the latest genome. In total, 6,861 QTXs, which covered 9,323 genes on the pig genome, were used. Combining the QTX hotspots and pathway analysis, we identified 180 candidate genes that may regulate the fat-related traits, and choose PNPLA2, PPARG, SREBF1, ACACA, PPARD and PPARA as credible candidate genes. In addition, we discussed the importance of incorporating transcriptome data and genomic data in causal gene identification, and the multi-omics information can effectively improve the credibility of identified candidate genes.
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Affiliation(s)
- Y Fu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - L Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - D Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Jain V, Kumar A, Ahmad N, Jana M, Kalaivani M, Kumar B, Shastri S, Jain O, Kabra M. Genetic polymorphisms associated with obesity and non-alcoholic fatty liver disease in Asian Indian adolescents. J Pediatr Endocrinol Metab 2019; 32:749-758. [PMID: 31216264 DOI: 10.1515/jpem-2018-0543] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/23/2019] [Indexed: 12/28/2022]
Abstract
Background The objective of this study was to investigate the association of polymorphisms in four genes, tumor necrosis factor-α (TNFA), patatin-like phospholipase domain containing 3 (PNPLA3), adiponectin (ADIPOQ) and apolipoprotein C3 (APOC3), with obesity and non-alcoholic fatty liver disease (NAFLD) in Asian Indian adolescents. Methods In this case-control study, 218 Asian Indian adolescents with overweight/obesity and 86 lean healthy adults without fatty liver were enrolled. Hepatic steatosis was assessed and graded by ultrasonography (USG). Serum insulin, lipids, alanine aminotransferase (ALT), aspartate aminotransferase (AST), TNF-α, adiponectin and apolipoprotein C3 were measured and genotyping was done. Frequencies of variant and wild genotypes in all adolescents and in the subgroups without steatosis, with grade 1 steatosis and with grade 2 or 3 steatosis were compared to those in the controls. The frequencies were also compared in the overweight adolescents with grade 2 or 3 steatosis and without steatosis. Results Variant genotypes of polymorphisms -863 C > A and -1031 T > C of the TNFA gene, 455 T > C of the APOC3 gene and the wild type of +276 G > T of the ADIPOQ gene were associated with obesity with odds ratios (OR, 95% confidence interval [CI]) of 2.5 (1.5-4.4), 2.5 (1.5-4.2), 2.0 (1.1-3.6) and 2.5 (1.4-5.0), respectively. Polymorphisms 455 T > C of APOC3 and rs738409 C > G of PNPLA3 were associated with NAFLD. Fasting insulin and triglycerides (TG) were higher in the adolescents with homozygous variant polymorphisms -1031 T > C of TNFA and 455 T > C of APOC3 genes, respectively. Conclusions Several polymorphisms were noted to have a significant association with obesity and NAFLD in Asian Indian adolescents.
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Affiliation(s)
- Vandana Jain
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Anil Kumar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Nayeem Ahmad
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Manisha Jana
- Department of Radiology, All India Institute of Medical Sciences, New Delhi, India
| | - Mani Kalaivani
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Brijesh Kumar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Shivaram Shastri
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Oshima Jain
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Larrieta-Carrasco E, Flores YN, Macías-Kauffer LR, Ramírez-Palacios P, Quiterio M, Ramírez-Salazar EG, León-Mimila P, Rivera-Paredez B, Cabrera-Álvarez G, Canizales-Quinteros S, Zhang ZF, López-Pérez TV, Salmerón J, Velázquez-Cruz R. Genetic variants in COL13A1, ADIPOQ and SAMM50, in addition to the PNPLA3 gene, confer susceptibility to elevated transaminase levels in an admixed Mexican population. Exp Mol Pathol 2018; 104:50-58. [PMID: 29307798 DOI: 10.1016/j.yexmp.2018.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/15/2017] [Accepted: 01/03/2018] [Indexed: 12/13/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the accumulation of extra fat in liver cells not caused by alcohol. Elevated transaminase levels are common indicators of liver disease, including NAFLD. Previously, we demonstrated that PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), and GCKR (rs780094) are associated with elevated transaminase levels in overweight/obese Mexican adults. We investigated the association between 288 SNPs identified in genome-wide association studies and risk of elevated transaminase levels in an admixed Mexican-Mestizo sample of 178 cases of NAFLD and 454 healthy controls. The rs2896019, rs12483959, and rs3810622 SNPs in PNPLA3 and rs1227756 in COL13A1 were associated with elevated alanine aminotransferase (ALT, ≥40IU/L). A polygenic risk score (PRS) based on six SNPs in the ADIPOQ, COL13A1, PNPLA3, and SAMM50 genes was also associated with elevated ALT. Individuals carrying 9-12 risk alleles had 65.8% and 48.5% higher ALT and aspartate aminotransferase (AST) levels, respectively, than those with 1-4 risk alleles. The PRS showed the greatest risk of elevated ALT levels, with a higher level of significance than the individual variants. Our findings suggest a significant association between variants in COL13A1, ADIPOQ, SAMM50, and PNPLA3, and risk of NAFLD/elevated transaminase levels in Mexican adults with an admixed ancestry. This is the first study to examine high-density single nucleotide screening for genetic variations in a Mexican-Mestizo population. The extent of the effect of these variations on the development and progression of NAFLD in Latino populations requires further analysis.
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Affiliation(s)
- Elena Larrieta-Carrasco
- Departamento de Gastroenterología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico
| | - Yvonne N Flores
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Instituto Mexicano del Seguro Social (IMSS), Blvd. Benito Juárez No. 31 Col. Centro, Cuernavaca, Morelos, Mexico; UCLA Department of Health Policy and Management, UCLA Kaiser Permanente Center for Health Equity, Fielding School of Public Health and Jonsson Comprehensive Cancer Center, Los Angeles, California, USA
| | - Luis R Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Paula Ramírez-Palacios
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Instituto Mexicano del Seguro Social (IMSS), Blvd. Benito Juárez No. 31 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Manuel Quiterio
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Eric G Ramírez-Salazar
- Consejo Nacional de Ciencia y Tecnología (CONACYT)-Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, México
| | - Paola León-Mimila
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Berenice Rivera-Paredez
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Instituto Mexicano del Seguro Social (IMSS), Blvd. Benito Juárez No. 31 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Guillermo Cabrera-Álvarez
- Clínica de Hígado, IMSS Hospital General Regional UMF, 1, Av. Plan de Ayala S/N, Cuernavaca, Morelos, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genomica (INMEGEN), Mexico City, Mexico
| | - Zuo-Feng Zhang
- UCLA Department of Epidemiology, Fielding School of Public Health, Los Angeles, California, USA
| | - Tania V López-Pérez
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Jorge Salmerón
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Instituto Mexicano del Seguro Social (IMSS), Blvd. Benito Juárez No. 31 Col. Centro, Cuernavaca, Morelos, Mexico; Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Rafael Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.
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Identification mouse patatin-like phospholipase domain containing protein 1 as a skin-specific and membrane-associated protein. Gene 2016; 591:344-50. [PMID: 27267404 DOI: 10.1016/j.gene.2016.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/28/2016] [Accepted: 06/03/2016] [Indexed: 11/21/2022]
Abstract
Patatin-like phospholipase domain containing protein 1 (PNPLA1) mutations have been identified to be associated with autosomal recessive congenital ichthyosis (ARCI) in recent years. However, its molecular characters have not been achieved until now. In the current study, the full length coding cDNA sequence of mouse PNPLA1 (mPNPLA1) was identified firstly. There were several putative transmembrane domains (TMDs) in mPNPLA1 by bioinformation analysis. mPNPLA1 was further found to be expressed exclusively in the membrane fraction in mammalian cells. However, it did not colocalized with the endoplasmic reticulum (ER) or lipid droplets (LDs). Moreover, the mRNA levels of mPNPLA1 was detected to be highly expressed in the skin, while very weak or even less in other mouse tissues by quantitative PCR. In addition, based on experiments with inhibitors and inducer of protein degradation pathways, mPNPLA1 was demonstrated to be degraded by macroautophagy, but not by the proteasome. These results indicated PNPLA1 was a skin-specific and membrane-associated protein for the first time, suggesting that it may mainly play a role in the skin.
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Rao KR, Lal N, Giridharan N. Genetic & epigenetic approach to human obesity. Indian J Med Res 2014; 140:589-603. [PMID: 25579139 PMCID: PMC4311311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Obesity is an important clinical and public health challenge, epitomized by excess adipose tissue accumulation resulting from an imbalance in energy intake and energy expenditure. It is a forerunner for a variety of other diseases such as type-2-diabetes (T2D), cardiovascular diseases, some types of cancer, stroke, hyperlipidaemia and can be fatal leading to premature death. Obesity is highly heritable and arises from the interplay of multiple genes and environmental factors. Recent advancements in Genome-wide association studies (GWAS) have shown important steps towards identifying genetic risks and identification of genetic markers for lifestyle diseases, especially for a metabolic disorder like obesity. According to the 12th Update of Human Obesity Gene Map there are 253 quantity trait loci (QTL) for obesity related phenotypes from 61 genome wide scan studies. Contribution of genetic propensity of individual ethnic and racial variations in obesity is an active area of research. Further, understanding its complexity as to how these variations could influence ones susceptibility to become or remain obese will lead us to a greater understanding of how obesity occurs and hopefully, how to prevent and treat this condition. In this review, various strategies adapted for such an analysis based on the recent advances in genome wide and functional variations in human obesity are discussed.
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Affiliation(s)
- K. Rajender Rao
- National Center for Laboratory Animal Sciences & National Institute of Nutrition (ICMR), Hyderabad, India
| | - Nirupama Lal
- National Center for Laboratory Animal Sciences & National Institute of Nutrition (ICMR), Hyderabad, India
| | - N.V. Giridharan
- National Center for Laboratory Animal Sciences & National Institute of Nutrition (ICMR), Hyderabad, India,Reprint requests: Dr N.V. Giridharan, National Center for Laboratory Animal Sciences (NCLAS), National Institute of Nutrition (ICMR) Hyderabad 500 008, Telangana, India e-mail:
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Identification of human patatin-like phospholipase domain-containing protein 1 and a mutant in human cervical cancer HeLa cells. Mol Biol Rep 2013; 40:5597-605. [PMID: 24057234 DOI: 10.1007/s11033-013-2661-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 09/14/2013] [Indexed: 01/04/2023]
Abstract
Recently members of mammalian patatin-like phospholipase domain containing (PNPLA) protein family have attracted attention for their critical roles in diverse aspects of lipid metabolism and signal pathway. Until now little has been known about the characteristics of PNPLA1. Here, the full length coding cDNA sequence of human PNPLA1 (hPNPLA1) was cloned for the first time, which encoded a polypeptide with 532 amino acids containing the whole patatin domain. Tissue expression profiles analysis showed that low mRNA levels of hPNPLA1 existed in various tissues, except high expression in the digestive system, bone marrow and spleen. Subcellular distribution of hPNPLA1 tagged with green fluorescence protein mainly localized to lipid droplets. Furthermore, a nonsense mutation of PNPLA1 in human cervical cancer HeLa cells was identified. The hPNPLA1 mutant encoded a protein of 412 amino acids without the C-terminal domain and did not colocalize to lipid droplets, which suggested that the C-terminal region of hPNPLA1 affected lipid droplet binding. These results identified hPNPLA1 and a mutant in HeLa cells, and provided insights into the structure and function of PNPLA1.
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Guichelaar MMJ, Gawrieh S, Olivier M, Viker K, Krishnan A, Sanderson S, Malinchoc M, Watt KD, Swain JM, Sarr M, Charlton MR. Interactions of allelic variance of PNPLA3 with nongenetic factors in predicting nonalcoholic steatohepatitis and nonhepatic complications of severe obesity. Obesity (Silver Spring) 2013; 21:1935-41. [PMID: 23418085 PMCID: PMC3896123 DOI: 10.1002/oby.20327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 11/24/2012] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Allelic variation (rs738409C→G) in adiponutrin (patatin-like phospholipase domain-containing protein 3, PNPLA3) has been associated with hepatic steatosis and liver fibrosis. The physiologic impact of the PNPLA3 G allele may be exacerbated in patients with severe obesity. In this study, we investigated the interactions of PNPLA3 rs738409 with a broad panel of metabolic and histologic characteristics of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (NASH) in patients with medically complicated obesity. DESIGN AND METHODS Consecutive patients undergoing bariatric surgery were selected for a prospective study. They underwent extensive laboratory and histologic (liver biopsy) assessment, as well as evaluation of rs738409 polymorphism by TaqMan assay. RESULTS Only 12 (8.3%) of the 144 patients had normal liver histology, with 72 (50%) NASH, of whom 15 (10.4% of total patients) had fibrosis stage 2-3. PNPLA3 GG genotype correlated positively (P < 0.05) with serum levels of alanine aminotransferase (ALT), asparate aminotransferase (AST), glucose, fibrinogen, and insulin-dependent diabetes mellitus, homeostasis model assessment-insulin resistance, and presence of NASH. Multivariate analysis indicated that PNPLA3 rs738409 G versus C allele remained an (independent) risk factor for NASH, in addition to CK-18 >145 IU/l, glucose >100 mg/dl, and C-reactive protein (CRP) >0.8 mg/dl. The probability of NASH increased from 9% (no risk factor) to 82% if all four risk factors were present. CONCLUSIONS In this cohort of patients with medically complicated obesity, PNPLA3 rs738409 G allelic expression is associated with hepatic (NASH) and nonhepatic complications of obesity, such as insulin resistance. These novel findings may be related to a greater impact of PNPLA3 variant in magnitude and scope in patients with severe obesity than in less obese populations. Further studies are needed to characterize the nature of these associations.
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Affiliation(s)
- M M J Guichelaar
- Division of Gastroenterology and Hepatology, Medical Spectrum Twente, Enschede, The Netherlands; Liver Transplantation, Mayo Clinic, Rochester, Minnesota, USA
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Gu D, Wang Z, Dou X, Zhang X, Li S, Vu L, Yao T, Song Z. Inhibition of ERK1/2 pathway suppresses adiponectin secretion via accelerating protein degradation by Ubiquitin-proteasome system: relevance to obesity-related adiponectin decline. Metabolism 2013; 62:1137-48. [PMID: 23490586 PMCID: PMC3718849 DOI: 10.1016/j.metabol.2013.01.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/03/2013] [Accepted: 01/08/2013] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Predominantly secreted by adipose tissue, adiponectin possesses insulin-sensitizing, anti-atherogenic, anti-inflammatory, and anti-angiogenic properties. Paradoxically, obesity is associated with declined plasma adiponectin levels; however, the underlying mechanisms remain elusive. In this study, we investigated the mechanistic involvement of MEK/ERK1/2 pathway in obesity-related adiponectin decrease. MATERIALS/METHODS C57 BL/6 mice exposed to a high-fat diet (HFD) were employed as animal obesity model. Both fully-differentiated 3T3-L1 and mouse primary adipocytes were used in the in vitro experiments. RESULTS Obesity and plasma adiponectin decline induced by prolonged HFD exposure were associated with suppressed ERK1/2 activation in adipose tissue. In adipocytes, specific inhibition of MEK/ERK1/2 pathway decreased intracellular and secretory adiponectin levels, whereas adiponectin gene expression was increased, suggesting that MEK/ERK1/2 inhibition may promote adiponectin protein degradation. Cycloheximide (CHX)-chase assay revealed that MEK/ERK1/2 inhibition accelerated adiponectin protein degradation, which was prevented by MG132, a potent proteasome inhibitor. Immunoprecipitation assay showed that intracellular MEK/ERK1/2 activity was negatively associated with ubiquitinated adiponectin protein levels. Consistently, long-term HFD feeing in mice increased ubiquitinated adiponectin levels in the epididymal fat pads. CONCLUSIONS Adipose tissue MEK/ERK1/2 activity can differentially regulate adiponectin gene expression and protein abundance and its suppression in obesity may play a mechanistic role in obesity-related plasma adiponectin decline.
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Affiliation(s)
- Dongfang Gu
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
- Key Laboratory of Cardiovascular Medicine Research (Harbin Medical University), Ministry of Education, P. R. China
| | - Zhigang Wang
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
| | - Xiaobing Dou
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P. R. China. 310053
| | - Ximei Zhang
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
| | - Songtao Li
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
| | - Lyndsey Vu
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
| | - Tong Yao
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
| | - Zhenyuan Song
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL 60612
- Department of Pathology, Medical Center, University of Illinois, Chicago, IL 60612
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Asai M, Ramachandrappa S, Joachim M, Shen Y, Zhang R, Nuthalapati N, Ramanathan V, Strochlic DE, Ferket P, Linhart K, Ho C, Novoselova TV, Garg S, Ridderstråle M, Marcus C, Hirschhorn JN, Keogh JM, O’Rahilly S, Chan LF, Clark AJ, Farooqi IS, Majzoub JA. Loss of function of the melanocortin 2 receptor accessory protein 2 is associated with mammalian obesity. Science 2013; 341:275-8. [PMID: 23869016 PMCID: PMC3788688 DOI: 10.1126/science.1233000] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Melanocortin receptor accessory proteins (MRAPs) modulate signaling of melanocortin receptors in vitro. To investigate the physiological role of brain-expressed melanocortin 2 receptor accessory protein 2 (MRAP2), we characterized mice with whole-body and brain-specific targeted deletion of Mrap2, both of which develop severe obesity at a young age. Mrap2 interacts directly with melanocortin 4 receptor (Mc4r), a protein previously implicated in mammalian obesity, and it enhances Mc4r-mediated generation of the second messenger cyclic adenosine monophosphate, suggesting that alterations in Mc4r signaling may be one mechanism underlying the association between Mrap2 disruption and obesity. In a study of humans with severe, early-onset obesity, we found four rare, potentially pathogenic genetic variants in MRAP2, suggesting that the gene may also contribute to body weight regulation in humans.
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Affiliation(s)
- Masato Asai
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
- Departments of Pathology, Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shwetha Ramachandrappa
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, CB2 0QQ, Cambridge, UK
| | - Maria Joachim
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Yuan Shen
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Rong Zhang
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Nikhil Nuthalapati
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Visali Ramanathan
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - David E. Strochlic
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Peter Ferket
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695
| | - Kirsten Linhart
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Caroline Ho
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
| | - Tatiana V. Novoselova
- William Harvey Research Institute, Centre for Endocrinology Queen Mary, University of London Barts and The London School of Medicine and Dentistry, London, EC1M 6BQ, UK
| | - Sumedha Garg
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, CB2 0QQ, Cambridge, UK
| | - Martin Ridderstråle
- Department of Clinical Sciences, Lund University, Malmö, Sweden and Steno Diabetes Center, Gentofte, Denmark
| | - Claude Marcus
- Department for Clinical Science, Intervention and Technology, Karolinska Institute, Division of Pediatrics, National Childhood Obesity Centre, Stockholm, Sweden
| | - Joel N. Hirschhorn
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
- Department of Genetics, Harvard Medical School and Broad Institute, Cambridge, MA
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, CB2 0QQ, Cambridge, UK
| | - Stephen O’Rahilly
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, CB2 0QQ, Cambridge, UK
| | - Li F. Chan
- William Harvey Research Institute, Centre for Endocrinology Queen Mary, University of London Barts and The London School of Medicine and Dentistry, London, EC1M 6BQ, UK
| | - Adrian J. Clark
- William Harvey Research Institute, Centre for Endocrinology Queen Mary, University of London Barts and The London School of Medicine and Dentistry, London, EC1M 6BQ, UK
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, CB2 0QQ, Cambridge, UK
| | - Joseph A. Majzoub
- Division of Endocrinology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115
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Xin YN, Zhao Y, Lin ZH, Jiang X, Xuan SY, Huang J. Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity. Proteins 2012; 81:406-14. [PMID: 23042597 DOI: 10.1002/prot.24199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 09/20/2012] [Accepted: 09/20/2012] [Indexed: 12/13/2022]
Abstract
A missense mutation I148M in PNPLA3 (patatin-like phospholipase domain-containing 3 protein) is significantly correlated with nonalcoholic fatty liver disease (NAFLD). To glean insights into mutation's effect on enzymatic activity, we performed molecular dynamics simulation and flexible docking studies. Our data show that the size of the substrate-access entry site is significantly reduced in mutants, which limits the access of palmitic acid to the catalytic dyad. Besides, the binding free energy calculations suggest low affinity for substrate to mutant enzyme. The substrate-bound system simulations reveal that the spatial arrangement of palmitic acid is distinct in wild-type from that in mutant. The substrate recognition specificity is lost due to the loop where the I148M mutation was located. Our results provide strong evidence for the mechanism by which I148M affects the enzyme activity and suggest that mediating the dynamics may offer a potential avenue for NAFLD.
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Affiliation(s)
- Yong-Ning Xin
- College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266003, Shandong Province, China
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11
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Krarup NT, Grarup N, Banasik K, Friedrichsen M, Færch K, Sandholt CH, Jørgensen T, Poulsen P, Witte DR, Vaag A, Sørensen T, Pedersen O, Hansen T. The PNPLA3 rs738409 G-allele associates with reduced fasting serum triglyceride and serum cholesterol in Danes with impaired glucose regulation. PLoS One 2012; 7:e40376. [PMID: 22792295 PMCID: PMC3390392 DOI: 10.1371/journal.pone.0040376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/04/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND AND AIM Non-alcoholic fatty liver disease (NAFLD) is a common condition, associated with hepatic insulin resistance and the metabolic syndrome including hyperglycaemia and dyslipidemia. We aimed at studying the potential impact of the NAFLD-associated PNPLA3 rs738409 G-allele on NAFLD-related metabolic traits in hyperglycaemic individuals. METHODS The rs738409 variant was genotyped in the population-based Inter99 cohort examined by an oral glucose-tolerance test, and a combined study-sample consisting of 192 twins (96 twin pairs) and a sub-set of the Inter99 population (n = 63) examined by a hyperinsulinemic euglycemic clamp (n(total) = 255). In Inter99, we analyzed associations of rs738409 with components of the WHO-defined metabolic syndrome (n = 5,847) and traits related to metabolic disease (n = 5,663). In the combined study sample we elucidated whether the rs738409 G-allele altered hepatic or peripheral insulin sensitivity. Study populations were divided into individuals with normal glucose-tolerance (NGT) and with impaired glucose regulation (IGR). RESULTS The case-control study showed no associations with components of the metabolic syndrome or the metabolic syndrome. Among 1,357 IGR individuals, the rs738409 G-allele associated with decreased fasting serum triglyceride levels (per allele effect(β) = -9.9% [-14.4%;-4.0% (95% CI)], p = 5.1×10(-5)) and fasting total cholesterol (β = -0.2 mmol/l [-0.3;-0.01 mmol/l(95% CI)], p = 1.5×10(-4)). Meta-analyses showed no impact on hepatic or peripheral insulin resistance in carriers of the rs738409 G-allele. CONCLUSION Our findings suggest that the G-allele of PNPLA3 rs738409 associates with reduced fasting levels of cholesterol and triglyceride in individuals with IGR.
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Affiliation(s)
- Nikolaj Thure Krarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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12
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Alisi A, Cianfarani S, Manco M, Agostoni C, Nobili V. Non-alcoholic fatty liver disease and metabolic syndrome in adolescents: pathogenetic role of genetic background and intrauterine environment. Ann Med 2012; 44:29-40. [PMID: 21355790 DOI: 10.3109/07853890.2010.547869] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In the last three decades the incidence of metabolic syndrome (MetS) has been growing worldwide along with an increase of obesity, type 2 diabetes mellitus, and non-alcoholic fatty liver disease (NAFLD). In children and adolescents such epidemics are particularly worrisome, since the metabolic consequences in adulthood will significantly burden the health care system. Although the definition of MetS in childhood is still controversial, there is agreement with respect to NAFLD being the hepatic manifestation of MetS. However, the molecular pathogenesis of MetS and its contribution to NAFLD is complex and closely related to the pre- and postnatal environment as well as to genetic predisposing factors. The analysis of the possible relationships between NAFLD and MetS is particularly interesting, not only from an epidemiological point of view, but also to better understand the genetic and environmental factors contributing to the development of both diseases. We here summarize the most recent epidemiological data on the incidence of both diseases in adolescents, and several aspects linking MetS with NAFLD, discussing the possible role played by genetics and intrauterine environment.
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Affiliation(s)
- Anna Alisi
- Liver Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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13
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Grall A, Guaguère E, Planchais S, Grond S, Bourrat E, Hausser I, Hitte C, Le Gallo M, Derbois C, Kim GJ, Lagoutte L, Degorce-Rubiales F, Radner FPW, Thomas A, Küry S, Bensignor E, Fontaine J, Pin D, Zimmermann R, Zechner R, Lathrop M, Galibert F, André C, Fischer J. PNPLA1 mutations cause autosomal recessive congenital ichthyosis in golden retriever dogs and humans. Nat Genet 2012; 44:140-7. [PMID: 22246504 DOI: 10.1038/ng.1056] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 12/05/2011] [Indexed: 01/04/2023]
Abstract
Ichthyoses comprise a heterogeneous group of genodermatoses characterized by abnormal desquamation over the whole body, for which the genetic causes of several human forms remain unknown. We used a spontaneous dog model in the golden retriever breed, which is affected by a lamellar ichthyosis resembling human autosomal recessive congenital ichthyoses (ARCI), to carry out a genome-wide association study. We identified a homozygous insertion-deletion (indel) mutation in PNPLA1 that leads to a premature stop codon in all affected golden retriever dogs. We subsequently found one missense and one nonsense mutation in the catalytic domain of human PNPLA1 in six individuals with ARCI from two families. Further experiments highlighted the importance of PNPLA1 in the formation of the epidermal lipid barrier. This study identifies a new gene involved in human ichthyoses and provides insights into the localization and function of this yet uncharacterized member of the PNPLA protein family.
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Affiliation(s)
- Anaïs Grall
- Centre National de la Recherche Scientifique, Institut de Génétique et Développement de Rennes, Rennes, France
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14
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Kuningas M, Estrada K, Hsu YH, Nandakumar K, Uitterlinden AG, Lunetta KL, van Duijn CM, Karasik D, Hofman A, Murabito J, Rivadeneira F, Kiel DP, Tiemeier H. Large common deletions associate with mortality at old age. Hum Mol Genet 2011; 20:4290-6. [PMID: 21835882 PMCID: PMC3188993 DOI: 10.1093/hmg/ddr340] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/01/2011] [Accepted: 08/01/2011] [Indexed: 12/13/2022] Open
Abstract
Copy-number variants (CNVs) are a source of genetic variation that increasingly are associated with human disease. However, the role of CNVs in human lifespan is to date unknown. To identify CNVs that influence mortality at old age, we analyzed genome-wide CNV data in 5178 participants of Rotterdam Study (RS1) and positive findings were evaluated in 1714 participants of the second cohort of the Rotterdam Study (RS2) and in 4550 participants of Framingham Heart Study (FHS). First, we assessed the total burden of rare (frequency <1%) and common (frequency >1%) CNVs for association with mortality during follow-up. These analyses were repeated by stratifying CNVs by type and size. Secondly, we assessed individual common CNV regions (CNVR) for association with mortality. We observed that the burden of common but not of rare CNVs influences mortality. A higher burden of large (≥ 500 kb) common deletions associated with 4% higher mortality [hazard ratio (HR) per CNV 1.04, 95% confidence interval (CI) 1.02-1.07, P = 5.82 × 10(-5)] in the 11 442 participants of RS1, RS2 and FHS. In the analysis of 312 individual common CNVRs, we identified two regions (11p15.5; 14q21.3) that associated with higher mortality in these cohorts. The 11p15.5 region (combined HR 1.59, 95% CI 1.31-1.93, P = 2.87 × 10(-6)) encompasses 41 genes, of which some have previously been related to longevity, whereas the 14q21.3 region (combined HR 1.57, 95% CI 1.19-2.07, P = 1.53 × 10(-3)) does not encompass any genes. In conclusion, the burden of large common deletions, as well as common CNVs in 11p15.5 and 14q21.3 region, associate with higher mortality.
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Affiliation(s)
- Maris Kuningas
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, CA 3000, The Netherlands.
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15
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Coleman RA, Mashek DG. Mammalian triacylglycerol metabolism: synthesis, lipolysis, and signaling. Chem Rev 2011; 111:6359-86. [PMID: 21627334 PMCID: PMC3181269 DOI: 10.1021/cr100404w] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rosalind A Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
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16
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Wang Z, Pini M, Yao T, Zhou Z, Sun C, Fantuzzi G, Song Z. Homocysteine suppresses lipolysis in adipocytes by activating the AMPK pathway. Am J Physiol Endocrinol Metab 2011; 301:E703-12. [PMID: 21750268 PMCID: PMC3191546 DOI: 10.1152/ajpendo.00050.2011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hyperhomocysteinemia (HHcy) is an independent risk factor for coronary artery disease. Emerging evidence suggests that HHcy is also associated with adipocyte tissue dysfunction. One of the principal functions of adipose tissue is to provide energy substrate via lipolysis. In the present study, we investigated the effects of homocysteine (Hcy) on lipolysis in adipocytes. We found that Hcy inhibited release of glycerol and fatty acids, two typical indicators of the lipolytic response, in primary adipocytes and fully differentiated 3T3-L1 adipocytes in a dose-dependent manner under both basal and isoproterenol-stimulated conditions. In differentiated 3T3-L1 adipocytes, decreased glycerol and free fatty acid (FFA) release was associated with elevation of intracellular TG content. Further studies showed that Hcy-mediated antilipolytic responses were independent of the cyclic AMP-PKA and MEK-ERK1/2 pathways. However, Hcy increased phosphorylation levels of AMP-activated protein kinase (AMPK) and its downstream enzyme acetyl-CoA carboxylase. Compound C, an AMPK inhibitor, abolished Hcy-induced reduction of glycerol and FFA release under both basal and isoproterenol-stimulated conditions. Furthermore, AMPKα1 siRNA reversed Hcy-inhibited glycerol release. Supplementation of exogenous Hcy in the diet for 2 wk lowered circulating glycerol and FFA levels. Moreover, Hcy supplementation was associated with elevated leptin levels and reduced adiponectin levels in plasma. These results show that Hcy inhibits lipolysis through a pathway that involves AMPK activation.
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Affiliation(s)
- Zhigang Wang
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, USA
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17
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Di Rosa M, Malaguarnera L. Genetic variants in candidate genes influencing NAFLD progression. J Mol Med (Berl) 2011; 90:105-18. [PMID: 21894552 DOI: 10.1007/s00109-011-0803-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/08/2011] [Accepted: 08/08/2011] [Indexed: 12/17/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a metabolic disorder including simple steatosis and nonalcoholic steatohepatitis (NASH). Advanced stages of NASH result ultimately in fibrosis, cirrhosis, and hepatocarcinoma. A diagnosis of NASH entails an increased risk of both liver-related and cardiovascular mortality as worsening of the metabolic syndrome. Because of its escalation, many investigations have been performed to elucidate the pathophysiologic origins of the disease progression. Human epidemiologic studies describing polymorphisms in a number of genes involved in metabolic dysfunctions have contributed to clarify the causes leading to the disease evolution. In this review, we attempt to outline critically the most recently identified genetic variants in NAFLD patients to identify possible risk factors promoting the progression of the disease. The evaluation of altered genotypes together with other clinical variables may facilitate the clinical management of these patients.
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Affiliation(s)
- Michelino Di Rosa
- Department of Biomedical Sciences, University of Catania, Via Androne, 83, 95124 Catania, Italy
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18
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Basantani MK, Sitnick MT, Cai L, Brenner DS, Gardner NP, Li JZ, Schoiswohl G, Yang K, Kumari M, Gross RW, Zechner R, Kershaw EE. Pnpla3/Adiponutrin deficiency in mice does not contribute to fatty liver disease or metabolic syndrome. J Lipid Res 2011; 52:318-29. [PMID: 21068004 PMCID: PMC3023552 DOI: 10.1194/jlr.m011205] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/02/2010] [Indexed: 12/11/2022] Open
Abstract
PNPLA3 (adiponutrin, calcium-independent phospholipase A(2) epsilon [iPLA(2)ε]) is an adipose-enriched, nutritionally regulated protein that belongs to the patatin-like phospholipase domain containing (PNPLA) family of lipid metabolizing proteins. Genetic variations in the human PNPLA3 gene (i.e., the rs738409 I148M allele) has been strongly and repeatedly associated with fatty liver disease. Although human PNPLA3 has triacylglycerol (TAG) hydrolase and transacylase activities in vitro, its in vivo function and physiological relevance remain controversial. The objective of this study was to determine the metabolic consequences of global targeted deletion of the Pnpla3 gene in mice. We found that Pnpla3 mRNA expression is altered in adipose tissue and liver in response to acute and chronic nutritional challenges. However, global targeted deletion of the Pnpla3 gene in mice did not affect TAG hydrolysis, nor did it influence energy/glucose/lipid homoeostasis or hepatic steatosis/injury. Experimental interventions designed to increase Pnpla3 expression (refeeding, high-sucrose diet, diet-induced obesity, and liver X receptor agonism) likewise failed to reveal differences in the above-mentioned metabolic phenotypes. Expression of the Pnpla3 paralog, Pnpla5, was increased in adipose tissue but not in liver of Pnpla3-deficient mice, but compensatory regulation of genes involved in TAG metabolism was not identified. Together these data argue against a role for Pnpla3 loss-of-function in fatty liver disease or metabolic syndrome in mice.
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Affiliation(s)
- Mahesh K. Basantani
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Mitch T. Sitnick
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Lingzhi Cai
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Daniel S. Brenner
- Division of Endocrinology and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Noah P. Gardner
- Division of Endocrinology and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - John Zhong Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Kui Yang
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Manju Kumari
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Richard W. Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Erin E. Kershaw
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Division of Endocrinology and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
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19
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Deng Y, Johnson DR, Guan X, Ang CY, Ai J, Perkins EJ. In vitro gene regulatory networks predict in vivo function of liver. BMC SYSTEMS BIOLOGY 2010; 4:153. [PMID: 21073692 PMCID: PMC2998496 DOI: 10.1186/1752-0509-4-153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 11/12/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Evolution of toxicity testing is predicated upon using in vitro cell based systems to rapidly screen and predict how a chemical might cause toxicity to an organ in vivo. However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed. RESULTS Here we use the nitroaromatic 2,4,6-trinitrotoluene (TNT) as a model chemical to compare and determine how we might extrapolate from in vitro data to in vivo effects. We found 341 transcripts differentially expressed in common among in vitro and in vivo assays in response to TNT. The major functional term corresponding to these transcripts was cell cycle. Similarly modulated common pathways were identified between in vitro and in vivo. Furthermore, we uncovered the conserved common transcriptional gene regulatory networks between in vitro and in vivo cellular liver systems that responded to TNT exposure, which mainly contain 2 subnetwork modules: PTTG1 and PIR centered networks. Interestingly, all 7 genes in the PTTG1 module were involved in cell cycle and downregulated by TNT both in vitro and in vivo. CONCLUSIONS The results of our investigation of TNT effects on gene expression in liver suggest that gene regulatory networks obtained from an in vitro system can predict in vivo function and mechanisms. Inhibiting PTTG1 and its targeted cell cycle related genes could be key mechanism for TNT induced liver toxicity.
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Affiliation(s)
- Youping Deng
- Rush University Medical Center, Chicago, IL 60612, USA.
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20
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Basantani MK, Sitnick MT, Cai L, Brenner DS, Gardner NP, Li JZ, Schoiswohl G, Yang K, Kumari M, Gross RW, Zechner R, Kershaw EE. Pnpla3/Adiponutrin deficiency in mice does not contribute to fatty liver disease or metabolic syndrome. J Lipid Res 2010. [PMID: 21068004 DOI: 10.1194/jlr.m01120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PNPLA3 (adiponutrin, calcium-independent phospholipase A(2) epsilon [iPLA(2)ε]) is an adipose-enriched, nutritionally regulated protein that belongs to the patatin-like phospholipase domain containing (PNPLA) family of lipid metabolizing proteins. Genetic variations in the human PNPLA3 gene (i.e., the rs738409 I148M allele) has been strongly and repeatedly associated with fatty liver disease. Although human PNPLA3 has triacylglycerol (TAG) hydrolase and transacylase activities in vitro, its in vivo function and physiological relevance remain controversial. The objective of this study was to determine the metabolic consequences of global targeted deletion of the Pnpla3 gene in mice. We found that Pnpla3 mRNA expression is altered in adipose tissue and liver in response to acute and chronic nutritional challenges. However, global targeted deletion of the Pnpla3 gene in mice did not affect TAG hydrolysis, nor did it influence energy/glucose/lipid homoeostasis or hepatic steatosis/injury. Experimental interventions designed to increase Pnpla3 expression (refeeding, high-sucrose diet, diet-induced obesity, and liver X receptor agonism) likewise failed to reveal differences in the above-mentioned metabolic phenotypes. Expression of the Pnpla3 paralog, Pnpla5, was increased in adipose tissue but not in liver of Pnpla3-deficient mice, but compensatory regulation of genes involved in TAG metabolism was not identified. Together these data argue against a role for Pnpla3 loss-of-function in fatty liver disease or metabolic syndrome in mice.
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Affiliation(s)
- Mahesh K Basantani
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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21
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Rotman Y, Koh C, Zmuda JM, Kleiner DE, Liang TJ. The association of genetic variability in patatin-like phospholipase domain-containing protein 3 (PNPLA3) with histological severity of nonalcoholic fatty liver disease. HEPATOLOGY (BALTIMORE, MD.) 2010. [PMID: 20684021 DOI: 10.1002/hep.23759.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
UNLABELLED Genome-wide association studies identified single-nucleotide polymorphisms (SNPs) that are associated with increased hepatic fat or elevated liver enzymes, presumably reflecting nonalcoholic fatty liver disease (NAFLD). To investigate whether these SNPs are associated with histological severity of NAFLD, 1117 (894 adults/223 children) individuals enrolled in the Nonalcoholic Steatohepatitis (NASH) Clinical Research Network and National Institutes of Health Clinical Center studies with histologically confirmed NAFLD were genotyped for six SNPs that are associated with hepatic fat or liver enzymes in genome-wide association studies. In adults, three SNPs on chromosome 22 showed associations with histological parameters of NASH. After adjustment for age, sex, diabetes, and alcohol consumption, the minor allele of rs738409 C/G, a nonsynonymous coding SNP in the patatin-like phospholipase domain-containing protein 3 (PNPLA3) (adiponutrin) gene encoding an Ile148Met change, was associated with steatosis (P = 0.03), portal inflammation (P = 2.5 x 10(-4)), lobular inflammation (P = 0.005), Mallory-Denk bodies (P = 0.015), NAFLD activity score (NAS, P = 0.004), and fibrosis (P = 7.7 x 10(-6)). Two other SNPs in the same region demonstrated similar associations. Three SNPs on chromosome 10 near the CHUK (conserved helix-loop-helix ubiquitous kinase) gene were independently associated with fibrosis (P = 0.010). In children, no SNP was associated with histological severity. However, the rs738409 G allele was associated with younger age at the time of biopsy in multivariate analysis (P = 0.045). CONCLUSION In this large cohort of histologically proven NAFLD, we confirm the association of the rs738409 G allele with steatosis and describe its association with histological severity. In pediatric patients, the high-risk rs738409 G allele is associated with an earlier presentation of disease. We also describe a hitherto unknown association between SNPs at a chromosome 10 locus and the severity of NASH fibrosis.
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Affiliation(s)
- Yaron Rotman
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-1800, USA
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22
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Speliotes EK, Butler JL, Palmer CD, Voight BF, Hirschhorn JN. PNPLA3 variants specifically confer increased risk for histologic nonalcoholic fatty liver disease but not metabolic disease. HEPATOLOGY (BALTIMORE, MD.) 2010. [PMID: 20648472 DOI: 10.1002/hep.23768.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
UNLABELLED Single nucleotide polymorphisms (SNPs) near 7 loci have been associated with liver function tests or with liver steatosis by magnetic resonance spectroscopy. In this study we aim to test whether these SNPs influence the risk of histologically-confirmed nonalcoholic fatty liver disease (NAFLD). We tested the association of histologic NAFLD with SNPs at 7 loci in 592 cases of European ancestry from the Nonalcoholic Steatohepatitis Clinical Research Network and 1405 ancestry-matched controls. The G allele of rs738409 in PNPLA3 was associated with increased odds of histologic NAFLD (odds ratio [OR] = 3.26, 95% confidence intervals [CI] = 2.11-7.21; P = 3.6 x 10(-43)). In a case only analysis of G allele of rs738409 in PNPLA3 was associated with a decreased risk of zone 3 centered steatosis (OR = 0.46, 95% CI = 0.36-0.58; P = 5.15 x 10(-11)). We did not observe any association of this variant with body mass index, triglyceride levels, high- and low-density lipoprotein levels, or diabetes (P > 0.05). None of the variants at the other 6 loci were associated with NAFLD. CONCLUSION Genetic variation at PNPLA3 confers a markedly increased risk of increasingly severe histological features of NAFLD, without a strong effect on metabolic syndrome component traits.
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Affiliation(s)
- Elizabeth K Speliotes
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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23
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Rotman Y, Koh C, Zmuda JM, Kleiner DE, Liang TJ. The association of genetic variability in patatin-like phospholipase domain-containing protein 3 (PNPLA3) with histological severity of nonalcoholic fatty liver disease. Hepatology 2010; 52:894-903. [PMID: 20684021 PMCID: PMC2932770 DOI: 10.1002/hep.23759] [Citation(s) in RCA: 355] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
UNLABELLED Genome-wide association studies identified single-nucleotide polymorphisms (SNPs) that are associated with increased hepatic fat or elevated liver enzymes, presumably reflecting nonalcoholic fatty liver disease (NAFLD). To investigate whether these SNPs are associated with histological severity of NAFLD, 1117 (894 adults/223 children) individuals enrolled in the Nonalcoholic Steatohepatitis (NASH) Clinical Research Network and National Institutes of Health Clinical Center studies with histologically confirmed NAFLD were genotyped for six SNPs that are associated with hepatic fat or liver enzymes in genome-wide association studies. In adults, three SNPs on chromosome 22 showed associations with histological parameters of NASH. After adjustment for age, sex, diabetes, and alcohol consumption, the minor allele of rs738409 C/G, a nonsynonymous coding SNP in the patatin-like phospholipase domain-containing protein 3 (PNPLA3) (adiponutrin) gene encoding an Ile148Met change, was associated with steatosis (P = 0.03), portal inflammation (P = 2.5 x 10(-4)), lobular inflammation (P = 0.005), Mallory-Denk bodies (P = 0.015), NAFLD activity score (NAS, P = 0.004), and fibrosis (P = 7.7 x 10(-6)). Two other SNPs in the same region demonstrated similar associations. Three SNPs on chromosome 10 near the CHUK (conserved helix-loop-helix ubiquitous kinase) gene were independently associated with fibrosis (P = 0.010). In children, no SNP was associated with histological severity. However, the rs738409 G allele was associated with younger age at the time of biopsy in multivariate analysis (P = 0.045). CONCLUSION In this large cohort of histologically proven NAFLD, we confirm the association of the rs738409 G allele with steatosis and describe its association with histological severity. In pediatric patients, the high-risk rs738409 G allele is associated with an earlier presentation of disease. We also describe a hitherto unknown association between SNPs at a chromosome 10 locus and the severity of NASH fibrosis.
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Affiliation(s)
- Yaron Rotman
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Joseph M. Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - David E. Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - T. Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD,Corresponding author: T. Jake Liang, NIH, NIDDK, Liver Diseases Branch, 10 Center Drive, Building 10, Room 9B16, Bethesda, MD, 20892-1800,
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Speliotes EK, Butler JL, Palmer CD, Voight BF, Hirschhorn JN. PNPLA3 variants specifically confer increased risk for histologic nonalcoholic fatty liver disease but not metabolic disease. Hepatology 2010; 52:904-12. [PMID: 20648472 PMCID: PMC3070300 DOI: 10.1002/hep.23768] [Citation(s) in RCA: 279] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED Single nucleotide polymorphisms (SNPs) near 7 loci have been associated with liver function tests or with liver steatosis by magnetic resonance spectroscopy. In this study we aim to test whether these SNPs influence the risk of histologically-confirmed nonalcoholic fatty liver disease (NAFLD). We tested the association of histologic NAFLD with SNPs at 7 loci in 592 cases of European ancestry from the Nonalcoholic Steatohepatitis Clinical Research Network and 1405 ancestry-matched controls. The G allele of rs738409 in PNPLA3 was associated with increased odds of histologic NAFLD (odds ratio [OR] = 3.26, 95% confidence intervals [CI] = 2.11-7.21; P = 3.6 x 10(-43)). In a case only analysis of G allele of rs738409 in PNPLA3 was associated with a decreased risk of zone 3 centered steatosis (OR = 0.46, 95% CI = 0.36-0.58; P = 5.15 x 10(-11)). We did not observe any association of this variant with body mass index, triglyceride levels, high- and low-density lipoprotein levels, or diabetes (P > 0.05). None of the variants at the other 6 loci were associated with NAFLD. CONCLUSION Genetic variation at PNPLA3 confers a markedly increased risk of increasingly severe histological features of NAFLD, without a strong effect on metabolic syndrome component traits.
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Affiliation(s)
- Elizabeth K. Speliotes
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA,Program in Medical and Population Genetics and Metabolism Initiative, Broad Institute, Cambridge, MA
| | - Johannah L. Butler
- Program in Medical and Population Genetics and Metabolism Initiative, Broad Institute, Cambridge, MA,Divisions of Endocrinology and Genetics and Program in Genomics, Children's Hospital, Boston, MA
| | - Cameron D. Palmer
- Program in Medical and Population Genetics and Metabolism Initiative, Broad Institute, Cambridge, MA,Divisions of Endocrinology and Genetics and Program in Genomics, Children's Hospital, Boston, MA
| | - Benjamin F. Voight
- Program in Medical and Population Genetics and Metabolism Initiative, Broad Institute, Cambridge, MA,Department of Molecular Medicine, Massachusetts General Hospital Boston, MA
| | | | | | | | - Joel N. Hirschhorn
- Program in Medical and Population Genetics and Metabolism Initiative, Broad Institute, Cambridge, MA,Divisions of Endocrinology and Genetics and Program in Genomics, Children's Hospital, Boston, MA,Department of Genetics, Harvard Medical School, Boston MA
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Chen W, Chang B, Li L, Chan L. Patatin-like phospholipase domain-containing 3/adiponutrin deficiency in mice is not associated with fatty liver disease. Hepatology 2010; 52:1134-42. [PMID: 20648554 PMCID: PMC2932863 DOI: 10.1002/hep.23812] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
UNLABELLED PNPLA3 (adiponutrin), a novel patatin-like phospholipase domain-containing enzyme, is expressed at high level in fat, but also in other tissues including liver. Polymorphisms in PNPLA3 have been linked to obesity and insulin sensitivity. Notably, a nonsynonymous variant rs738409(G) allele of the PNPLA3 gene was found to be strongly associated with both nonalcoholic and alcoholic fatty liver disease. We have generated Pnpla3(-/-) mice by gene targeting. Loss of Pnpla3 has no effect on body weight or composition, adipose mass, or development, whether the mice were fed regular chow or high-fat diet or bred into the genetic obese Lep(ob/ob) background. Plasma and liver triglyceride content and plasma aspartate aminotransferase and alanine aminotransferase levels were not different between Pnpla3(+/+) and Pnpla3(-/-) mice while they were on regular chow, fed three different fatty liver-inducing diets, or after they were bred into Lep(ob/ob) background. Hepatic Pnpla5 messenger RNA (mRNA) levels were similar in wild-type and Pnpla3(-/-) mice, although adipose Pnpla5 mRNA level was increased in Pnpla3(-/-) mice. A high-sucrose lipogenic diet stimulated hepatic Pnpla3 and Pnpla5 mRNA levels to a similar degree, but it did not affect adipose or liver triglyceride lipase (ATGL, known also as Pnpla2) mRNA in Pnpla3(+/+) and Pnpla3(-/-) mice. Finally, Pnpla3(+/+) and Pnpla3(-/-) mice displayed similar glucose tolerance and insulin tolerance tests while on regular chow or three different fatty liver-inducing diets. CONCLUSION Loss of Pnpla3 does not cause fatty liver, liver enzyme elevation, or insulin resistance in mice.
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Affiliation(s)
- Weiqin Chen
- Diabetes and Endocrinology Research Center (DERC), Section of Diabetes and Endocrinology, Departments of Medicine, Molecular & Cellular Biology and Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Benny Chang
- Diabetes and Endocrinology Research Center (DERC), Section of Diabetes and Endocrinology, Departments of Medicine, Molecular & Cellular Biology and Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Lan Li
- Diabetes and Endocrinology Research Center (DERC), Section of Diabetes and Endocrinology, Departments of Medicine, Molecular & Cellular Biology and Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Lawrence Chan
- Diabetes and Endocrinology Research Center (DERC), Section of Diabetes and Endocrinology, Departments of Medicine, Molecular & Cellular Biology and Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA, St. Luke’s Episcopal Hospital, Houston, Texas, USA,Contact Information: Lawrence Chan, Diabetes and Endocrinology Research Center R614, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA. Tel: 713-798-4478, Fax: 713-798-8764,
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