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Hubacek JA, Adamkova V, Lanska V, Staněk V, Mrázková J, Gebauerová M, Kettner J, Kautzner J, Pitha J. Cholesterol associated genetic risk score and acute coronary syndrome in Czech males. Mol Biol Rep 2024; 51:164. [PMID: 38252350 PMCID: PMC10803395 DOI: 10.1007/s11033-023-09128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Despite a general decline in mean levels across populations, LDL-cholesterol levels remain a major risk factor for acute coronary syndrome (ACS). The APOB, LDL-R, CILP, and SORT-1 genes have been shown to contain variants that have significant effects on plasma cholesterol levels. METHODS AND RESULTS We examined polymorphisms within these genes in 1191 controls and 929 patients with ACS. Only rs646776 within SORT-1 was significantly associated with a risk of ACS (P < 0.05, AA vs. + G comparison; OR 1.21; 95% CI 1.01-1.45). With regard to genetic risk score (GRS), the presence of at least 7 alleles associated with elevated cholesterol levels was connected with increased risk (P < 0.01) of ACS (OR 1.26; 95% CI 1.06-1.52). Neither total mortality nor CVD mortality in ACS subjects (follow up-9.84 ± 3.82 years) was associated with the SNPs analysed or cholesterol-associated GRS. CONCLUSIONS We conclude that, based on only a few potent SNPs known to affect plasma cholesterol, GRS has the potential to predict ACS risk, but not ACS associated mortality.
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Affiliation(s)
- Jaroslav A Hubacek
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, IKEM-CEM-LMG, Videnska 1958/9, 140 21, Prague 4, Czech Republic.
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Vera Adamkova
- Preventive Cardiology Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vera Lanska
- Information Technology Division, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vladimir Staněk
- Cardiac Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jolana Mrázková
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, IKEM-CEM-LMG, Videnska 1958/9, 140 21, Prague 4, Czech Republic
| | - Marie Gebauerová
- Cardiac Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jiri Kettner
- Cardiac Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Josef Kautzner
- Cardiac Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jan Pitha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, IKEM-CEM-LMG, Videnska 1958/9, 140 21, Prague 4, Czech Republic
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AKADAM-TEKER AB, TEKER E. Effect of SORT1 rs599839 Polymorphism on Lipid Profiles: A Single City Experience. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.38079/igusabder.987894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Amaç: VPS10p ailesinin bir reseptörü olan Sortilin-1(SORT1)’i kodlayan SORT1 geni 1p13.3’de lokalizedir. SORT1 genom çapında ilişkilendirme çalışmalarında (GWAS) hepatik lipit metabolizması ve düşük dansiteli lipoprotein-kolesterol (LDL-K) seviyeleri ile olan ilişkisinden dolayı koroner kalp hastalığı (KKH) oluşturma riski ile ilişkilendirilmiştir. SORT1 gen bölgesi üzerindeki çeşitli varyasyonlar lipit profilleri üzerinde farklı etkilere neden olmaktadır. Bizim bu çalışmadaki amacımız; Giresun ilinde SORT1 rs599839 gen varyantlarının KKH gelişimi ve lipit parametreleri üzerine bir etkisinin olup olmadığını belirlemektir.Yöntem: Bu vaka-kontrol çalışmasında 396 kişiden oluşan erkek çalışma grubunda (209 KKH /187 kontrol) SORT1 rs599839 polimorfizmi için TaqMan 5’ Allelik Ayrım Testi ile genotipleme yapıldı.Bulgular: Hasta ve kontrol grupları arasında SORT1 rs599839 genotip dağılımları açısından istatistiksel olarak fark bulunmamaktadır (p=0.81). G allel varlığı hem hasta hem de kontrol grubunda daha düşük Total-Kolesterol (TK) (sırasıyla; p=0.005,p=0.032) ve LDL-K (sırasıyla; p=0.005,p=0.040) seviyelerine sebep olurken daha yüksek yüksek dansiteli lipoprotein-kolesterol (HDL-K) (sırasıyla; p=0.001,p=0.006) seviyeleri gözlenmiştir.Sonuç: Bulgularımız SORT1 rs599839 polimorfizminin direk olarak KKH patogenezine katkısının olmadığı yönündedir. Ancak, minör G allel varlığının TK ve LDL-K seviyelerini düşürürken, HDL-K seviyelerinde yükselmeye sebep olduğu görülmüştür. Bu durum minör G allel varlığının lipit profili üzerine olumlu etki gösterdiği ve KKH’a karşı koruyucu olduğu izlenimini vermiştir.
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Affiliation(s)
| | - Erhan TEKER
- Dr. Ali Menekşe Göğüs Hastalıkları Hastanesi
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3
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Jurado-Camacho PA, Cid-Soto MA, Barajas-Olmos F, García-Ortíz H, Baca-Peynado P, Martínez-Hernández A, Centeno-Cruz F, Contreras-Cubas C, González-Villalpando ME, Saldaña-Álvarez Y, Salas-Martinez G, Mendoza-Caamal EC, González-Villalpando C, Córdova EJ, Orozco L. Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci. Front Genet 2022; 13:807381. [PMID: 35669185 PMCID: PMC9164108 DOI: 10.3389/fgene.2022.807381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Plasma lipid levels are a major risk factor for cardiovascular diseases. Although international efforts have identified a group of loci associated with the risk of dyslipidemia, Latin American populations have been underrepresented in these studies.Objective: To know the genetic variation occurring in lipid-related loci in the Mexican population and its association with dyslipidemia.Methods: We searched for single-nucleotide variants in 177 lipid candidate genes using previously published exome sequencing data from 2838 Mexican individuals belonging to three different cohorts. With the extracted variants, we performed a case-control study. Logistic regression and quantitative trait analyses were implemented in PLINK software. We used an LD pruning using a 50-kb sliding window size, a 5-kb window step size and a r2 threshold of 0.1.Results: Among the 34251 biallelic variants identified in our sample population, 33% showed low frequency. For case-control study, we selected 2521 variants based on a minor allele frequency ≥1% in all datasets. We found 19 variants in 9 genes significantly associated with at least one lipid trait, with the most significant associations found in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster on chromosome 11. Notably, all 11 variants associated with hypertriglyceridemia were within this cluster; whereas variants associated with hypercholesterolemia were located at chromosome 2 and 19, and for low high density lipoprotein cholesterol were in chromosomes 9, 11, and 19. No significant associated variants were found for low density lipoprotein. We found several novel variants associated with different lipemic traits: rs3825041 in BUD13 with hypertriglyceridemia, rs7252453 in CILP2 with decreased risk to hypercholesterolemia and rs11076176 in CETP with increased risk to low high density lipoprotein cholesterol.Conclusions: We identified novel variants in lipid-regulation candidate genes in the Mexican population, an underrepresented population in genomic studies, demonstrating the necessity of more genomic studies on multi-ethnic populations to gain a deeper understanding of the genetic structure of the lipemic traits.
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Affiliation(s)
- Pedro A. Jurado-Camacho
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Miguel A. Cid-Soto
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Humberto García-Ortíz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Paulina Baca-Peynado
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- Posgraduate in Biomedical Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Federico Centeno-Cruz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - María Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Yolanda Saldaña-Álvarez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Guadalupe Salas-Martinez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | | | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigación en Diabetes y Riesgo Cardiovascular, Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova, ; Lorena Orozco,
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Zago VHS, Scherrer DZ, Parra ES, Vieira IC, Marson FAL, de Faria EC. Effects of SNVs in ABCA1, ABCG1, ABCG5, ABCG8, and SCARB1 Genes on Plasma Lipids, Lipoproteins, and Adiposity Markers in a Brazilian Population. Biochem Genet 2021; 60:822-841. [PMID: 34505223 DOI: 10.1007/s10528-021-10131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Several proteins are involved in cholesterol homeostasis, as scavenger receptor class B type I and ATP-binding cassette (ABC) transporters including ABCA1, ABCG1, ABCG5, and ABCG8. This study aimed to determine the effects of single nucleotide variants (SNVs) rs2275543 (ABCA1), rs1893590 (ABCG1), rs6720173 (ABCG5), rs6544718 (ABCG8), and rs5888 (SCARB1) on plasma lipids, lipoproteins, and adiposity markers in an asymptomatic population and its sex-specific effects. Volunteers (n = 590) were selected and plasma lipids, lipoproteins, and adiposity markers (waist-to-hip and waist-to-height ratios, lipid accumulation product and body adiposity index) were measured. Genomic DNA was isolated from peripheral blood cells according to the method adapted from Gross-Bellard. SNVs were detected in the TaqMan® OpenArray® Real-Time polymerase chain reaction platform and data analyses were performed using the TaqMan® Genotyper Software. The rs2275543*C point to an increase of high-density lipoprotein size in females while in males very-low-density lipoprotein, cholesterol, and triglycerides were statistically lower (P value < 0.05). The rs1893590*C was statistically associated with lower apolipoprotein A-I levels and higher activities of paraoxonase-1 and cholesteryl ester transfer protein (P value < 0.05). The rs6720173 was statistically associated with an increase in cholesterol and low-density lipoprotein cholesterol in males; moreover, rs6544718*T reduced adiposity markers in females (P value < 0.05). Regarding the rs5888, a decreased adiposity marker in the total population and in females occurred (P value < 0.05). Multivariate analysis of variance showed that SNVs could influence components of high-density lipoprotein metabolism, mainly through ABCG1 (P value < 0.05). The ABCA1 and ABCG5 variants showed sex-specific effects on lipids and lipoproteins, while SCARB1 and ABCG8 variants might influence adiposity markers in females. Our data indicate a possible role of ABCG1 on HDL metabolism.
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Affiliation(s)
- Vanessa Helena Souza Zago
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Daniel Zanetti Scherrer
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Eliane Soler Parra
- Department of Cardiology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Isabela Calanca Vieira
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Laboratory of Human and Medical Genetics and Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.
| | - Eliana Cotta de Faria
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil.
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5
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Coto E, Lorca R, Rodríguez-Reguero J, Martín M, Pascual I, Avanzas P, Cuesta-Llavona E, Vázquez-Coto D, Díaz-Corte C, Tranche S, Alonso B, Iglesias S, Morís C, Gómez J. The APOB polymorphism rs1801701 A/G (p.R3638Q) is an independent risk factor for early-onset coronary artery disease: Data from a Spanish cohort. Nutr Metab Cardiovasc Dis 2021; 31:1564-1568. [PMID: 33810965 DOI: 10.1016/j.numecd.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/30/2020] [Accepted: 02/03/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND AND AIMS Apoliprotein B (ApoB) has been associated with hypercholesterolemia and ischemic coronary disease. This study was aimed to determine the effect of two APOB gene variants in the risk of developing early-onset coronary artery disease (EO-CAD) in a Spanish population. The association of these polymorphisms with hypercholesterolemia was also analysed. METHODS AND RESULTS The study involved a total of 889 healthy population controls (397 male) and 790 EO-CAD cases (636 male; EO-CAD was defined as male <60 years and women <65 years). All the patients had at least one vessel with angiography documented atherosclerotic lesion. Patients and controls were genotyped for the APOB variants rs1801701 A/G (p.R3638Q) and rs1367117 C/T (p.T98I). Allele and genotype frequencies were compared between the groups (patients vs. controls, hyper-vs. normo-cholesterolemia) by logistic regression. The rs1801701 was significantly associated with EO-CAD in male (OR = 1.44, 95%CI = 1.05-1.99) and female (OR = 2.22, 95%CI = 1.58-3.14). This SNP was significantly associated with hypercholesterolemia in female, with a trend in male. The association with EO-CAD was independent of hypercholesterolemia (multiple logistic regression). CONCLUSION A common APOB polymorphism (rs1801701) was an independent risk factor for EO-CAD in our population. The risk-effect was more significant in female than in male.
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Affiliation(s)
- Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Departamento Medicina, Universidad de Oviedo, Oviedo, Spain; Red de Investigación Renal (REDINREN), Madrid, Spain.
| | - Rebeca Lorca
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Julián Rodríguez-Reguero
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - María Martín
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Isaac Pascual
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Pablo Avanzas
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Elías Cuesta-Llavona
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | | | - Carmen Díaz-Corte
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Departamento Medicina, Universidad de Oviedo, Oviedo, Spain; Red de Investigación Renal (REDINREN), Madrid, Spain; Nefrología, Hospital Universitario Central Asturias, Oviedo, Spain
| | | | - Belén Alonso
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Red de Investigación Renal (REDINREN), Madrid, Spain
| | - Sara Iglesias
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Red de Investigación Renal (REDINREN), Madrid, Spain
| | - César Morís
- Cardiología, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Departamento Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain; Red de Investigación Renal (REDINREN), Madrid, Spain
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Interaction between Sex and LDLR rs688 Polymorphism on Hyperlipidemia among Taiwan Biobank Adult Participants. Biomolecules 2020; 10:biom10020244. [PMID: 32033407 PMCID: PMC7072141 DOI: 10.3390/biom10020244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/25/2020] [Accepted: 02/03/2020] [Indexed: 01/04/2023] Open
Abstract
Hyperlipidemia is one of the strong risk factors for ischemic heart disease. Using the Taiwan Biobank (TWB) database, we evaluated the risk of hyperlipidemia and its interaction with sex and rs688 polymorphism on the low-density lipoprotein receptor (LDLR) gene. Data collection in the biobank started in 2008 and is ongoing. Data analysis was performed on the participants’ data collected between 2008 and 2015. In general, 27.92% of the 9237 female participants and 32.65% of the 8690 male participants were identified with hyperlipidemia. Compared to the C/C genotype, C/T and T/T genotypes were not significant risk factors for hyperlipidemia (OR = 1.061, CI: 0.976–1.153 for C/T and OR = 1.052, CI: 0.845–1.309 for T/T genotype) in the general model. However, there was a significant interaction between sex and rs6888 on hyperlipidemia risk (p-interaction = 0.0321). With the male sex/CC genotype being the reference group, only the female sex/CT and T/T genotypes were closely associated with hyperlipidemia, with respective ORs of 1.153 (CI: 1.014–1.311) and 1.423 (CI: 1.056–1.917). Our data indicate that rs688 C/T and T/T genotypes may be associated with increased risk of hyperlipidemia in Taiwanese women. These findings may be relevant in lipid-modification therapy.
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7
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Genome-wide Association Study of Change in Fasting Glucose over time in 13,807 non-diabetic European Ancestry Individuals. Sci Rep 2019; 9:9439. [PMID: 31263163 PMCID: PMC6602949 DOI: 10.1038/s41598-019-45823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/29/2019] [Indexed: 01/13/2023] Open
Abstract
Type 2 diabetes (T2D) affects the health of millions of people worldwide. The identification of genetic determinants associated with changes in glycemia over time might illuminate biological features that precede the development of T2D. Here we conducted a genome-wide association study of longitudinal fasting glucose changes in up to 13,807 non-diabetic individuals of European descent from nine cohorts. Fasting glucose change over time was defined as the slope of the line defined by multiple fasting glucose measurements obtained over up to 14 years of observation. We tested for associations of genetic variants with inverse-normal transformed fasting glucose change over time adjusting for age at baseline, sex, and principal components of genetic variation. We found no genome-wide significant association (P < 5 × 10-8) with fasting glucose change over time. Seven loci previously associated with T2D, fasting glucose or HbA1c were nominally (P < 0.05) associated with fasting glucose change over time. Limited power influences unambiguous interpretation, but these data suggest that genetic effects on fasting glucose change over time are likely to be small. A public version of the data provides a genomic resource to combine with future studies to evaluate shared genetic links with T2D and other metabolic risk traits.
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8
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Kovac U, Jasper EA, Smith CJ, Baer RJ, Bedell B, Donovan BM, Weathers N, Prosenc Zmrzljak U, Jelliffe-Pawlowski LL, Rozman D, Ryckman KK. The Association of Polymorphisms in Circadian Clock and Lipid Metabolism Genes With 2 nd Trimester Lipid Levels and Preterm Birth. Front Genet 2019; 10:540. [PMID: 31249592 PMCID: PMC6584752 DOI: 10.3389/fgene.2019.00540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
Deregulation of the circadian system in humans and animals can lead to various adverse reproductive outcomes due to genetic mutations and environmental factors. In addition to the clock, lipid metabolism may also play an important role in influencing reproductive outcomes. Despite the importance of the circadian clock and lipid metabolism in regulating birth timing few studies have examined the relationship between circadian genetics with lipid levels during pregnancy and their relationship with preterm birth (PTB). In this study we aimed to determine if single nucleotide polymorphisms (SNPs) in genes from the circadian clock and lipid metabolism influence 2nd trimester maternal lipid levels and if this is associated with an increased risk for PTB. We genotyped 72 SNPs across 40 genes previously associated with various metabolic abnormalities on 930 women with 2nd trimester serum lipid measurements. SNPs were analyzed for their relationship to levels of total cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL) and triglycerides (TG) using linear regression. SNPs were also evaluated for their relationship to PTB using logistic regression. Five SNPs in four genes met statistical significance after Bonferroni correction (p < 1.8 × 10-4) with one or more lipid levels. Of these, four SNPs were in lipid related metabolism genes: rs7412 in APOE with total cholesterol, HDL and LDL, rs646776 and rs599839 in CELSR2-PSRC1-SORT1 gene cluster with total cholesterol, HDL and LDL and rs738409 in PNPLA3 with HDL and TG and one was in a circadian clock gene: rs228669 in PER3 with TG. Of these SNPs only PER3 rs228669 was marginally associated with PTB (p = 0.02). In addition, PER3 rs228669 acts as an effect modifier on the relationship between TG and PTB.
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Affiliation(s)
- Ursa Kovac
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Elizabeth A Jasper
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
| | - Caitlin J Smith
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
| | - Rebecca J Baer
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States.,California Preterm Birth Initiative, University of California, San Francisco, San Francisco, CA, United States
| | - Bruce Bedell
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
| | - Brittney M Donovan
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
| | - Nancy Weathers
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
| | - Ursula Prosenc Zmrzljak
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Laura L Jelliffe-Pawlowski
- California Preterm Birth Initiative, University of California, San Francisco, San Francisco, CA, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kelli K Ryckman
- Department of Epidemiology, The University of Iowa, Iowa City, IA, United States
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Jha RM, Desai SM, Zusman BE, Koleck TA, Puccio AM, Okonkwo DO, Park SY, Shutter LA, Kochanek PM, Conley YP. Downstream TRPM4 Polymorphisms Are Associated with Intracranial Hypertension and Statistically Interact with ABCC8 Polymorphisms in a Prospective Cohort of Severe Traumatic Brain Injury. J Neurotrauma 2019; 36:1804-1817. [PMID: 30484364 PMCID: PMC6551973 DOI: 10.1089/neu.2018.6124] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Sulfonylurea-receptor-1(SUR1) and its associated transient-receptor-potential cation channel subfamily-M (TRPM4) channel are key contributors to cerebral edema and intracranial hypertension in traumatic brain injury (TBI) and other neurological disorders. Channel inhibition by glyburide is clinically promising. ABCC8 (encoding SUR1) single-nucleotide polymorphisms (SNPs) are reported as predictors of raised intracranial pressure (ICP). This project evaluated whether TRPM4 SNPs predicted ICP and TBI outcome. DNA was extracted from 435 consecutively enrolled severe TBI patients. Without a priori selection, all 11 TRPM4 SNPs available on the multiplex platform (Illumina:Human-Core-Exome v1.0) were genotyped spanning the 25 exon gene. A total of 385 patients were analyzed after quality control. Outcomes included ICP and 6 month Glasgow Outcome Scale (GOS) score. Proxy SNPs, spatial modeling, and functional predictions were determined using established software programs. rs8104571 (intron-20) and rs150391806 (exon-24) were predictors of ICP. rs8104571 heterozygotes predicted higher average ICP (β = 10.3 mm Hg, p = 0.00000029), peak ICP (β = 19.6 mm Hg, p = 0.0007), and proportion ICP >25 mm Hg (β = 0.16 p = 0.004). rs150391806 heterozygotes had higher mean (β = 7.2 mm Hg, p = 0.042) and peak (β = 28.9 mm Hg, p = 0.0015) ICPs. rs8104571, rs150391806, and 34 associated proxy SNPs in linkage-disequilibrium clustered downstream. This region encodes TRPM4's channel pore and a region postulated to juxtapose SUR1 sequences encoded by an ABCC8 DNA segment containing previously identified relevant SNPs. There was an interaction effect on ICP between rs8104571 and a cluster of predictive ABCC8 SNPs (rs2237982, rs2283261, rs11024286). Although not significant in univariable or a basic multivariable model, in an expanded model additionally accounting for injury pattern, computed tomographic (CT) appearance, and intracranial hypertension, heterozygous rs8104571 was associated with favorable 6 month GOS (odds ratio [OR] = 16.7, p = 0.007951). This trend persisted in a survivor-only subcohort (OR = 20.67, p = 0.0168). In this cohort, two TRPM4 SNPs predicted increased ICP with large effect sizes. Both clustered downstream, spanning a region encoding the channel pore and interacting with SUR1. If validated, this may guide risk stratification and eventually inform treatment-responder classification for SUR1-TRPM4 inhibition in TBI. Larger studies are warranted.
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Affiliation(s)
- Ruchira M. Jha
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Safar Center for Resuscitation Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shashvat M. Desai
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Benjamin E. Zusman
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Ava M. Puccio
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David O. Okonkwo
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seo-Young Park
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lori A. Shutter
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Patrick M. Kochanek
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Safar Center for Resuscitation Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Anesthesia, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania
- University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yvette P. Conley
- Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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10
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Steba GS, Koekkoek SM, Tanck MWT, Vanhommerig JW, van der Meer JTM, Kwa D, Brinkman K, Prins M, Berkhout B, Pollakis G, Molenkamp R, Schinkel J, Paxton WA. SNP rs688 within the low-density lipoprotein receptor (LDL-R) gene associates with HCV susceptibility. Liver Int 2019; 39:463-469. [PMID: 30260075 PMCID: PMC6588020 DOI: 10.1111/liv.13978] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Despite high-risk behaviour, 10%-20% of HCV multiple exposed individuals remain uninfected (MEU), whilst the remainder become infected (MEI). We hypothesize that host factors play a role in HCV susceptibility. We aimed to identify polymorphisms in host genes that encode for proteins involved in viral entry: CD81, Scavenger receptor 1 (SR-1), Low-density lipoprotein receptor (LDL-R), Claudin-1 (CLDN1), Occludin (OCLN) and Niemann-Pick C1-like 1 (NPC1L1). METHODS Multiple exposed infected and MEU from two observational cohorts were selected. From the MSM study of acute infection with HCV (MOSAIC), HIV-1 infected MEU cases (n = 30) and HIV-1 infected MEI controls (n = 32) were selected based on reported high-risk behaviour. From the Amsterdam Cohorts Studies (ACS) injecting drug users (IDU) cohort, MEU cases (n = 40) and MEI controls (n = 22) were selected who injected drugs for ≥2 years, in the nineties, when HCV incidence was high. Selected single nucleotide polymorphisms (SNPs) were determined by sequencing or SNP assays. RESULTS No associations were found for SNPs within genes coding for CD81, SR-1, Claudin-1 or Occludin between the MEU and MEI individuals from either cohort. We did observe a significant association for rs688 within the LDL-R gene with HCV infection (OR: 0.41 P = 0.001), however, LDL cholesterol levels did not vary between individuals carrying the differential SNPs. Additionally, a marginal significant effect was found for rs217434 and rs2072183 (OR: 2.07 P = 0.032 and OR: 1.76 P = 0.039, respectively) within NPC1L1. CONCLUSIONS Our results demonstrate that the rs688 SNP within the LDL-R gene associates with HCV susceptibility through mucosal as well as intravenous exposure.
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Affiliation(s)
- Gaby S. Steba
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Sylvie M. Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Michael W. T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Joost W. Vanhommerig
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Infectious DiseasesPublic Health Service of AmsterdamAmsterdamThe Netherlands
| | - Jan T. M. van der Meer
- Division of Infectious Diseases, Tropical Medicine and AIDS, Department of Internal Medicine, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - David Kwa
- Department of MicrobiologyOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Kees Brinkman
- Department of Internal MedicineOnze Lieve Vrouwe GasthuisAmsterdamThe Netherlands
| | - Maria Prins
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Epidemiology, Biostatistics and Bioinformatics (CEBB), Amsterdam UMCAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
| | - Richard Molenkamp
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - William A. Paxton
- Department of Medical Microbiology, Amsterdam UMC, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands,Department of Clinical Infection, Microbiology and ImmunologyInstitute of Infection and Global HealthUniversity of LiverpoolLiverpoolUK
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11
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Do DN, Schenkel FS, Miglior F, Zhao X, Ibeagha-Awemu EM. Genome wide association study identifies novel potential candidate genes for bovine milk cholesterol content. Sci Rep 2018; 8:13239. [PMID: 30185830 PMCID: PMC6125589 DOI: 10.1038/s41598-018-31427-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/14/2018] [Indexed: 12/31/2022] Open
Abstract
This study aimed to identify single nucleotide polymorphisms (SNPs) associated with milk cholesterol (CHL) content via a genome wide association study (GWAS). Milk CHL content was determined by gas chromatography and expressed as mg of CHL in 100 g of fat (CHL_fat) or in 100 mg of milk (CHL_milk). GWAS was performed with 1,183 cows and 40,196 SNPs using a univariate linear mixed model. Two and 20 SNPs were significantly associated with CHL_fat and CHL_milk, respectively. The important regions for CHL_fat and CHL_milk were at 41.9 Mb on chromosome (BTA) 17 and 1.6-3.2 Mb on BTA 14, respectively. DGAT1, PTPN1, INSIG1, HEXIM1, SDS, and HTR5A genes, also known to be associated with human plasma CHL phenotypes, were identified as potential candidate genes for bovine milk CHL. Additional new potential candidate genes for milk CHL were RXFP1, FAM198B, TMEM144, CXXC4, MAML2 and CDH13. Enrichment analyses suggested that identified candidate genes participated in cell-cell signaling processes and are key members in tight junction, focal adhesion, Notch signaling and glycerolipid metabolism pathways. Furthermore, identified transcription factors such as PPARD, LXR, and NOTCH1 might be important in the regulation of bovine milk CHL content. The expression of several positional candidate genes (such as DGAT1, INSIG1 and FAM198B) and their correlation with milk CHL content were further confirmed with RNA sequence data from mammary gland tissues. This is the first GWAS on bovine milk CHL. The identified markers and candidate genes need further validation in a larger cohort for use in the selection of cows with desired milk CHL content.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada
- Department of Animal Science, McGill University, Ste-Anne-de-, Bellevue, QC, H9X 3V9, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-de-, Bellevue, QC, H9X 3V9, Canada.
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada.
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12
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Varga TV, Kurbasic A, Aine M, Eriksson P, Ali A, Hindy G, Gustafsson S, Luan J, Shungin D, Chen Y, Schulz CA, Nilsson PM, Hallmans G, Barroso I, Deloukas P, Langenberg C, Scott RA, Wareham NJ, Lind L, Ingelsson E, Melander O, Orho-Melander M, Renström F, Franks PW. Novel genetic loci associated with long-term deterioration in blood lipid concentrations and coronary artery disease in European adults. Int J Epidemiol 2018; 46:1211-1222. [PMID: 27864399 DOI: 10.1093/ije/dyw245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2016] [Indexed: 11/14/2022] Open
Abstract
Background Cross-sectional genome-wide association studies have identified hundreds of loci associated with blood lipids and related cardiovascular traits, but few genetic association studies have focused on long-term changes in blood lipids. Methods Participants from the GLACIER Study (Nmax = 3492) were genotyped with the MetaboChip array, from which 29 387 SNPs (single nucleotide polymorphisms; replication, fine-mapping regions and wildcard SNPs for lipid traits) were extracted for association tests with 10-year change in total cholesterol (ΔTC) and triglycerides (ΔTG). Four additional prospective cohort studies (MDC, PIVUS, ULSAM, MRC Ely; Nmax = 8263 participants) were used for replication. We conducted an in silico look-up for association with coronary artery disease (CAD) in the Coronary ARtery DIsease Genome-wide Replication and Meta-analysis (CARDIoGRAMplusC4D) Consortium (N ∼ 190 000) and functional annotation for the top ranking variants. Results In total, 956 variants were associated (P < 0.01) with either ΔTC or ΔTG in GLACIER. In GLACIER, chr19:50121999 at APOE was associated with ΔTG and multiple SNPs in the APOA1/A4/C3/A5 region at genome-wide significance (P < 5 × 10-8), whereas variants in four loci, DOCK7, BRE, SYNE1 and KCNIP1, reached study-wide significance (P < 1.7 × 10-6). The rs7412 variant at APOE was associated with ΔTC in GLACIER (P < 1.7 × 10-6). In pooled analyses of all cohorts, 139 SNPs at six and five loci were associated with ΔTC and for ΔTG, respectively (P < 10-3). Of these, a variant at CAPN3 (P = 1.2 × 10-4), multiple variants at HPR (Pmin = 1.5 × 10-6) and a variant at SIX5 (P = 1.9 × 10-4) showed evidence for association with CAD. Conclusions We identified seven novel genomic regions associated with long-term changes in blood lipids, of which three also raise CAD risk.
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Affiliation(s)
- Tibor V Varga
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Azra Kurbasic
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Aine
- Division of Oncology and Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology and Pathology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Ashfaq Ali
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - George Hindy
- Diabetes and Cardiovascular Disease - Genetic Epidemiology, Skåne University Hospital, Malmö, Sweden
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jian'an Luan
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Dmitry Shungin
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden.,Department of Odontology.,Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
| | - Yan Chen
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | | | - Peter M Nilsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Göran Hallmans
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Metabolic Research Laboratories.,NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, London, UK.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Claudia Langenberg
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Olle Melander
- Department of Clinical Sciences, Hypertension and Cardiovascular Diseases, Skåne University Hospital, Malmö, Sweden
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease - Genetic Epidemiology, Skåne University Hospital, Malmö, Sweden
| | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden.,Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden.,Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden.,Department of Nutrition, Harvard T.H Chan School of Public Health, Boston, MA, USA
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13
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ArulJothi KN, Suruthi Abirami B, Devi A. Genetic spectrum of low density lipoprotein receptor gene variations in South Indian population. Clin Chim Acta 2017; 478:28-36. [PMID: 29269200 DOI: 10.1016/j.cca.2017.12.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Low density lipoprotein receptor (LDLR) is a membrane bound receptor maintaining cholesterol homeostasis along with Apolipoprotein B (APOB), Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) and other genes of lipid metabolism. Any pathogenic variation in these genes alters the function of the receptor and leads to Familial Hypercholesterolemia (FH) and other cardiovascular diseases. OBJECTIVE This study was aimed at screening the LDLR, APOB and PCSK9 genes in Hypercholesterolemic patients to define the genetic spectrum of FH in Indian population. METHODS Familial Hypercholesterolemia patients (n=78) of South Indian Tamil population with LDL cholesterol and Total cholesterol levels above 4.9mmol/l and 7.5mmol/l with family history of Myocardial infarction were involved. DNA was isolated by organic extraction method from blood samples and LDLR, APOB and PCSK9 gene exons were amplified using primers that cover exon-intron boundaries. The amplicons were screened using High Resolution Melt (HRM) Analysis and the screened samples were sequenced after purification. RESULTS This study reports 20 variations in South Indian population for the first time. In this set of variations 9 are novel variations which are reported for the first time, 11 were reported in other studies also. The in silico analysis for all the variations detected in this study were done to predict the probabilistic effect in pathogenicity of FH. CONCLUSION This study adds 9 novel variations and 11 recurrent variations to the spectrum of LDLR gene mutations in Indian population. All these variations are reported for the first time in Indian population. This spectrum of variations was different from the variations of previous Indian reports.
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Affiliation(s)
- K N ArulJothi
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India
| | - B Suruthi Abirami
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India
| | - Arikketh Devi
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India.
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14
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Leduc V, Bourque L, Poirier J, Dufour R. Role of rs3846662 and HMGCR alternative splicing in statin efficacy and baseline lipid levels in familial hypercholesterolemia. Pharmacogenet Genomics 2016; 26:1-11. [PMID: 26466344 DOI: 10.1097/fpc.0000000000000178] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To assess the contribution of the rs3846662 polymorphism of HMGCR on serum lipid levels and statin efficacy, we measured in vivo HMGCR mRNA and lipid levels in French Canadian individuals affected by heterozygous familial hypercholesterolemia due to the deletion of more than 15 kb of the LDLR gene. RESULTS Men and women carrying the AA genotype at rs3846662, and no APOE4 allele, had higher levels of total cholesterol (5.43 vs. 4.58 mmol/l, P<0.05) and LDL-cholesterol (5.20 vs. 4.39 mmol/l, P<0.05) at baseline. However, with regard to statin efficacy, the penetrance of the AA genotype was sex dependent. Indeed, the percentage reduction in LDL-cholesterol upon statin treatment was significantly decreased in women with the AA genotype compared with women without it (38.4 vs. 46.2%, P<0.05), whereas this was not observed in men. Although both men and women bearing the AA genotype showed a higher ratio of full-length HMGCR mRNA/total HMGCR mRNA compared with individuals without it (n=37, P<0.05), overall transcription of HMGCR was decreased and increased in men and women carrying this genotype, respectively (n=37, P<0.01 and P<0.05). Finally, in our familial hypercholesterolemia cohort, HMGCR alternative splicing explained between 22 and 55% of the variance in statin response. CONCLUSION rs3846662 polymorphism and the alternative splicing of HMGCR mRNA significantly impact women's response to statin therapy.
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Affiliation(s)
- Valerie Leduc
- aCentre for Studies in Alzheimer's disease prevention bDouglas Mental Health University Institute, McGill University cDepartment of Nutrition, Clinical Research Institute of Montreal (IRCM), Montreal University, Montreal, Quebec, Canada
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15
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Miranzadeh-Mahabadi H, Emadi-Baygi M, Nikpour P, Kelishadi R. Association Study Between Metabolic Syndrome and rs8066560 Polymorphism in the Promoter Region of Sterol Regulatory Element-binding Transcription Factor 1 Gene in Iranian Children and Adolescents. Int J Prev Med 2016; 7:41. [PMID: 27076879 PMCID: PMC4809125 DOI: 10.4103/2008-7802.177314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/22/2015] [Indexed: 11/17/2022] Open
Abstract
Background: Metabolic syndrome (MetS) is a prevalent disorder in pediatric age groups, described by a combination of genetic and environmental factors. Sterol regulatory element-binding transcription factor 1 (SREBF-1) induces the expression of a family of genes involved in fatty acid synthesis. Moreover, dysregulation of miR-33b, which is located within the intron 17 of the SREBF-1 gene, disrupts fatty acid oxidation and insulin signaling, thus leading to MetS. The aim of the present study was to investigate the association between SREBF-1 rs8066560 polymorphism and MetS in Iranian children and adolescents. Methods: This study includes 100 MetS and 100 normal individuals aged 9–19 years. Anthropological and biochemical indexes were measured. The -1099G > A polymorphism was genotyped by TaqMan real-time polymerase chain reaction. Results: Significant differences were observed in anthropometric measurements and lipid profiles between MetS and normal children. There were no differences in the genotype frequencies or allele distribution for -1099G > A polymorphism between MetS and control groups. High-density lipoprotein cholesterol levels were significantly higher in the MetS GG group than in the A allele carrier group. The genotype AA controls had significantly increased cholesterol and low-density lipoprotein cholesterol levels than AG genotypes. By logistic regression using different genetic models, no significant association was observed between SREBF-1 rs8066560 polymorphism and the risk of MetS. Conclusions: We conclude that the -1099G > A variant on SREBF-1 gene associated with serum lipid profiles, however, it may not be a major risk factor for the MetS in Iranian children and adolescents.
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Affiliation(s)
- Hajar Miranzadeh-Mahabadi
- Department of Genetics, School of Basic Sciences, Shahrekord University, Shahrekord, Iran; Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, School of Basic Sciences, Shahrekord University, Shahrekord, Iran; Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Parvaneh Nikpour
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran; Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Roya Kelishadi
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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16
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Koleck TA, Bender CM, Sereika SM, Brufsky AM, Lembersky BC, McAuliffe PF, Puhalla SL, Rastogi P, Conley YP. Polymorphisms in DNA repair and oxidative stress genes associated with pre-treatment cognitive function in breast cancer survivors: an exploratory study. SPRINGERPLUS 2016; 5:422. [PMID: 27099827 PMCID: PMC4826652 DOI: 10.1186/s40064-016-2061-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/27/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE The purpose of this exploratory candidate gene association study was to examine relationships between polymorphisms in oxidative stress and DNA repair genes and pre-adjuvant therapy cognitive function (CF) in postmenopausal women diagnosed with early stage-breast cancer. METHODS Using a neuropsychological test battery, CF was assessed in 138 women diagnosed with breast cancer prior to initiation of adjuvant therapy and 81 age- and education-matched controls and summarized across eight composites. Participants were genotyped for 39 functional or tagging single nucleotide polymorphisms (SNPs) of select oxidative stress (CAT, GPX1, SEPP1, SOD1, and SOD2) and DNA repair (ERCC2, ERCC3, ERCC5, and PARP1) genes. Multiple linear regression was used to determine if the presence or absence of one or more minor alleles account for variability in CF composite scores. Based on regression findings from the analysis of individual SNPs, weighted multi-gene, multi-polymorphism genetic risk scores (GRSs) were calculated to evaluate the collective effect of possession of multiple protective and/or risk alleles. RESULTS Each CF composite was significantly (p < 0.05) associated with one or more oxidative stress and DNA repair gene polymorphisms evaluated either by SNP main effects and/or SNP-by-prescribed breast cancer treatment group interactions. Each computed GRS was found to be significantly (p < 0.001) related to its corresponding CF composite. All associations were positive suggesting that as overall genetic protection increases, CF composite score increases (indicating better performance). CONCLUSIONS These findings suggest that genetic variation in the oxidative stress and DNA repair pathways may play an important role in pre-adjuvant therapy CF in breast cancer survivors.
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Affiliation(s)
- Theresa A Koleck
- School of Nursing, University of Pittsburgh, 3500 Victoria Street, Pittsburgh, PA 15261 USA
| | - Catherine M Bender
- School of Nursing, University of Pittsburgh, 3500 Victoria Street, Pittsburgh, PA 15261 USA
| | - Susan M Sereika
- School of Nursing, University of Pittsburgh, 3500 Victoria Street, Pittsburgh, PA 15261 USA ; Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA ; Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
| | - Adam M Brufsky
- Division of Hematology/Oncology, Magee-Womens Hospital of University of Pittsburgh Medical Center (UPMC), 300 Halket Street, Pittsburgh, PA 15213 USA ; University of Pittsburgh Cancer Institute, 5150 Centre Avenue, Pittsburgh, PA 15232 USA ; School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261 USA
| | - Barry C Lembersky
- Division of Hematology/Oncology, Magee-Womens Hospital of University of Pittsburgh Medical Center (UPMC), 300 Halket Street, Pittsburgh, PA 15213 USA ; University of Pittsburgh Cancer Institute, 5150 Centre Avenue, Pittsburgh, PA 15232 USA
| | - Priscilla F McAuliffe
- University of Pittsburgh Cancer Institute, 5150 Centre Avenue, Pittsburgh, PA 15232 USA ; School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261 USA ; Division of Breast Surgical Oncology, Magee-Womens Hospital of University of Pittsburgh Medical Center (UPMC), 300 Halket Street, Pittsburgh, PA 15213 USA
| | - Shannon L Puhalla
- Division of Hematology/Oncology, Magee-Womens Hospital of University of Pittsburgh Medical Center (UPMC), 300 Halket Street, Pittsburgh, PA 15213 USA ; School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261 USA
| | - Priya Rastogi
- Division of Hematology/Oncology, Magee-Womens Hospital of University of Pittsburgh Medical Center (UPMC), 300 Halket Street, Pittsburgh, PA 15213 USA ; School of Medicine, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261 USA
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, 3500 Victoria Street, Pittsburgh, PA 15261 USA ; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261 USA
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17
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Lu X, Huang J, Mo Z, He J, Wang L, Yang X, Tan A, Chen S, Chen J, Gu CC, Chen J, Li Y, Zhao L, Li H, Hao Y, Li J, Hixson JE, Li Y, Cheng M, Liu X, Cao J, Liu F, Huang C, Shen C, Shen J, Yu L, Xu L, Mu J, Wu X, Ji X, Guo D, Zhou Z, Yang Z, Wang R, Yang J, Yan W, Peng X, Gu D. Genetic Susceptibility to Lipid Levels and Lipid Change Over Time and Risk of Incident Hyperlipidemia in Chinese Populations. ACTA ACUST UNITED AC 2015; 9:37-44. [PMID: 26582766 DOI: 10.1161/circgenetics.115.001096] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 11/13/2015] [Indexed: 01/19/2023]
Abstract
BACKGROUND Multiple genetic loci associated with lipid levels have been identified predominantly in Europeans, and the issue of to what extent these genetic loci can predict blood lipid levels increases over time and the incidence of future hyperlipidemia remains largely unknown. METHODS AND RESULTS We conducted a meta-analysis of genome-wide association studies of lipid levels in 8344 subjects followed by replication studies including 14 739 additional individuals. We replicated 17 previously reported loci. We also newly identified 3 Chinese-specific variants in previous regions (HLA-C, LIPG, and LDLR) with genome-wide significance. Almost all the variants contributed to lipid levels change and incident hyperlipidemia >8.1-year follow-up among 6428 individuals of a prospective cohort study. The strongest associations for lipid levels change were detected at LPL, TRIB1, APOA1-C3-A4-A5, LIPC, CETP, and LDLR (P range from 4.84×10(-4) to 4.62×10(-18)), whereas LPL, TRIB1, ABCA1, APOA1-C3-A4-A5, CETP, and APOE displayed significant strongest associations for incident hyperlipidemia (P range from 1.20×10(-3) to 4.67×10(-16)). The 4 lipids genetic risk scores were independently associated with linear increases in their corresponding lipid levels and risk of incident hyperlipidemia. A C-statistics analysis showed significant improvement in the prediction of incident hyperlipidemia on top of traditional risk factors including the baseline lipid levels. CONCLUSIONS These findings identified some evidence for allelic heterogeneity in Chinese when compared with Europeans in relation to lipid associations. The individual variants and those cumulative effects were independent risk factors for lipids increase and incident hyperlipidemia.
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18
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Leduc V, Théroux L, Dea D, Dufour R, Poirier J. Effects of rs3846662 Variants on HMGCR mRNA and Protein Levels and on Markers of Alzheimer's Disease Pathology. J Mol Neurosci 2015; 58:109-19. [PMID: 26541602 DOI: 10.1007/s12031-015-0666-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/09/2015] [Indexed: 01/23/2023]
Abstract
3-Hydroxy-3-methyglutaryl coenzyme A reductase (HMGCR) is a cholesterol-regulating gene with statin relevance. rs3846662 being involved in regulation of HMGCR alternative splicing, we explored its impact on HMGCR messenger RNA (mRNA) and protein levels in the brain and the associations between those levels and levels of Alzheimer's disease pathological markers. We used brain samples derived from a cohort of 33 non-demented controls and 90 Alzheimer's disease autopsied-confirmed cases. HMGCR mRNA levels were determined in the frontal cortex (n = 114) and cerebellum (n = 110) using Taqman-qPCR, and HMGCR protein levels were determined in the frontal cortex (n = 117) using a commercial enzyme immunoassay. While densities of neurofibrillary tangles and senile plaques were determined in the frontal cortex (n = 74), total tau, phosphorylated Tau, and beta-amyloid 1-42 levels were determined in the frontal cortex (n = 94) and cerebellum (n = 91) using commercial enzyme immunoassays. Despite an increase in full-length HMGCR mRNA ratio in the frontal cortex of women carrying the AA genotype, there were no associations between rs3846662 and HMGCR mRNA or protein levels. An increased Δ13 HMGCR mRNA ratio was associated with increased levels of HMGCR proteins and neurofibrillary tangles in the frontal cortex but with reduced beta-amyloid 1-42 levels in the cerebellum, suggesting a brain cell type- or a disease progression-dependent association.
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Affiliation(s)
- Valerie Leduc
- Centre for Studies on Prevention of Alzheimer's Disease (StoP-AD Centre), Douglas Mental Health University Institute, 6875 Lasalle, Verdun, Quebec, H4H 1R3, Canada.,Institut de Recherches Cliniques de Montréal, Department of Nutrition, Université de Montréal, Montréal, Quebec, Canada
| | - Louise Théroux
- Centre for Studies on Prevention of Alzheimer's Disease (StoP-AD Centre), Douglas Mental Health University Institute, 6875 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Doris Dea
- Centre for Studies on Prevention of Alzheimer's Disease (StoP-AD Centre), Douglas Mental Health University Institute, 6875 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Robert Dufour
- Institut de Recherches Cliniques de Montréal, Department of Nutrition, Université de Montréal, Montréal, Quebec, Canada
| | - Judes Poirier
- Centre for Studies on Prevention of Alzheimer's Disease (StoP-AD Centre), Douglas Mental Health University Institute, 6875 Lasalle, Verdun, Quebec, H4H 1R3, Canada. .,Centre for Studies in the Prevention of Alzheimer's Disease, McGill University, Montréal, Quebec, Canada.
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19
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Fan W, Shen C, Wu M, Zhou ZY, Guo ZR. Association and interaction of PPARα, δ, and γ gene polymorphisms with low-density lipoprotein-cholesterol in a Chinese Han population. Genet Test Mol Biomarkers 2015; 19:379-86. [PMID: 26098621 DOI: 10.1089/gtmb.2015.0002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIMS Elevated low-density lipoprotein-cholesterol (LDL-C) is regarded as one of major risks of cardiovascular diseases and atherosclerotic events. It has been previously reported that peroxisome proliferator-activated receptors (PPARs) play an important role in the regulation of lipid metabolism. In this study, we aimed to investigate the influence of PPARα/δ/γ gene polymorphisms on LDL-C level. Eight hundred twenty unrelated participants were recruited. Ten single-nucleotide polymorphisms (SNPs) were genotyped to analyze the gene-gene interactions among these polymorphisms using the generalized multifactor dimensionality reduction (GMDR) method. RESULTS The results of single-locus analyses indicated that the genotypes with minor allele variants at the rs1800206, rs9794, rs1805192, rs709158, and rs3856806 loci are associated with higher LDL-C levels (p<0.05) after adjusting for covariates. In contrast, individuals that were homozygous for the major allele (CC) of rs10865710 had significantly higher LDL-C than those with either one or more minor type alleles (CG+GG, mean difference: -0.21 mM; 95% confidence interval [CI]: -0.37 to -0.04 mM; p=0.013). Significant gene-gene interactions among PPAR gene polymorphisms on LDL-C were identified by a generalized multifactor dimensionality reduction (GMDR) approach in 2- to 8-locus models (p<0.05). CONCLUSION Our results provide evidence that multiple PPARα/δ/γ gene polymorphisms are individually associated with increased LDL-C, and that interactions, among these alleles result in additional increased risk suggesting that PPAR genes may contribute substantially to the risk of cardiovascular diseases and atherosclerosis.
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Affiliation(s)
- Wei Fan
- 1 Department of Epidemiology, School of Public Health, Medical College of Soochow University , Suzhou, China
| | - Chao Shen
- 1 Department of Epidemiology, School of Public Health, Medical College of Soochow University , Suzhou, China
| | - Ming Wu
- 2 Center for Disease Control of Jiangsu Province , Nanjing, China
| | | | - Zhi-Rong Guo
- 1 Department of Epidemiology, School of Public Health, Medical College of Soochow University , Suzhou, China
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20
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Parihar A, Wood GC, Chu X, Jin Q, Argyropoulos G, Still CD, Shuldiner AR, Mitchell BD, Gerhard GS. Extension of GWAS results for lipid-related phenotypes to extreme obesity using electronic health record (EHR) data and the Metabochip. Front Genet 2014; 5:222. [PMID: 25147553 PMCID: PMC4123014 DOI: 10.3389/fgene.2014.00222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/26/2014] [Indexed: 12/18/2022] Open
Abstract
A variety of health-related data are commonly deposited into electronic health records (EHRs), including laboratory, diagnostic, and medication information. The digital nature of EHR data facilitates efficient extraction of these data for research studies, including genome-wide association studies (GWAS). Previous GWAS have identified numerous SNPs associated with variation in total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG). These findings have led to the development of specialized genotyping platforms that can be used for fine-mapping and replication in other populations. We have combined the efficiency of EHR data and the economic advantages of the Illumina Metabochip, a custom designed SNP chip targeted to traits related to coronary artery disease, myocardial infarction, and type 2 diabetes, to conduct an array-wide analysis of lipid traits in a population with extreme obesity. Our analyses identified associations with 12 of 21 previously identified lipid-associated SNPs with effect sizes similar to prior results. Association analysis using several approaches to account for lipid-lowering medication use resulted in fewer and less strongly associated SNPs. The availability of phenotype data from the EHR and the economic efficiency of the specialized Metabochip can be exploited to conduct multi-faceted genetic association analyses.
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Affiliation(s)
- Ankita Parihar
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine Baltimore, MD, USA
| | - G Craig Wood
- Geisinger Clinic, Geisinger Obesity Institute Danville, PA, USA
| | - Xin Chu
- Geisinger Clinic, Geisinger Obesity Institute Danville, PA, USA
| | - Qunjan Jin
- Department of Pathology and Laboratory Medicine, Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine Hershey, PA, USA
| | | | | | - Alan R Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine Baltimore, MD, USA ; Geriatric Research and Education Clinical Center, Veterans Administration Medical Center Baltimore, MD, USA
| | - Braxton D Mitchell
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine Baltimore, MD, USA ; Geriatric Research and Education Clinical Center, Veterans Administration Medical Center Baltimore, MD, USA
| | - Glenn S Gerhard
- Department of Pathology and Laboratory Medicine, Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, Pennsylvania State University College of Medicine Hershey, PA, USA
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Walia GK, Gupta V, Aggarwal A, Asghar M, Dudbridge F, Timpson N, Singh NS, Kumar MR, Kinra S, Prabhakaran D, Reddy KS, Chandak GR, Smith GD, Ebrahim S. Association of common genetic variants with lipid traits in the Indian population. PLoS One 2014; 9:e101688. [PMID: 24991929 PMCID: PMC4081649 DOI: 10.1371/journal.pone.0101688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 06/10/2014] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies (GWAS) have been instrumental in identifying novel genetic variants associated with altered plasma lipid levels. However, these quantitative trait loci have not been tested in the Indian population, where there is a poorly understood and growing burden of cardiometabolic disorders. We present the association of six single nucleotide polymorphisms in 1671 sib pairs (3342 subjects) with four lipid traits: total cholesterol, triglycerides, high density lipoprotein cholesterol (HDL-C) and low density lipoprotein cholesterol (LDL-C). We also investigated the interaction effects of gender, location, fat intake and physical activity. Each copy of the risk allele of rs964184 at APOA1 was associated with 1.06 mmol/l increase in triglycerides (SE = 0.049; p = 0.006), rs3764261 at CETP with 1.02 mmol/l increase in both total cholesterol (SE = 0.042; p = 0.017) and HDL-C (SE = 0.041; p = 0.008), rs646776 at CELSR2-PSRC1-SORT1 with 0.96 mmol/l decrease in cholesterol (SE = 0.043; p = 0.0003) and 0.15 mmol/l decrease in LDL-C levels (SE = 0.043; p = 0.0003) and rs2954029 at TRIB1 with 1.02 mmol/l increase in HDL-C (SE = 0.039; p = 0.047). A combined risk score of APOA1 and CETP loci predicted an increase of 1.25 mmol/l in HDL-C level (SE = 0.312; p = 0.0007). Urban location and sex had strong interaction effects on the genetic association of most of the studied loci with lipid traits. To conclude, we validated four genetic variants (identified by GWAS in western populations) associated with lipid traits in the Indian population. The interaction effects found here may explain the sex-specific differences in lipid levels and their heritability. Urbanization appears to influence the nature of the association with GWAS lipid loci in this population. However, these findings will require replication in other Indian populations.
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Affiliation(s)
- Gagandeep Kaur Walia
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- * E-mail: (GKW); (VG)
| | - Vipin Gupta
- Department of Anthropology, University of Delhi, Delhi, India
- * E-mail: (GKW); (VG)
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
| | - Mohammad Asghar
- Department of Anthropology, Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India
| | - Frank Dudbridge
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicholas Timpson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | | | - M. Ravi Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Sanjay Kinra
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dorairaj Prabhakaran
- Centre for Chronic Disease Control, New Delhi, India
- Public Health Foundation of India, New Delhi, India
| | | | | | - George Davey Smith
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Shah Ebrahim
- South Asia Network for Chronic Disease (SANCD), Public Health Foundation of India (PHFI), New Delhi, India
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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22
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Varga TV, Sonestedt E, Shungin D, Koivula RW, Hallmans G, Escher SA, Barroso I, Nilsson P, Melander O, Orho-Melander M, Renström F, Franks PW. Genetic determinants of long-term changes in blood lipid concentrations: 10-year follow-up of the GLACIER study. PLoS Genet 2014; 10:e1004388. [PMID: 24922540 PMCID: PMC4055682 DOI: 10.1371/journal.pgen.1004388] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/01/2014] [Indexed: 01/04/2023] Open
Abstract
Recent genome-wide meta-analyses identified 157 loci associated with cross-sectional lipid traits. Here we tested whether these loci associate (singly and in trait-specific genetic risk scores [GRS]) with longitudinal changes in total cholesterol (TC) and triglyceride (TG) levels in a population-based prospective cohort from Northern Sweden (the GLACIER Study). We sought replication in a southern Swedish cohort (the MDC Study; N = 2,943). GLACIER Study participants (N = 6,064) were genotyped with the MetaboChip array. Up to 3,495 participants had 10-yr follow-up data available in the GLACIER Study. The TC- and TG-specific GRSs were strongly associated with change in lipid levels (β = 0.02 mmol/l per effect allele per decade follow-up, P = 2.0×10−11 for TC; β = 0.02 mmol/l per effect allele per decade follow-up, P = 5.0×10−5 for TG). In individual SNP analysis, one TC locus, apolipoprotein E (APOE) rs4420638 (β = 0.12 mmol/l per effect allele per decade follow-up, P = 2.0×10−5), and two TG loci, tribbles pseudokinase 1 (TRIB1) rs2954029 (β = 0.09 mmol/l per effect allele per decade follow-up, P = 5.1×10−4) and apolipoprotein A-I (APOA1) rs6589564 (β = 0.31 mmol/l per effect allele per decade follow-up, P = 1.4×10−8), remained significantly associated with longitudinal changes for the respective traits after correction for multiple testing. An additional 12 loci were nominally associated with TC or TG changes. In replication analyses, the APOE rs4420638, TRIB1 rs2954029, and APOA1 rs6589564 associations were confirmed (P≤0.001). In summary, trait-specific GRSs are robustly associated with 10-yr changes in lipid levels and three individual SNPs were strongly associated with 10-yr changes in lipid levels. Although large cross-sectional studies have proven highly successful in identifying gene variants related to lipid levels and other cardiometabolic traits, very few examples of well-designed longitudinal studies exist where associations between genotypes and long-term changes in lipids have been assessed. Here we undertook analyses in the GLACIER Study to determine whether the 157 previously identified lipid-associated genes variants associate with changes in blood lipid levels over 10-yr follow-up. We identified a variant in APOE that is robustly associated with total cholesterol change and two variants in TRIB1 and APOA1 respectively that are robustly associated with triglyceride change. We replicated these findings in a second Swedish cohort (the MDC Study). The identified genes had previously been associated with cardiovascular traits such as myocardial infarction or coronary heart disease; hence, these novel lipid associations provide additional insight into the pathogenesis of atherosclerotic heart and large vessel disease. By incorporating all 157 established variants into gene scores, we also observed strong associations with 10-yr lipid changes, illustrating the polygenic nature of blood lipid deterioration.
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Affiliation(s)
- Tibor V Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Emily Sonestedt
- Department of Clinical Sciences, Diabetes and Cardiovascular Disease - Genetic Epidemiology, Skåne University Hospital, Malmö, Sweden
| | - Dmitry Shungin
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden; Department of Odontology, Umeå University, Umeå, Sweden; Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
| | - Robert W Koivula
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Göran Hallmans
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Stefan A Escher
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Inês Barroso
- NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom; University of Cambridge, Metabolic Research Laboratories Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Peter Nilsson
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Hypertension and Cardiovascular Diseases, Skåne University Hospital, Malmö, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences, Diabetes and Cardiovascular Disease - Genetic Epidemiology, Skåne University Hospital, Malmö, Sweden
| | - Frida Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden; Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, Malmö, Sweden; Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden; Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
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23
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Scientific reporting is suboptimal for aspects that characterize genetic risk prediction studies: a review of published articles based on the Genetic RIsk Prediction Studies statement. J Clin Epidemiol 2014; 67:487-99. [DOI: 10.1016/j.jclinepi.2013.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 10/03/2013] [Accepted: 10/09/2013] [Indexed: 12/29/2022]
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Milton JN, Gordeuk VR, Taylor JG, Gladwin MT, Steinberg MH, Sebastiani P. Prediction of fetal hemoglobin in sickle cell anemia using an ensemble of genetic risk prediction models. ACTA ACUST UNITED AC 2014; 7:110-5. [PMID: 24585758 DOI: 10.1161/circgenetics.113.000387] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Fetal hemoglobin (HbF) is the major modifier of the clinical course of sickle cell anemia. Its levels are highly heritable, and its interpersonal variability is modulated in part by 3 quantitative trait loci that affect HbF gene expression. Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) in these quantitative trait loci that are highly associated with HbF but explain only 10% to 12% of the variance of HbF. Combining SNPs into a genetic risk score can help to explain a larger amount of the variability of HbF level, but the challenge of this approach is to select the optimal number of SNPs to be included in the genetic risk score. METHODS AND RESULTS We developed a collection of 14 models with genetic risk score composed of different numbers of SNPs and used the ensemble of these models to predict HbF in patients with sickle cell anemia. The models were trained in 841 patients with sickle cell anemia and were tested in 3 independent cohorts. The ensemble of 14 models explained 23.4% of the variability in HbF in the discovery cohort, whereas the correlation between predicted and observed HbF in the 3 independent cohorts ranged between 0.28 and 0.44. The models included SNPs in BCL11A, the HBS1L-MYB intergenic region, and the site of the HBB gene cluster, quantitative trait loci previously associated with HbF. CONCLUSIONS An ensemble of 14 genetic risk models can predict HbF levels with accuracy between 0.28 and 0.44, and the approach may also prove useful in other applications.
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Affiliation(s)
- Jacqueline N Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
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25
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Abstract
Bipolar disorder is a common, complex genetic disorder, but the mode of transmission remains to be discovered. Many researchers assume that common genomic variants carry some risk for manifesting the disease. The research community has celebrated the first genome-wide significant associations between common single nucleotide polymorphisms (SNPs) and bipolar disorder. Currently, attempts are under way to translate these findings into clinical practice, genetic counseling, and predictive testing. However, some experts remain cautious. After all, common variants explain only a very small percentage of the genetic risk, and functional consequences of the discovered SNPs are inconclusive. Furthermore, the associated SNPs are not disease specific, and the majority of individuals with a "risk" allele are healthy. On the other hand, population-based genome-wide studies in psychiatric disorders have rediscovered rare structural variants and mutations in genes, which were previously known to cause genetic syndromes and monogenic Mendelian disorders. In many Mendelian syndromes, psychiatric symptoms are prevalent. Although these conditions do not fit the classic description of any specific psychiatric disorder, they often show nonspecific psychiatric symptoms that cross diagnostic boundaries, including intellectual disability, behavioral abnormalities, mood disorders, anxiety disorders, attention deficit, impulse control deficit, and psychosis. Although testing for chromosomal disorders and monogenic Mendelian disorders is well established, testing for common variants is still controversial. The standard concept of genetic testing includes at least three broad criteria that need to be fulfilled before new genetic tests should be introduced: analytical validity, clinical validity, and clinical utility. These criteria are currently not fulfilled for common genomic variants in psychiatric disorders. Further work is clearly needed before genetic testing for common variants in psychiatric disorders should be established.
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Affiliation(s)
- Berit Kerner
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
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26
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Uhl GR, Walther D, Musci R, Fisher C, Anthony JC, Storr CL, Behm FM, Eaton WW, Ialongo N, Rose JE. Smoking quit success genotype score predicts quit success and distinct patterns of developmental involvement with common addictive substances. Mol Psychiatry 2014; 19:50-4. [PMID: 23128154 PMCID: PMC3922203 DOI: 10.1038/mp.2012.155] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 11/11/2022]
Abstract
Genotype scores that predict relevant clinical outcomes may detect other disease features and help direct prevention efforts. We report data that validate a previously established v1.0 smoking cessation quit success genotype score and describe striking differences in the score in individuals who display differing developmental trajectories of use of common addictive substances. In a cessation study, v1.0 genotype scores predicted ability to quit with P=0.00056 and area under receiver-operating characteristic curve 0.66. About 43% vs 13% quit in the upper vs lower genotype score terciles. Latent class growth analyses of a developmentally assessed sample identified three latent classes based on substance use. Higher v1.0 scores were associated with (a) higher probabilities of participant membership in a latent class that displayed low use of common addictive substances during adolescence (P=0.0004) and (b) lower probabilities of membership in a class that reported escalating use (P=0.001). These results indicate that: (a) we have identified genetic predictors of smoking cessation success, (b) genetic influences on quit success overlap with those that influence the rate at which addictive substance use is taken up during adolescence and (c) individuals at genetic risk for both escalating use of addictive substances and poor abilities to quit may provide especially urgent focus for prevention efforts.
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Affiliation(s)
- George R Uhl
- Molecular Neurobiology Branch, NIH-IRP, NIDA, Baltimore, Maryland 21224,Corresponding Author: George Uhl, Molecular Neurobiology, Box 5180, Baltimore, MD 21224, phone: (443) 740-2799, fax: (443) 740-2122, (GRU)
| | - Donna Walther
- Molecular Neurobiology Branch, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | - Rashelle Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21221
| | - Christian Fisher
- Molecular Neurobiology Branch, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | - James C Anthony
- Dept of Epidemiology, Michigan State University, East Lansing, MI 48824
| | - Carla L Storr
- Department of Family and Community Health, University of Maryland School of Nursing, Baltimore, MD 21201,Dept of Psychiatry and Center for Nicotine and Smoking Cessation Research, Duke University, Durham NC 27705
| | - Frederique M. Behm
- Dept of Psychiatry and Center for Nicotine and Smoking Cessation Research, Duke University, Durham NC 27705
| | - William W Eaton
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21221
| | - Nicholas Ialongo
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21221
| | - Jed E. Rose
- Dept of Psychiatry and Center for Nicotine and Smoking Cessation Research, Duke University, Durham NC 27705
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27
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Gelissen IC, McLachlan AJ. The pharmacogenomics of statins. Pharmacol Res 2013; 88:99-106. [PMID: 24365577 DOI: 10.1016/j.phrs.2013.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/06/2013] [Accepted: 12/12/2013] [Indexed: 12/24/2022]
Abstract
The statin class of cholesterol-lowering drugs have been used for decades to successfully lower plasma cholesterol concentrations and cardiovascular risk. Adverse effects of statins are generally considered mild, but increase with age of patients and polypharmacy. One aspect of statin therapy that is still difficult for prescribers to predict is the individual's response to statin therapy. Recent advances in the field of pharmacogenomics have indicated variants of candidate genes that affect statin efficacy and safety. In this review, a number of candidates that affect statin pharmacokinetics and pharmacodynamics are discussed. Some of these candidates, in particular those involved in import and efflux of statins, have now been linked to increased risk of side effects. Furthermore, pharmacogenomic studies continue to reveal new players that are involved in the fine-tuning of the complex regulation of cholesterol homeostasis and response to statins.
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Affiliation(s)
| | - Andrew J McLachlan
- Faculty of Pharmacy, University of Sydney, NSW, Australia; Centre for Education and Research on Ageing, Concord Hospital, Sydney, NSW, Australia
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van Zyl T, Jerling JC, Conradie KR, Feskens EJM. Common and rare single nucleotide polymorphisms in the LDLR gene are present in a black South African population and associate with low-density lipoprotein cholesterol levels. J Hum Genet 2013; 59:88-94. [DOI: 10.1038/jhg.2013.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 10/18/2013] [Accepted: 10/30/2013] [Indexed: 11/09/2022]
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Xiong X, Xu C, Zhang Y, Li X, Wang B, Wang F, Yang Q, Wang D, Wang X, Li S, Chen S, Zhao Y, Yin D, Huang Y, Zhu X, Wang L, Wang L, Chang L, Xu C, Li H, Ke T, Ren X, Wu Y, Zhang R, Wu T, Xia Y, Yang Y, Ma X, Tu X, Wang QK. BRG1 variant rs1122608 on chromosome 19p13.2 confers protection against stroke and regulates expression of pre-mRNA-splicing factor SFRS3. Hum Genet 2013; 133:499-508. [PMID: 24190014 DOI: 10.1007/s00439-013-1389-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 10/26/2013] [Indexed: 01/31/2023]
Abstract
A single nucleotide polymorphism (SNP) rs1122608 on chromosome 19p13.2 and in the BRG1/SMARCA4 gene was previously associated with coronary artery disease (CAD). CAD and ischemic stroke are both associated with atherosclerosis. Thus, we tested the hypothesis that rs1122608 is associated with ischemic stroke. Further studies were used to identify the most likely mechanism by which rs1122608 regulates atherosclerosis. For case-control association studies, two independent Chinese Han GeneID cohorts were used, including a Central cohort with 1,075 cases and 2,685 controls and the Northern cohort with 1,208 cases and 824 controls. eQTL and real-time RT-PCR analyses were used to identify the potential candidate gene(s) affected by rs1122608. The minor allele T of SNP rs1122608 showed significant association with a decreased risk of ischemic stroke in the Central GeneID cohort (adjusted P adj = 2.1 × 10(-4), OR 0.61). The association was replicated in an independent Northern GeneID cohort (P adj = 6.00 × 10(-3), OR 0.69). The association became more significant in the combined population (P adj = 7.86 × 10(-5), OR 0.73). Allele T of SNP rs1122608 also showed significant association with a decreased total cholesterol level (P adj = 0.013). Allele T of rs1122608 was associated with an increased expression level of SFRS3 encoding an mRNA splicing regulator, but not with the expression of BRG1/SMARCA4 or LDLR (located 36 kb from rs1122608). Increased expression of SFSR3 may decrease IL-1β expression and secretion, resulting in reduced risk of atherosclerosis and stroke. This is the first study that demonstrates that rs1122608 confers protection against ischemic stroke and implicates splicing factor SFSR3 in the disease process.
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Affiliation(s)
- Xin Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, China
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Perisic L, Hedin E, Razuvaev A, Lengquist M, Osterholm C, Folkersen L, Gillgren P, Paulsson-Berne G, Ponten F, Odeberg J, Hedin U. Profiling of atherosclerotic lesions by gene and tissue microarrays reveals PCSK6 as a novel protease in unstable carotid atherosclerosis. Arterioscler Thromb Vasc Biol 2013; 33:2432-43. [PMID: 23908247 DOI: 10.1161/atvbaha.113.301743] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Carotid plaque instability is a major cause of ischemic stroke, but detailed knowledge about underlying molecular pathways is still lacking. Here, we evaluated large-scale transcriptomic and protein expression profiling in a biobank of carotid endarterectomies followed by characterization of identified candidates, as a platform for discovery of novel proteins differentially regulated in unstable carotid lesions. APPROACH AND RESULTS Genes highly upregulated in symptomatic versus asymptomatic plaques were selected from Affymetrix microarray analyses (n=127 plaques), and tissue microarrays constructed from 34 lesions were assayed for 21 corresponding proteins by immunohistochemistry. Quantification of stainings demonstrated differential expression of CD36, CD137, and DOCK7 (P<0.05) in unstable versus stable lesions and the most significant upregulation of a proprotein convertase, PCSK6 (P<0.0001). Increased expression of PCSK6 in symptomatic lesions was verified by quantitative real-time polymerase chain reaction (n=233), and the protein was localized to smooth muscle α-actin positive cells and extracellular matrix of the fibrous cap by immunohistochemistry. PCSK6 expression positively correlated to genes associated with inflammation, matrix degradation, and mitogens in microarrays. Stimulation of human carotid smooth muscle cells in vitro with cytokines caused rapid induction of PCSK6 mRNA. CONCLUSIONS Using a combination of transcriptomic and tissue microarray profiling, we demonstrate a novel approach to identify proteins differentially expressed in unstable carotid atherosclerosis. The proprotein convertase PCSK6 was detected at increased levels in the fibrous cap of symptomatic carotid plaques, possibly associated with key processes in plaque rupture such as inflammation and extracellular matrix remodeling. Further studies are needed to clarify the role of PCSK6 in atherosclerosis.
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Affiliation(s)
- Ljubica Perisic
- From the Department of Molecular Medicine and Surgery (L.P., E.H., A.R., M.L., C.O., U.H.), and Department of Medicine (G.P.-B., J.O.), Karolinska Institute, Stockholm, Sweden; Department of Molecular Genetics, Novo Nordisk, Copenhagen, Denmark (L.F.); Department of Surgery, Södersjukhuset, Stockholm, Sweden (P.G.); Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden (F.P.); and Department of Proteomics, Royal Institute of Technology, Stockholm, Sweden (J.O.)
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Cederberg H, Gylling H, Miettinen TA, Paananen J, Vangipurapu J, Pihlajamäki J, Kuulasmaa T, Stančáková A, Smith U, Kuusisto J, Laakso M. Non-cholesterol sterol levels predict hyperglycemia and conversion to type 2 diabetes in Finnish men. PLoS One 2013; 8:e67406. [PMID: 23840693 PMCID: PMC3696087 DOI: 10.1371/journal.pone.0067406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/16/2013] [Indexed: 11/24/2022] Open
Abstract
We investigated the levels of non-cholesterol sterols as predictors for the development of hyperglycemia (an increase in the glucose area under the curve in an oral glucose tolerance test) and incident type 2 diabetes in a 5-year follow-up study of a population-based cohort of Finnish men (METSIM Study, N = 1,050) having non-cholesterol sterols measured at baseline. Additionally we determined the association of 538,265 single nucleotide polymorphisms (SNP) with non-cholesterol sterol levels in a cross-sectional cohort of non-diabetic offspring of type 2 diabetes (the Kuopio cohort of the EUGENE2 Study, N = 273). We found that in a cross-sectional METSIM Study the levels of sterols indicating cholesterol absorption were reduced as a function of increasing fasting glucose levels, whereas the levels of sterols indicating cholesterol synthesis were increased as a function of increasing 2-hour glucose levels. A cholesterol synthesis marker desmosterol significantly predicted an increase, and two absorption markers (campesterol and avenasterol) a decrease in the risk of hyperglycemia and incident type 2 diabetes in a 5-year follow-up of the METSIM cohort, mainly attributable to insulin sensitivity. A SNP of ABCG8 was associated with fasting plasma glucose levels in a cross-sectional study but did not predict hyperglycemia or incident type 2 diabetes. In conclusion, the levels of some, but not all non-cholesterol sterols are markers of the worsening of hyperglycemia and type 2 diabetes.
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Affiliation(s)
- Henna Cederberg
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Helena Gylling
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Division of Internal Medicine, University of Helsinki, Helsinki, Finland
| | - Tatu A. Miettinen
- Department of Medicine, Division of Internal Medicine, University of Helsinki, Helsinki, Finland
| | - Jussi Paananen
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Teemu Kuulasmaa
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
- * E-mail:
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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Lutsey PL, Rasmussen-Torvik LJ, Pankow JS, Alonso A, Smolenski DJ, Tang W, Coresh J, Volcik KA, Ballantyne CM, Boerwinkle E, Folsom AR. Relation of lipid gene scores to longitudinal trends in lipid levels and incidence of abnormal lipid levels among individuals of European ancestry: the Atherosclerosis Risk in Communities (ARIC) study. ACTA ACUST UNITED AC 2011; 5:73-80. [PMID: 22057756 DOI: 10.1161/circgenetics.111.959619] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Multiple genetic loci have been associated with blood lipid levels. We tested the hypothesis that persons with an unfavorable lipid gene profile would experience a greater increase in lipid levels and a higher incidence of abnormal lipid levels relative to those with more-favorable lipid gene profiles. METHODS AND RESULTS A total of 9328 individuals of European descent (aged 45-64 years) in the ARIC (Atherosclerosis Risk in Communities) study were followed for 9 years. Separate gene scores were created for each lipid phenotype on the basis of 95 loci identified in a published genome-wide association study of >100 000 people of European-descent. Adjusted linear and survival models were used to estimate associations with lipid levels and incidence of lipid-lowering medication or abnormal lipid levels. Age and sex interactions were also explored. The cross-sectional difference (mg/dL) per 1 SD was -1.89 for high-density lipoprotein cholesterol (HDL-C), 9.5 for low-density lipoprotein cholesterol (LDL-C), and 22.8 for triglycerides (P<5×10(-34) for all). Longitudinally, overall triglyceride levels rose over time, and each 1-SD greater triglyceride gene score was associated with an average increase in triglyceride levels of 0.3 mg/dL (P=0.003) over 3 years. The HDL-C, LDL-C, and total cholesterol gene scores were not related to change. All lipid gene scores were positively related to incidence of abnormal lipid levels over follow-up (hazard ratios per SD range, 1.15-1.36). CONCLUSIONS Associations of genetic variants with lipid levels over time are complex. The triglyceride gene score was positively related to change in triglycerides levels, but similar longitudinal results were not observed for LDL-C or HDL-C levels. Unfavorable gene scores were nevertheless related to higher incidence of abnormal levels.
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Affiliation(s)
- Pamela L Lutsey
- Division of Epidemiology and Community Health, University of Minnesota, 1300 S 2nd Street, Minneapolis, MN 55454, USA.
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Chang MH, Ned RM, Hong Y, Yesupriya A, Yang Q, Liu T, Janssens ACJW, Dowling NF. Racial/ethnic variation in the association of lipid-related genetic variants with blood lipids in the US adult population. CIRCULATION. CARDIOVASCULAR GENETICS 2011; 4:523-33. [PMID: 21831959 DOI: 10.1161/circgenetics.111.959577] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified a number of single-nucleotide polymorphisms (SNPs) associated with serum lipid level in populations of European descent. The individual and the cumulative effect of these SNPs on blood lipids are largely unclear for the US population. METHODS AND RESULTS Using data from the second phase (1991-1994) of the Third National Health and Nutrition Examination Survey (NHANES III), a nationally representative survey of the US population, we examined associations of 57 GWAS-identified or well-established lipid-related genetic loci with plasma concentrations of high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol, total cholesterol, triglycerides, total cholesterol/HDL-C ratio, and non-HDL-C. We used multivariable linear regression to examine single SNP associations and the cumulative effect of multiple SNPs (using a genetic risk score [GRS]) on blood lipid levels. Analyses were conducted in adults from each of the 3 major racial/ethnic groups in the United States: non-Hispanic whites (n=2296), non-Hispanic blacks (n=1699), and Mexican Americans (n=1713). Allele frequencies for all SNPs varied significantly by race/ethnicity, except rs3764261 in CETP. Individual SNPs had very small effects on lipid levels, effects that were generally consistent in direction across racial/ethnic groups. More GWAS-validated SNPs were replicated in non-Hispanic whites (<67%) than in non-Hispanic blacks (<44%) or Mexican Americans (<44%). GRSs were strongly associated with increased lipid levels in each racial/ethnic group. The combination of all SNPs into a weighted GRS explained no more than 11% of the total variance in blood lipid levels. CONCLUSIONS Our findings show that the combined association of SNPs, based on a GRS, was strongly associated with increased blood lipid measures in all major race/ethnic groups in the United States, which may help in identifying subgroups with a high risk for an unfavorable lipid profile.
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Affiliation(s)
- Man-huei Chang
- Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Carrasquillo MM, Nicholson AM, Finch N, Gibbs JR, Baker M, Rutherford NJ, Hunter TA, DeJesus-Hernandez M, Bisceglio GD, Mackenzie IR, Singleton A, Cookson MR, Crook JE, Dillman A, Hernandez D, Petersen RC, Graff-Radford NR, Younkin SG, Rademakers R. Genome-wide screen identifies rs646776 near sortilin as a regulator of progranulin levels in human plasma. Am J Hum Genet 2010; 87:890-7. [PMID: 21087763 DOI: 10.1016/j.ajhg.2010.11.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 11/04/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022] Open
Abstract
Recent studies suggest progranulin (GRN) is a neurotrophic factor. Loss-of-function mutations in the progranulin gene (GRN) cause frontotemporal lobar degeneration (FTLD), a progressive neurodegenerative disease affecting ∼10% of early-onset dementia patients. Using an enzyme-linked immunosorbent assay, we previously showed that GRN is detectable in human plasma and can be used to predict GRN mutation status. This study also showed a wide range in plasma GRN levels in non-GRN mutation carriers, including controls. We have now performed a genome-wide association study of 313,504 single-nucleotide polymorphisms (SNPs) in 533 control samples and identified on chromosome 1p13.3 two SNPs with genome-wide significant association with plasma GRN levels (top SNP rs646776; p = 1.7 × 10⁻³⁰). The association of rs646776 with plasma GRN levels was replicated in two independent series of 508 controls (p = 1.9 × 10⁻¹⁹) and 197 FTLD patients (p = 6.4 × 10⁻¹²). Overall, each copy of the minor C allele decreased GRN levels by ∼15%. SNP rs646776 is located near sortilin (SORT1), and the minor C allele of rs646776 was previously associated with increased SORT1 mRNA levels. Supporting these findings, overexpression of SORT1 in cultured HeLa cells dramatically reduced GRN levels in the conditioned media, whereas knockdown of SORT1 increased extracellular GRN levels. In summary, we identified significant association of a locus on chromosome 1p13.3 with plasma GRN levels through an unbiased genome-wide screening approach and implicated SORT1 as an important regulator of GRN levels. This finding opens avenues for future research into GRN biology and the pathophysiology of neurodegenerative diseases.
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