Genome-Wide Association Study on Adiponectin-Mediated Suppression of HDL-C Levels in Taiwanese Individuals Identifies Functional Haplotypes in CDH13

CDH13 encodes T-cadherin, which is expressed in the vasculature and cardiac myocytes and is the receptor for hexameric and high-molecular-weight adiponectin. The CDH13 region is the most pivotal locus associated with adiponectin level. Mediation analysis is a method to explore the effect of a third variable, it is assumed that the magnitude of the relationship between the independent and dependent variables will be reduced by statistical adjustment for a third variable. In addition, mediation can further occur in the case when the mediator acts as a pathway-suppressor variable that means a suppression effect may be suggested if the statistical removal of a mediation effect could increase the magnitude of the relationship between the independent and dependent variables. Here, we aimed to explore the suppression effect in a genome-wide association study, and investigate possible mechanisms that may link adiponectin to CDH13 variants and high-density lipoprotein cholesterol (HDL-C). Genome-wide association data for adiponectin and HDL-C were accessible for 2349 Taiwan-biobank participants. The mediation analysis was conducted with the CDH13 lead single nucleotide polymorphism (SNP) rs4783244. The cloned constructs of CDH13 haplotypes (GG and TT) identified from the rs4783244 G/T and rs12051272 G/T SNPs were transiently expressed in HEK293T cells and investigated using the luciferase reporter assay. Genome-wide association analysis showed that HDL-C is significantly associated with variants in CDH13 after adjusting for the adiponectin level. The lead SNP rs4783244 was significantly associated with lower adiponectin levels and exhibited a suppression effect on HDL-C when adiponectin was included as a third factor in the mediation analysis. Luciferase reporter assay results further demonstrated that the GG haplotype increased enhancer activity, whereas the haplotype TT significantly reduced the activity of this enhancer. We present the first evidence of the suppressive role of adiponectin in the genome-wide association between CDH13 and HDL-C. CDH13 may increase the HDL-C levels, and its expression is suppressed by adiponectin.

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Functional validation of a finding from a mouse genome-wide association study demonstrates that a mutant allele of Azi2 alters sensitivity to methamphetamine

10.1101/2020.08.22.262709 ◽

2020 ◽

Author(s):

Xinzhu Zhou ◽

Amanda Barkley-Levenson ◽

Patricia Montilla-Perez ◽

Francesca Telese ◽

Abraham A. Palmer

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Metabotropic Glutamate Receptor ◽

Mouse Genome ◽

Genome Wide Association ◽

Group Iii ◽

Metabotropic Glutamate ◽

Genome Wide ◽

Receptor Signaling Pathway ◽

The Relationship

AbstractMethamphetamine is a widely abused psychostimulant. In a previous genome-wide association study (GWAS), we identified a locus that influenced the stimulant response to methamphetamine. That locus was also an eQTL for the gene Azi2. Based on those findings, we hypothesized that heritable differences in the expression of Azi2 were causally related to the differential response to methamphetamine. In this study, we created a mutant Azi2 allele that caused lower Azi2 expression and enhanced the locomotor response to methamphetamine; however, based on the GWAS findings, we had expected lower Azi2 to decrease rather than increase the stimulant response to methamphetamine. We then sought to explore the mechanism by which Azi2 influenced methamphetamine sensitivity. A recent publication had reported that the 3’UTR of Azi2 mRNA downregulates the expression of Slc6a3, which encodes the dopamine transporter (DAT), which is a key target of methamphetamine. We evaluated the relationship between Azi2/Azi2 3’UTR and Slc6a3 expression in the VTA in the mutant Azi2 mice and in a new cohort of CFW mice. We did not observe any correlation between Azi2 and Slc6a3 in the VTA in either cohort. However, RNA sequencing confirmed that the Azi2 mutation altered Azi2 expression and also revealed a number of potentially important genes and pathways that were regulated by Azi2, including the metabotropic glutamate receptor group III pathway and nicotinic acetylcholine receptor signaling pathway. Our results support a role for Azi2 in methamphetamine sensitivity; however, the exact mechanism does not appear to involve regulation of Slc6a3 and thus remains unknown.

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Periodontitis Risk Variants at SIGLEC5 Impair ERG and MAFB Binding

Journal of Dental Research ◽

10.1177/00220345211049984 ◽

2021 ◽

pp. 002203452110499

Author(s):

R. Mueller ◽

A. Chopra ◽

H. Dommisch ◽

A.S. Schaefer

Keyword(s):

Association Study ◽

Target Gene ◽

Genome Wide Association Study ◽

Biological Effects ◽

Regulatory Elements ◽

Genome Wide Association ◽

Luciferase Reporter ◽

Genome Wide ◽

A Genome ◽

Allele Specific

Periodontitis is a common complex inflammatory disease of the oral cavity. It is characterized by inflammation of gingival tissues and alveolar bone loss. Recently, a genome-wide association study and 2 genome-wide association study meta-analyses found 2 associated regions (haplotype blocks) at the inhibitory immune receptor gene SIGLEC5 to increase the risk for periodontitis. The aims of the current study were the identification of the putative causal variants underlying these associations, characterization of their molecular biological effects, and validation of SIGLEC5 as the target gene. We mapped the associated single-nucleotide polymorphisms to DNA elements with predictive features of regulatory functions and screened the associated alleles for transcription factor (TF) binding sites. Antibody electrophoretic mobility shift assays (EMSAs) with allele-specific probes were used to identify TF binding and to quantify allele-specific effects on binding affinities. Luciferase reporter assays were used to quantify the effect directions and allele-specific strength of the associated regulatory elements. We used CRISPR-dCas9 gene activation to validate SIGLEC5 as a target of the association. EMSA in peripheral blood mononuclear cells showed that E-26 transformation–specific TF-related gene (ERG) binds at rs11084095, with almost complete loss of binding at the minor A-allele. Allele-specific reporter genes showed enhancer function of the DNA sequence at rs11084095, which was abrogated in the background of the A-allele. EMSA in B lymphocytes showed that TF MAF bZIP (MAFB) binds at the common G-allele of rs4284742, whereas the minor A-allele reduced TF binding by 69%, corresponding to 9-fold reduction of luciferase reporter gene activity by the A-allele. Using CRISPR-dCas9, we showed that the enhancer at rs4284742 strongly activated SIGLEC5 expression, validating this gene as the target gene of the association. We conclude that rs11084095 and rs4284742 are putatively causal for the genome-wide significant associations with periodontitis at SIGLEC5 that impair ERG and MAFB binding, respectively.

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Functional Haplotype of LIPC Induces Triglyceride-Mediated Suppression of HDL-C Levels According to Genome-Wide Association Studies

Genes ◽

10.3390/genes12020148 ◽

2021 ◽

Vol 12 (2) ◽

pp. 148

Author(s):

Yu-Huang Liao ◽

Leay-Kiaw Er ◽

Semon Wu ◽

Yu-Lin Ko ◽

Ming-Sheng Teng

Keyword(s):

Hepatic Lipase ◽

Association Studies ◽

Luciferase Reporter Assay ◽

Genome Wide Association ◽

Luciferase Reporter ◽

Genome Wide Association Studies ◽

Reporter Assay ◽

Triacylglycerol Lipase ◽

Genome Wide ◽

A Genome

Hepatic lipase (encoded by LIPC) is a glycoprotein in the triacylglycerol lipase family and mainly synthesized in and secreted from the liver. Previous studies demonstrated that hepatic lipase is crucial for reverse cholesterol transport and modulating metabolism and the plasma levels of several lipoproteins. This study was conducted to investigate the suppression effect of high-density lipoprotein cholesterol (HDL-C) levels in a genome-wide association study and explore the possible mechanisms linking triglyceride (TG) to LIPC variants and HDL-C. Genome-wide association data for TG and HDL-C were available for 4657 Taiwan-biobank participants. The prevalence of haplotypes in the LIPC promoter region and their effects were calculated. The cloned constructs of the haplotypes were expressed transiently in HepG2 cells and evaluated in a luciferase reporter assay. Genome-wide association analysis revealed that HDL-C was significantly associated with variations in LIPC after adjusting for TG. Three haplotypes (H1: TCG, H2: CTA and H3: CCA) in LIPC were identified. H2: CTA was significantly associated with HDL-C levels and H1: TCG suppressed HDL-C levels when a third factor, TG, was included in mediation analysis. The luciferase reporter assay further showed that the H2: CTA haplotype significantly inhibited luciferase activity compared with the H1: TCG haplotype. In conclusion, we identified a suppressive role for TG in the genome-wide association between LIPC and HDL-C. A functional haplotype of hepatic lipase may reduce HDL-C levels and is suppressed by TG.

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Genome-wide association study of corneal biomechanical properties identifies over 200 loci providing insight into the genetic etiology of ocular diseases

Human Molecular Genetics ◽

10.1093/hmg/ddaa155 ◽

2020 ◽

Vol 29 (18) ◽

pp. 3154-3164 ◽

Cited By ~ 2

Author(s):

Mark J Simcoe ◽

Anthony P Khawaja ◽

Pirro G Hysi ◽

Christopher J Hammond ◽

Keyword(s):

Association Study ◽

Genetic Architecture ◽

Genome Wide Association Study ◽

Biomechanical Properties ◽

Genome Wide Association ◽

Corneal Resistance Factor ◽

Genome Wide ◽

Candidate Loci ◽

The Relationship ◽

Insight Into

Abstract Corneal hysteresis and corneal resistance factor are parameters that reflect the dynamic biomechanical properties of the cornea and have been shown to be biomarkers of corneal disease. In this genome-wide association study of over 100 000 participants, we identified over 200 genetic loci, all but eight novel, significantly associated with either one or both of these traits. In addition to providing key insights into the genetic architecture underlying normal corneal function, these results identify many candidate loci in the study of corneal diseases that lead to severe visual impairment. Additionally, using Mendelian randomization, we were able to identify causal relationships between corneal biomechanics and intraocular pressure measurements, which help elucidate the relationship between corneal properties and glaucoma.

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Genome-wide association study of plasma resistin levels identified rs1423096 and rs10401670 as possible functional variants in the Japanese population

Physiological Genomics ◽

10.1152/physiolgenomics.00040.2016 ◽

2016 ◽

Vol 48 (11) ◽

pp. 874-881 ◽

Cited By ~ 5

Author(s):

Ryoichi Kawamura ◽

Yasuharu Tabara ◽

Akiko Tsukada ◽

Michiya Igase ◽

Jun Ohashi ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Association Study ◽

Japanese Population ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Luciferase Reporter ◽

Strong Linkage Disequilibrium ◽

Functional Variants ◽

Genome Wide ◽

A Genome

Resistin is a cytokine inducing insulin resistance in mice. We previously identified single nucleotide polymorphisms (SNPs) at −420 (rs1862513) and −358 (rs3219175) located in the human resistin gene ( RETN) promoter as strong determinants for circulating resistin in the Japanese population. The objective was to identify additional functional variants for circulating resistin. We conducted a genome-wide association study in 448 Japanese subjects. A peak association signal was found on chromosome 19 where RETN is located. The top-hit SNP was SNP −358 G>A, followed by rs1423096 C>T, SNP −420 C>G, and rs10401670 C>T ( P = 5.39×10−47, 1.81×10−22, 2.09×10−16, and 9.25×10−15, respectively). Meta-analysis including another two independent general Japanese populations showed that circulating resistin was most strongly associated with SNP-358, followed by SNP-420, rs1423096, and rs10401670. Rs1423096 and rs10401670 were located in the 3′-region of RETN and were in strong linkage disequilibrium. Although these SNPs were also in linkage disequilibrium with the promoter SNPs, conditional and haplotype association analyses identified rs1423096 and rs10401670 as independent determinants for circulating resistin. Functionally, nuclear proteins specifically recognized T but not C at rs10401670 as evidenced by an electrophoretic mobility shift assay. The promoter activity of a luciferase reporter with T at either rs1423096 or rs10401670 was lower than that with C in THP-1 human monocytes. Therefore, rs1423096 and rs10401670, in addition to SNP-420 and SNP-358, were identified as possible functional variants affecting circulating resistin by the genome-wide search in the Japanese population.

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A genome-wide association study uncovers a critical role of the RsPAP2 gene in red-skinned Raphanus sativus L.

Horticulture Research ◽

10.1038/s41438-020-00385-y ◽

2020 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Lianxue Fan ◽

Yan Wang ◽

Liang Xu ◽

Mingjia Tang ◽

Xiaoli Zhang ◽

...

Keyword(s):

Association Study ◽

Skin Color ◽

Raphanus Sativus ◽

Genome Wide Association Study ◽

Critical Role ◽

Genome Wide Association ◽

Genetic Enhancement ◽

Luciferase Reporter ◽

Genome Wide ◽

A Genome

Abstract Radish (Raphanus sativus L.) taproot contains high concentrations of flavonoids, including anthocyanins (ATCs), in red-skinned genotypes. However, little information on the genetic regulation of ATC biosynthesis in radish is available. A genome-wide association study of radish red skin color was conducted using whole-genome sequencing data derived from 179 radish genotypes. The R2R3-MYB transcription factor production of anthocyanin pigment 2 (PAP2) gene was found in the region associated with a leading SNP located on chromosome 2. The amino acid sequence encoded by the RsPAP2 gene was different from those of the other published RsMYB genes responsible for the red skin color of radish. The overexpression of the RsPAP2 gene resulted in ATC accumulation in Arabidopsis and radish, which was accompanied by the upregulation of several ATC-related structural genes. RsPAP2 was found to bind the RsUFGT and RsTT8 promoters, as shown by a dual-luciferase reporter system and a yeast one-hybrid assay. The promoter activities of the RsANS, RsCHI, RsPAL, and RsUFGT genes could be strongly activated by coinfiltration with RsPAP2 and RsTT8. These findings showed the effectiveness of GWAS in identifying candidate genes in radish and demonstrated that RsPAP2 could (either directly or together with its cofactor RsTT8) regulate the transcript levels of ATC-related genes to promote ATC biosynthesis, facilitating the genetic enhancement of ATC contents and other related traits in radish.

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Mendelian randomization analyses show that higher acetyl-carnitine and carnitine levels in blood protect against severe Covid19

10.1101/2021.05.31.21257910 ◽

2021 ◽

Author(s):

Nabila Kazmi ◽

George Davey Smith ◽

Sarah J Lewis

Keyword(s):

Protective Effect ◽

Odds Ratio ◽

Genome Wide Association Study ◽

Mendelian Randomization ◽

Genome Wide Association ◽

Protective Effects ◽

Genome Wide ◽

Essential Nutrient ◽

The Relationship ◽

Genome Wide Study

Background: Severe Covid19 is characterised by a hyperactive immune response. Carnitine, an essential nutrient, and its derivative acetyl-carnitine can downregulate proinflammatory cytokines and has been suggested as a potential treatment for the disease. Methods: We carried out Mendelian randomization analyses using publicly available data from a large genome wide association study (GWAS) of metabolites and a collaborative genome wide study of Covid19 to investigate the nature of the relationship between carnitine and acetyl-carnitine and Covid19 infection, hospitalisation with Covid19 and very severe Covid19. We used the same methodology to determine whether carnitine was associated with co-morbidities commonly found among those with severe Covid19. Results: We found evidence of a protective effect against very severe Covid19 for both carnitine and acetyl-carnitine, with around a 40% reduction in risk associated with a doubling of carnitine or acetyl-carnitine (carnitine odds ratio (OR) = 0.56, 95% confidence intervals (CI) 0.33 to 0.95, p=0.03 and acetyl-carnitine OR=0.60, 95% CI 0.35 to 1.02, p=0.06), and evidence of protective effects on hopitalisation with Covid19. For acetyl-carnitine the largest protective effect was seen in the comparison between those hospitalised with Covid19 and those infected but not hospitalised (OR=0.34, 95%CI 0.18 to 0.62, p=0.0005). Conclusion: Carnitine and acetyl-carnitine merit further investigation in respect to the prevention of severe Covid19.

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