Coding variant Met72Thr in the PEDF gene and risk of neovascular age-related macular degeneration and polypoidal choroidal vasculopathy.

PURPOSE: Using a candidate-gene approach, a recent case-control study identified a previously unknown association between neovascular age-related macular degeneration (AMD) and the coding Met72Thr variant in the pigment epithelium-derived factor (PEDF) gene in a Taiwan Chinese population. However, a subsequent replication study failed to see this association in a white European population. We noted an important difference in the sample ascertainment scheme between these two studies. The original study did not consider findings of indocyanine green (ICG) angiography for disease classification, which is the only way to obtain a clear image of polypoidal choroidal vasculopathy (PCV) lesions. This suggests that their cohort might include a considerable amount of PCV, given its high prevalence in the Chinese population. In contrast, the replication study intentionally excluded PCV from the case cohort on the basis of ICG angiograms. Therefore, the inconsistent finding might be caused by potential sample heterogeneity between these two studies. In this respect, this association needed to be examined in a case series of clearly defined individuals with neovascular AMD and PCV. The aim of this study was to validate the previously reported association of the PEDF Met72Thr variant in a well characterized Japanese population with neovascular AMD and PCV. METHODS: We genotyped the Met72Thr variant (rs1136287) in 116 patients with neovascular AMD, 140 patients with PCV, and 189 control participants in a Japanese population. Genotyping was performed using TaqMan technology. We tested for an association of this variant with neovascular AMD and PCV separately. We also evaluated population stratification in our study cohort. RESULTS: We found no statistically significant evidence for association between rs1136287 and either neovascular AMD or PCV under any genetic models (trend, genotypic, dominant, and recessive genetic models; p>0.05). Population structure analyses excluded stratification artifact in our study population. CONCLUSIONS: We report a lack of association between the PEDF Met72Thr variant and either neovascular AMD or PCV in a Japanese population. We conclude that the Met72Thr variant does not play a significant role in the risk of developing neovascular AMD or PCV.

Role of RDBP and SKIV2L variants in the major histocompatibility complex class III region in polypoidal choroidal vasculopathy etiology.

PURPOSE: To investigate whether polymorphisms in 4 tightly linked genes of the major histocompatibility complex class III--complement component 2 (C2), complement factor B (CFB), RD RNA-binding protein (RDBP), and superkiller viralicidic activity 2-like (SKIV2L)--are associated with polypoidal choroidal vasculopathy (PCV). DESIGN: Cross-sectional study. PARTICIPANTS: A case-control group of 136 PCV subjects and 183 unrelated controls. METHODS: We performed an association analysis between PCV and polymorphisms across the C2-CFB-RDBP-SKIV2L region in a Japanese population, genotyping 13 single nucleotide polymorphisms (SNPs) spanning this region, including rs9332739 (E318D), rs547154, rs4151667 (L9H), and rs641153 (R32Q) that are known to be associated with age-related macular degeneration (AMD). Genotyping was conducted using TaqMan technology (Applied Biosystems, Foster City, CA). We also examined population stratification in our study cohort. MAIN OUTCOME MEASURES: Allele and haplotype frequencies of the variants across the C2-CFB-RDBP-SKIV2L region. RESULTS: We initially scanned the C2-CFB locus using 11 SNPs that capture the majority of common variations in this locus. We found a significant omnibus haplotype association and a single disease-protective haplotype, but individually, none of the 11 SNPs were associated with PCV. Further studies led to the identification of 2 untested allelic variants in RDBP (rs3880457) and SKIV2L (rs2075702) that were located on the protective haplotype. We also analyzed these 2 SNPs, detecting a significant association with a decreased risk of developing PCV (for both SNPs, allelic P = 0.0038 and per allele odds ratio = 0.31 [95% confidence interval, 0.13-0.71]). The 2 SNPs were correlated (r(2) = 1) in our dataset. Haplotype analysis and conditional testing demonstrated that either rs3880457 or rs2075702 could fully account for the omnibus haplotype association detected across the C2-CFB-RDBP-SKIV2L region. Population stratification analyses excluded stratification artifacts in our study cohort. CONCLUSIONS: Our results do not support any major role of the 4 AMD-associated variants in the risk of developing PCV, but favor a predominant association with the RDBP-SKIV2L variants, which has some potential implications for pathobiological differences between PCV and neovascular AMD. Further genetic characterization of this locus will provide additional insights into the genetic basis of PCV susceptibility.

Coding variant I62V in the complement factor H gene is strongly associated with polypoidal choroidal vasculopathy.

PURPOSE: To investigate whether variants in the complement factor H (CFH) gene are associated with polypoidal choroidal vasculopathy (PCV). DESIGN: Cross-sectional study. PARTICIPANTS: A case-control group of 130 PCV subjects and 173 unrelated controls. METHODS: We conducted an association analysis between CFH variants and PCV in a Japanese population, genotyping 12 tag single nucleotide polymorphisms (SNPs)-including rs3753394, rs800292 (I62V), and rs1061170 (Y402H)-that are highly representative of the common genetic variation in the CFH region. Genotyping was performed using TaqMan technology. MAIN OUTCOME MEASURES: Allele and haplotype frequencies of the CFH variants. RESULTS: A highly significant association with PCV was observed across the CFH region. The strongest association was observed at I62V (P = 1.7 x 10(-7)). Six other SNPs (rs3753394, rs6680396, rs1410996, rs2284664, rs1329428, and rs1065489) also showed significant association (10(-3) < P < 10(-6)). These associations became nonsignificant after accounting for rs800292 in a conditional logistic regression analysis. A significant omnibus haplotype association was detected in the entire CFH region (omnibus P = 1.6 x 10(-5) at 7 degrees of freedom). Conditional haplotype-based likelihood ratio tests revealed that the significant omnibus haplotype association disappeared when it was estimated conditional on I62V (omnibus P = 0.20, 6 degrees of freedom, post-I62V dependency), whereas the omnibus haplotype association remained significant when it was estimated conditional on any SNP other than I62V. These findings indicate that multiple observed effects were caused by linkage disequilibrium with I62V, and that this variant fully accounts for the association signals observed at the set of SNPs examined at this locus. CONCLUSIONS: The present study provides evidence that the complement pathway plays a substantial role in the pathogenesis of PCV. The nonsynonymous variant I62V is a plausible candidate for a causal polymorphism leading to the development of PCV, given its potential for functional consequences on the CFH protein and our own statistical evidence. FINANCIAL DISCLOSURE(S): The authors have to proprietary or commercial interest in any materials discussed in this article.

Positive association of common variants in CD36 with neovascular age-related macular degeneration.

Age-related macular degeneration (AMD) is a leading cause of legal blindness among older individuals of industrialized countries. In neovascular AMD, which is an advanced stage of AMD, choroidal neovascularization develops underneath the macula and destroys central vision. Oxidative stress is a hypothesized pathway for the pathophysiology of AMD. CD36 was chosen as a candidate gene for neovascular AMD because the protein plays an important role in this pathway as well as in angiogenesis and in maintaining chorioretinal homeostasis. We tested 19 tag single nucleotide polymorphisms (SNPs) across CD36 for their association with the disease in a Japanese population comprising 109 neovascular AMD subjects and 182 unrelated controls. Five of the 19 SNPs demonstrated a nominally significant association with neovascular AMD (P < 0.05), of which two (rs3173798 and rs3211883) withstood Bonferroni correction for multiple testing (rs3173798, nominal P = 9.96 x 10-4, allele-specific odds ratio = 0.55; rs3211883, nominal P = 2.09 x 10-4, allele-specific odds ratio = 0.50). Population structure analyses excluded stratification artifacts in our study cohort. This study supports the candidacy of CD36 as a novel susceptibility gene for neovascular AMD. Replication of our results in other populations will provide further convincing evidence for the genetic association.

Lack of association of CPT1A polymorphisms or haplotypes on hepatic lipid content or insulin resistance in Japanese individuals with type 2 diabetes mellitus.

Accumulation of fat in the liver is associated with insulin resistance and type 2 diabetes mellitus. The carnitine palmitoyltransferase (CPT) enzyme system facilitates the transport of long-chain fatty acids into mitochondria, and the gene for the hepatic isoform of CPT1 (CPT1A) is a candidate gene for metabolic disorders such as insulin resistance associated with fatty liver. We have now investigated the contribution of the CPT1A locus to hepatic lipid content (HLC), insulin resistance, and susceptibility to type 2 diabetes mellitus. A total of 324 type 2 diabetic patients and 300 nondiabetic individuals were enrolled in the study. Eighty-seven of the type 2 diabetic patients who had not been treated with insulin or lipid-lowering drugs were evaluated by homeostasis model assessment for insulin resistance and were subjected to nuclear magnetic resonance for determination of HLC. A total of 19 single nucleotide polymorphisms (SNPs) were identified at the CPT1A locus, and linkage disequilibrium analysis revealed a strong linkage disequilibrium block between SNP8 (intron 5) and SNP17 (intron 14). Neither haplotypes nor SNPs of CPT1A were found to be associated either with susceptibility to type 2 diabetes mellitus or with HLC or insulin resistance in type 2 diabetic patients.

Combination of multiple genetic risk factors is synergistically associated with carotid atherosclerosis in Japanese subjects with type 2 diabetes.

OBJECTIVE: Several genetic risk factors, such as single nucleotide polymorphisms (SNPs), in candidate genes have been reported to be responsible for intima-media thickness (IMT), which is one of the surrogate end points of cardiovascular events. However, the synergistic effects of SNPs have not been evaluated in detail. RESEARCH DESIGN AND METHODS: We measured the average IMT of the common and internal carotid artery in Japanese type 2 diabetic patients (n = 690) (>50 years old) using ultrasonography. We also determined their genotypes regarding 106 SNPs in candidate genes responsible for cardiovascular diseases. Among the 106 SNPs, we selected 40 common (frequency of minor allele >/=10%) SNPs. We compared the average IMT of subjects with and without any pairs of four genotypes selected from the 40 common SNPs. RESULTS: The combination of methylen-tetrahydrofolate reductase 677 TT genotype and lymphotoxin-alpha (LTA) 252 GG genotype and that of ACE DD genotype and LTA 252 GG genotype were evaluated as responsible for a statistically significant (P = 2.7 x 10(-9) and 3.5 x 10(-6), respectively) increase in average IMT (mean [+/-SD] 1.54 +/- 0.60 and 1.43 +/- 0.58 mm, respectively) compared with those of the subjects without these combinations (1.04 +/- 0.34 and 1.04 +/- 0.34 mm, respectively). No single genotype was shown to be responsible for the statistically significant difference in average IMT after Bonferroni's multiple comparison procedure. CONCLUSIONS: The present analysis demonstrates an approach to evaluate combinations of multiple genetic risk factors that are synergistically associated with carotid atherosclerosis.

Unified method for Bayesian calculation of genetic risk.

Bayesian inference has been used for genetic risk calculation. In this traditional method, inheritance events are divided into a number of cases under the inheritance model, and some elements of the inheritance model are usually disregarded. We developed a genetic risk calculation program, GRISK, which contains an improved Bayesian risk calculation algorithm to express the outcome of inheritance events with inheritance vectors, a set of ordered genotypes of founders, and mutation vectors, which represent a new idea for description of mutations in a pedigree. GRISK can calculate genetic risk in a common format that allows users to execute the same operation in every case, whereas the traditional risk calculation method requires construction of a calculation table in which the inheritance events are variously divided in each respective case. In addition, GRISK does not disregard any possible events in inheritance. This program was developed as a Japanese macro for Excel to run on Windows.

Association of the -112A>C polymorphism of the uncoupling protein 1 gene with insulin resistance in Japanese individuals with type 2 diabetes.

The -112A>C polymorphism (rs10011540) of the gene for uncoupling protein 1 (UCP1) has been associated with type 2 diabetes mellitus in Japanese individuals. The aim of the present study was to investigate the effects of this polymorphism, as well as the well-known -3826A>G polymorphism (rs1800592), on clinical characteristics of type 2 diabetes. We determined the genotypes of the two polymorphisms in 93 Japanese patients with type 2 diabetes. Intramyocellular lipid content and hepatic lipid content (HLC) were measured by magnetic resonance spectroscopy. No significant differences in age, sex, BMI, or HbA1c level were detected between type 2 diabetic patients with the -112C allele and those without it. However, homeostasis model assessment for insulin resistance (p=0.0089) and HLC (p=0.012) was significantly greater in patients with the -112C allele. We did not detect an association of the -3826A>G polymorphism (rs1800592) of UCP1 gene with any measured parameters. These results suggest that insulin resistance caused by the -112C allele influences the susceptibility to type 2 diabetes.

Division of linkage disequilibrium between absolute linkage disequilibrium and linkage equilibrium.

Linkage disequilibrium is the association between alleles in the allele distributions across linked loci and is intermediate in character between the dependence and the independence of allele distribution. This ambivalence makes linkage disequilibrium difficult to understand and to treat mathematically. To overcome this difficulty, an attempt was made to divide linkage disequilibrium between absolute linkage disequilibrium, which is a complete dependence of allele distribution, and linkage equilibrium, which is a complete independence. A matrix description of linkage disequilibrium showed that (1) linkage disequilibrium is divided between absolute linkage disequilibrium and linkage equilibrium, (2) a linkage disequilibrium state is characterized by the allele frequency in the first locus p, the relative content of absolute linkage disequilibrium d and the linkage equilibrium variable c, and (3) r is the geometric mean of both orientation's d. Division of linkage disequilibrium may make linkage disequilibrium straightforward to understand and to treat mathematically.

Identification of two novel mutations in adenine phosphoribosyltransferase gene in patients with 2,8-dihydroxyadenine urolithiasis.

Five mutations in the adenine phosphoribosyltransferase (APRT) gene have been described in Japanese patients with APRT deficiency. We investigated the APRT gene from three patients with APRT deficiency and two novel mutations, G133D and V84M, were determined.

Comparison between various strategies for the disease-gene mapping using linkage disequilibrium analyses: studies on adenine phosphoribosyltransferase deficiency used as an example.

Recently, linkage disequilibrium analyses have been used to detect disease-causing loci based on the common disease-common variant hypothesis. To see what methods can effectively identify the genes, we have to apply them to the practical data obtained from the human population. We extensively performed linkage disequilibrium and haplotype analyses on adenine phosphoribosyltransferase ( APRT) genes in both control and deficient subjects. To examine the power to detect disease-causing loci, we analyzed SNPs, STRPs, and VNTR within and around the APRT gene. When only SNPs were used, P values did not necessarily show significant difference, even at loci close to the mutation site for APRT*J that is exclusively observed among Japanese. However, the examination of the same samples with haplotypes based on the haplotype block data gave sufficient significance. In the case of STRP and VNTR, some single-marker loci showed significant difference. Our study suggested that the use of haplotype analysis based on the haplotype-block structure is more powerful than single-marker locus analysis for the detection of disease-related loci.

Does phosphatidylinositol 3-kinase play a role in insulin-induced outgrowth of pseudopodial cables in cultured cells derived from micromeres of sea urchin embryos?

Cultured cells derived from micromeres isolated from sea urchin embryos at the 16-cell stage, which have insulin receptors, undergo pseudopodial cable growth and spicule rod formation in culture with horse serum and only cable growth in culture with insulin. Genistein, an inhibitor of protein tyrosine kinase, and wortmannin, an inhibitor of phosphatidylinositol 3-kinase (PI3kinase), inhibited pseudopodial cable growth in micromere-derived cells cultured with insulin and also growth accompanied by spicule rod formation in horse serum-treated cells. The PI3kinase activity in the immunoprecipitates obtained by anti-phosphotyrosine antibody from the cells cultured with insulin was higher than that in cells cultured without insulin or with insulin and genistein. Following immunoblotting with antibody of SH-2, Src homology 2 domains in PI3kinase regulatory subunit, a band appeared at 85 kDa in SDS-PAGE of the immunoprecipitate, obtained from the micromere-derived cells by anti-phosphotyrosine antibody. This SDS-PAGE also showed protein bands at molecular weights similar to IRS-1 and the insulin receptor ß subunit. These indicate that the insulin signal transduction pathway in micromere-derived cells is somewhat similar to the pathway, in which PI3kinase is involved, in mammalian cells.

Insulin-Induced Outgrowth of Pseudopodial Cables from Cultured Micromere-Derived Cells Isolated from Sea Urchin Embryos at the 16 Cell Stage, with Special Reference to the Insulin-Receptor.: (sea urchin/micromere/insulin/psedopodial cable/receptor).

Cultured cells derived from micromeres isolated from sea urchin embryos at the 16 cell stage are known to show outgrowth of pseudopodial cables followed by spicule rod formation when cultured in the presence of horse serum. Micromere-derived cells cultured with bovine insulin showed pseudopodial cable growth but did not produce spicule rods. Micromere-derived cells reversibly bound to insulin through out the period between 3 and 20 hr of culture. The dissociation constant of insulin with these cells was about 5.1 × 10-10 M during the whole culture period examined. Horse serum, as well as blastocoelic fluid obtained from early gastrulae, concentration-dependently reduced the amount of insulin bound to these cells, but the bound insulin was scarcely replaced by any proteins tested, such as bovine serum albumin. The micromere-derived cells were bound to have an insulin-binding protein, that may be the receptor for insulin or insulin-like proteins. The insulin-binding protein had a smaller molecular weight than the insulin receptor of mammalian cells. The binding of insulin with this protein in micromere-derived cells probably results in pseudopodial cable growth.

Changes in Insulin-Binding Capacity of the Plasma Membrane Fraction during Culture in vitro of Cells Derived from Micromeres of 16-Cell-Stage Sea Urchin Embryos: (sea urchin/development/micromere/insulin/insulin receptor).

In cultured cells derived from isolated micromeres of 16-cell stage sea urchin embryos, which undergo insulin-induced pseudopodial cable growth, specific and reversible insulin binding by a 52-kDa protein, probably an insulin receptor in the plasma membrane, is augmented during 5 h of culture without any change in the dissociation constant (Kuno et al : 1994). The increase in insulin-binding capacity in micromere-derived cells was only minimally blocked by actinomycin D and cycloheximide, which inhibited [U-3 H]uridine incorporation into RNA and [35 S]methionine incorporation into protein, respectively. Insulin binding capacity was found in the plasma membrane fraction and the microsome fraction of isolated micromeres. The capacity in the plasma membrane fraction increased, accompanied by its decrease in the microsome fraction, during 5 h of culture of micromere-derived cells. The insulin receptor is probably accumulated in microsomes of presumptive micromeres prior to the 16-cell stage and transferred to the plasma membrane, resulting in an increase in the insulin binding capacity of micromere-derived cells during 5 h of culture.

Several Cell Responses to Insulin of Cultured Cells Derived from Micromeres, Isolated from Sea Urchin Embryos at the 16 Cell Stage: (Sea urchin/development/morphogenesis/insulin/micromere).

In micromere-derived cells of sea urchin embryos, treatment with insulin started for up to 24 h during culture at 20°C resulted in augmentation of 32 P incorporation into protein (protein phosphorylation) followed by activation of 32 P incorporation into RNA (RNA synthesis) and then induced pseudopodial cable growth, accompanied by considerable decreases in the rates of protein phosphorylation and RNA synthesis. This augmentation of RNA synthesis and cable growth induced by insulin were blocked by H-7, which inhibited protein phosphorylation, and were also inhibited by actinomycin D without any inhibition of protein phosphorylation. Similar results were obtained on treatment with horse serum, found to contain insulin-like compounds. In cells treated with horse serum treated cells, high rates of protein phosphorylation and RNA synthesis were maintained even after the initiation of cable growth and about 5 h later, spicule rods were produced. Insulin treatment did not induce spicule rod formation. In cells treated with horse serum, actinomycin D treatment started at the time of initiation of cable growth, cables were formed but formation of spicule rods was blocked. These results suggest that horse serum contains some other substance besides insulin-like ones, which induces expression of genes that are indispensable for spicule rod formation.