Henian Cao

Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia

Genome-wide association studies (GWAS) have identified multiple loci associated with plasma lipid concentrations. Common variants at these loci together explain <10% of variation in each lipid trait. Rare variants with large individual effects may also contribute to the heritability of lipid traits; however, the extent to which rare variants affect lipid phenotypes remains to be determined. Here we show an accumulation of rare variants, or a mutation skew, in GWAS-identified genes in individuals with hypertriglyceridemia (HTG). Through GWAS, we identified common variants in APOA5, GCKR, LPL and APOB associated with HTG. Resequencing of these genes revealed a significant burden of 154 rare missense or nonsense variants in 438 individuals with HTG, compared to 53 variants in 327 controls (P = 6.2 × 10−8), corresponding to a carrier frequency of 28.1% of affected individuals and 15.3% of controls (P = 2.6 × 10−5). Considering rare variants in these genes incrementally increased the proportion of genetic variation contributing to HTG.

LMNA is mutated in Hutchinson-Gilford progeria (MIM 176670) but not in Wiedemann-Rautenstrauch progeroid syndrome (MIM 264090)

AbstractHutchinson-Gilford progeria syndrome (HGPS; MIM 176670) is an extremely rare disease that is characterized by accelerated aging and early death, frequently from coronary artery disease. Wiedemann-Rautenstrauch syndrome (WRS; MIM 264090) is another extremely rare disease that is characterized by progeroid features from birth with multiple somatic anomalies and paucity of subcutaneous fat. Because mutations in LMNA, encoding nuclear lamin A/C, cause other lipodystrophy syndromes, we sequenced LMNA (MIM 150330) from the genomic DNAs of seven unrelated HGPS probands and two unrelated WRS probands. We found four novel LMNA coding sequence variants among the HGPS probands, namely R471C, R527C, G608S and c.2036C>T. All seven HGPS probands had at least one LMNA variant, which were found in none of the genomes of 100 normal subjects (P<4×10−11). In contrast, neither of the WRS proband genomes had any LMNA sequence abnormality. The strong association of rare LMNA coding sequence mutations with HGPS implicates this syndrome as a laminopathy, while WRS is most probably due to mutations in another gene.

Polygenic determinants of severe hypertriglyceridemia

Recent genome-wide association (GWA) studies have identified new genetic determinants of complex quantitative traits, including plasma triglyceride (TG). We hypothesized that common variants associated with mild TG variation identified in GWA studies would also be associated with severe hypertriglyceridemia (HTG). We studied 132 patients of European ancestry with severe HTG (fasting plasma TG > 10 mmol/l), who had no mutations found by resequencing of candidate genes, and 351 matched normolipidemic controls. We determined genotypes for: GALNT2 rs4846914, TBL2/MLXIPL rs17145738, TRIB1 rs17321515, ANGPTL3 rs12130333, GCKR rs780094, APOA5 rs3135506 (S19W), APOA5 rs662799 (-1131T > C), APOE (isoforms) and LPL rs328 (S447X). We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T > C, APOE, GCKR, TRIB1 and TBL2/MLXIPL, were significantly associated with severe HTG; (ii) odds ratios for these genetic variables were significant in both univariate and multivariate regression analyses, irrespective of the presence or absence of diabetes or obesity; (iii) a significant fraction-about one-quarter-of the explained variation in disease status was associated with these genotypes. Therefore, common SNPs (single nucleotide polymorphisms) that are associated with mild TG variation in GWA studies of normolipidemic subjects are also associated with severe HTG. Our findings are consistent with the emerging model of a complex genetic trait. At the extremes of a quantitative trait, such as severe HTG, are found the cumulative contributions of both multiple rare alleles with large genetic effects and common alleles with small effects.

Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia.

BackgroundMice with a deleted Cav1 gene encoding caveolin-1 develop adipocyte abnormalities and insulin resistance. From genomic DNA of patients with atypical lipodystrophy and hypertriglyceridemia who had no mutations in any known lipodystrophy gene, we used DNA sequence analysis to screen the coding regions of human CAV1 (MIM 601047).ResultsWe found a heterozygous frameshift mutation in CAV1, designated I134fsdelA-X137, in a female patient who had atypical partial lipodystrophy, with subcutaneous fat loss affecting the upper part of her body and face, but sparing her legs, gluteal region and visceral fat stores. She had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis. In addition, she had some atypical features, including congenital cataracts and neurological findings. Her father was also heterozygous for this mutation, and had a similar pattern of fat redistribution, hypertriglyceridemia and congenital cataracts, with milder neurological involvement. An unrelated patient had a different heterozygous frameshift mutation in the CAV1 gene, designated -88delC. He also had a partial lipodystrophy phenotype, with subcutaneous fat loss affecting the arms, legs and gluteal region, but sparing his face, neck and visceral fat stores. He also had severe type 5 hyperlipoproteinemia, with recurrent pancreatitis; however he had no clinically apparent neurological manifestations. The mutations were absent from the genomes of 1063 healthy individuals.ConclusionThus, very rare CAV1 frameshift mutations appear to be associated with atypical lipodystrophy and hypertriglyceridemia.

Resequencing Genomic DNA of Patients With Severe Hypertriglyceridemia (MIM 144650)

Objective—The genetic determinants of severe hypertriglyceridemia (HTG; MIM 144650) in adults are poorly defined. We therefore resequenced 3 candidate genes, namely LPL, APOC2, and APOA5, to search for accumulation of missense mutations in patients with severe HTG compared with normolipidemic subjects. Methods and Results—We resequenced >2 million base pairs of genomic DNA from 110 nondiabetic patients with severe HTG and determined the prevalence of coding sequence variants compared with 472 age- and sex-matched normolipidemic controls. We found: (1) heterozygous mutations (LPL p.Q-12E >11X, p.D25H, p.W86R, p.G188E, p.I194T and p.P207L; APOC2 p.K19T and IVS2–30G>A) in 10.0% of severe HTG patients compared with 0.2% of controls (carrier odds ratio [OR] 52, 95% confidence interval [CI] 8.6 to 319); and (2) an association of the APOA5 p.S19W missense variant with severe HTG (carrier OR 5.5 95% CI 3.3 to 9.1). Furthermore, either rare mutations or the APOA5 p.S19W variant were found in 41.8% of HTG subjects compared with 8.9% of controls (carrier OR 7.4, 95% CI 4.5 to 12.0). Also, heterozygotes for rare mutations had a significantly reduced plasma triglyceride response to fibrate monotherapy. Conclusions—Both common and rare DNA variants in candidate genes were found in a substantial proportion of severe HTG patients. The findings underscore the value of candidate gene resequencing to understand the genetic contribution in complex lipoprotein and metabolic disorders.

DNA polymorphisms in ITPA including basis of inosine triphosphatase deficiency

AbstractIntracellular concentrations of the nucleotide inosine triphosphate (ITP) are regulated by ITP-ase (EC 3.6.1.19), which is encoded by ITPA on chromosome 20p. Subjects with complete deficiency of ITP-ase activity (MIM 147520) have elevated ITP concentrations in erythrocytes, but no obvious clinical abnormalities. Based on biochemical screening, complete ITP-ase deficiency has been postulated to result from homozygosity for a dysfunctional allele, with an estimated frequency of 0.05 in Caucasians. ITP-ase deficiency has not yet been characterized at the molecular genetic level. Sequencing of the genomic DNA from a Caucasian subject with complete ITP-ase deficiency revealed homozygosity for missense mutation 198C>A, which predicted a threonine for proline substitution at codon 32 (P32T), whereas among 125 normal Caucasians, there were no homozygotes for P32T (P = 0.0079). The P32T allele frequency of 0.07 in Caucasians was similar to the estimates derived from earlier biochemical studies. P32T was found to be present at varying frequency in other ethnic groups. Two common synonymous single-nucleotide polymorphisms were also identified. These ITPA markers, including P32T, provide tools for further study of association with clinical and biochemical phenotypes.

G Protein β3 Subunit Gene Variant and Blood Pressure Variation in Canadian Oji-Cree

The subunits of the heterotrimeric G proteins are attractive candidate gene products for both susceptibility to essential hypertension and interindividual variation in blood pressure. There is alternative splicing of exon 9 of the gene encoding the beta3 subunit of heterotrimeric G proteins (GNB3) associated with a C-->T change at nucleotide 825, which activates a cryptic splice site. The 825T allele results in a gene product that is 41 amino acids smaller than the wild-type gene product. G protein heterotrimers containing the shorter variant are more reactive than those containing the wild type, and the 825T allele appears to be associated with essential hypertension. To evaluate whether this variant is associated with hypertension or blood pressure in other human samples, we genotyped 447 young adult Oji-Cree for the GNB3 C825T variation. We found that the frequency of the GNB3 825T allele was 0.501 in the Oji-Cree, which is considerably higher than the frequency observed in whites. Furthermore, genetic variation of the GNB3 nucleotide 825 was significantly associated with variation in systolic pressure but not diastolic pressure. Specifically, subjects with the 825T/T genotype had significantly lower systolic pressure than subjects with the 825C/T and 825C/C genotypes; the association was independent of sex. Furthermore, the 825T allele frequency tended to be higher in subjects who took antihypertensive medications than in subjects who did not (0.571 versus 0.496; P=NS), although this young sample had relatively few subjects with hypertension. The findings support an association of variation in this gene with variation in blood pressure.

Human C-reactive protein (CRP) 1059G/C polymorphism

AbstractWe found a novel G → C change at nucleotide 1059 within exon 2 of the CRP gene encoding the C-reactive protein. The CRP 1059G/C polymorphism could be detected by digestion with endonuclease MaeIII. The frequency of the CRP 1059C allele was 0.109 in Caucasians, but it was absent from Canadian Oji-Cree. Because of the importance of the CRP gene product in inflammation and its recent association with ischemic heart disease syndromes, this polymorphism may be useful in the association studies of atherosclerosis and its related phenotypes.

A polygenic basis for four classical Fredrickson hyperlipoproteinemia phenotypes that are characterized by hypertriglyceridemia

Numerous single nucleotide polymorphisms (SNPs) have been found in recent genome wide association studies (GWAS) to be associated with subtle plasma triglyceride (TG) variation in normolipidemic subjects. However, since these GWAS did not specifically evaluate patients with rare disorders of lipoprotein metabolism—‘hyperlipoproteinemia’ (HLP)—it remains largely unresolved whether any of these SNP determinants of modest physiological changes in TG are necessarily also determinants of most HLP phenotypes. To address this question, we evaluated 28 TG-associated SNPs from GWAS in 386 unrelated adult patients with one of five Fredrickson phenotypes (HLP types 2A, 2B, 3, 4 and 5) and 242 matched normolipidemic controls. We found that several SNPs associated with TG in normolipidemic samples, including APOA5 p.S19W and -1131T>C, TRIB1 rs17321515, TBL2 rs17145738, GCKR rs780094, GALNT2 rs4846914 and ANGPTL3 rs12130333, were significantly associated with HLP types 2B, 3, 4 and 5. The findings indicate that: (i) the TG-associated Fredrickson HLP types 2B, 3, 4 and 5 are polygenic traits; (ii) these Fredrickson HLP types share numerous genetic determinants among themselves; and (iii) genetic determinants of modest TG variation in normolipidemic population samples also underlie—to an apparently even greater degree—susceptibility to these rare HLP phenotypes. Thus, the TG-associated Fredrickson HLP types 2B, 3, 4 and 5, although historically considered to be distinct are actually complex traits sharing among them several common genetic determinants seen in GWAS of normolipidemic population samples.

Elevated Serum C-Reactive Protein and Free Fatty Acids Among Nondiabetic Carriers of Missense Mutations in the Gene Encoding Lamin A/C (LMNA) With Partial Lipodystrophy

Objective—Dunnigan-type familial partial lipodystrophy (FPLD) due to mutant LMNA is a monogenic form of insulin resistance. Affected subjects, especially women, are at increased risk of early coronary heart disease (CHD). Although common insulin resistance is associated with several biochemical perturbations, including elevated C-reactive protein (CRP), the biochemical profile in subjects with mutant LMNA is incompletely defined. Methods and Results—We studied 35 nondiabetic adult FPLD subjects (of whom 24 were women) with either the LMNA R482Q or R482W missense mutations and 51 matched normal first-degree relatives (of whom 27 were women). Compared with normal controls, LMNA mutation carriers had significantly higher plasma insulin and more dyslipidemia, higher mean triglycerides and lower HDL cholesterol, significantly higher nonesterified free fatty acids and CRP, and significantly lower leptin and adiponectin than controls. Subgroup analyses showed that these differences were more pronounced in women. Other biomarkers such as resistin, fibrinogen, and plasminogen activator inhibitor-1 were not different between groups. Conclusions—LMNA mutations in nondiabetic patients with FPLD are associated with several metabolic and biochemical changes, particularly in women. The unfavorable profile might contribute to the increased susceptibility to CHD seen in LMNA mutation carriers.