Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed eQTL analysis and bioinformatics network analysis.
We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS-) and femoral neck (FN-) BMD, in 25,353 individuals from eight cohorts. In a second stage, we followed up the 12 top SNPs (P<1×10−5) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs.
We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 & p-value = 3.0×10−5; female effect = −0.007 & p-value=3.3×10−2) and eleven suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (P<5×10−8) gene-by-sex interaction in the joint analysis of discovery and replication cohorts.
Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found influencing BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP.
gene-by-sex; interaction; BMD; association; aging
Osteocalcin (OC) is a protein constituent of bone matrix and a marker of bone formation. We characterized the heritability of serum OC measures and identified genomic regions potentially involved in the regulation of OC via high-density genome-wide linkage analysis in African ancestry individuals.
African ancestry individuals (n=459) were recruited, without regard to health status, from seven probands (mean family size = 66; 4,373 relative pairs). Residual heritability of serum OC measures was estimated and multipoint quantitative trait linkage analysis was performed using pedigree-based maximum likelihood methods.
Residual heritabilities of total OC, uncarboxylated OC, carboxylated OC and percent uncarboxylated OC were: 0.74±0.10, 0.89±0.08, 0.46±0.10 and 0.41±0.09, respectively. All OC measures were genetically correlated with whole body bone mineral content (BMC). We obtained strong evidence of bivariate linkage for percent uncarboxylated OC and whole body BMC on chromosome 17 (LOD=3.15, 99cM).
All forms of OC were highly heritable and genetically correlated with total body BMC in these African ancestry families. The identified linkage region contains several candidate genes for bone and energy metabolism including COL1A1 and TNFRSF11A. Further studies of this genomic region may reveal novel insight into the genetic regulation of OC and bone mineralization.
osteocalcin; genome-wide linkage; African ancestry; bone mineral
Vertebral bone mineral density (BMD) and cross-sectional area (CSA) are important determinants of vertebral bone strength. Little is known about the specific genetic variants that influence these phenotypes in humans. We investigated the potential genetic variants associated with vertebral trabecular volumetric BMD (vBMD) and CSA measured by quantitative computed tomography (QCT). We initially tested for association between these phenotypes and 4608 tagging and potentially functional single nucleotide polymorphisms (SNPs) in 383 candidate genes in 862 community-dwelling Caucasian men aged ≥65 years in the Osteoporotic Fractures in Men Study (MrOS). The most promising SNP associations (P<0.01) were then validated by genotyping an additional 1,156 randomly sampled men from the same cohort. We identified 11 SNPs in 10 genes (TGFBR3, SOST, KL, CALCR, LEP, CSF1R, PTN, GNRH2, FGFR2, MEPE) that were consistently associated with trabecular vBMD and 5 SNPs in 5 genes (CYP11B1, DVL2, DLX5, WNT4, PAX7) that were consistently associated with CSA in both samples (p<0.005). None of the SNPs associated with trabecular vBMD were associated with CSA. Our findings raise the possibility that at least some of the loci for vertebral trabecular BMD and bone size may be distinct.
Osteoporosis; Genetics; BMD; men; QCT; Polymorphism
Background. Toll-like receptors (TLRs) are involved in the innate immune response. We examined whether TLR variants are associated with Chlamydia trachomatis infection among women with pelvic inflammatory disease (PID).
Methods. We tested whether 18 tagging single nucleotide polymorphisms (tagSNPs) assayed in 4 TLR genes (TLR1, TLR2, TLR4, TLR6) and 2 adaptor molecules (TIRAP, MyD88) were associated with C. trachomatis among 205 African American women with clinically suspected PID from the PID Evaluation and Clinical Health Study. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs). An empirical P value of <.004 was considered significant.
Results. Women with PID who carried the TLR4 rs1927911 CC genotype had significantly increased odds of C. trachomatis (OR, 3.7; 95% CI, 1.6–8.8; P = .002). The TLR1 rs5743618TT genotype was also associated with C. trachomatis (OR, 2.8; 95% CI, 1.3–6.2; P = .008).
Conclusions. Among African American women with PID, variants in the TLR1 and TLR4 genes, which may increase signaling, were associated with increased C. trachomatis infection.
One challenge in understanding the polygenic disease of hypertension is elucidating the genes involved and defining responses to environmental factors. Many studies focus on animal models of hypertension; however, this does not necessarily extrapolate to humans.
Current technology and cost limitations are prohibitive in fully evaluating hypertension within humans. Thus, we have designed a single array platform that allows direct comparison of genes relevant to hypertension in animal models and non-human primates/human hypertension. The custom array is targeted to 328 genes known to be potentially related to blood pressure control.
Studies compared gene expression in the kidney from normotensive rats and baboons. We found 74 genes expressed in both the rat and baboon kidney, 41 genes expressed in the rat kidney that were not detected in the baboon kidney and 34 genes expression in the baboon kidney that were not detected in the rat kidney.
To begin the evaluation of the array in a pathological condition, kidney gene expression was compared between the salt sensitive DOCA rat model of hypertension and sham animals. Gene expression in renal cortex and medulla from hypertensive DOCA compared with sham rats revealed 3 genes differentially expressed in the renal cortex: Annexin A1 (up-regulated; relative intensity: 1.316 ± 0.321 vs. 2.312 ± 0.283), Glutamate-cysteine ligase (down-regulated; relative intensity: 3.738 ± 0.174 vs. 2.645 ± 0.364) and Glutathione-S transferase (down-regulated; relative intensity: 5.572 ± 0.246 vs. 4.215 ± 0.411) and 21 genes differentially expressed in renal medulla. Interestingly, few genes were differentially expressed in the kidney in the DOCA-salt model of hypertension; this may suggest that the complexity of hypertension may be the result of only a few gene-by-environment responsive events.
hypertension; gene array; kidney; rat; baboon
Skeletal muscle adipose tissue (AT) infiltration, or myosteatosis, appears to be greater in African compared with European ancestry individuals and may play a role in type 2 diabetes mellitus (T2DM), a disease that disproportionally affects African ancestry populations. Inflammation is one mechanism that may link myosteatosis with increased T2DM risk, but studies examining the relationship between inflammation and myosteatosis are lacking.
To examine these associations, we measured skeletal muscle subcutaneous AT, intermuscular AT, and skeletal muscle density using quantitative computed tomography and serum markers of inflammation in 471 individuals from 8 Afro-Caribbean multigenerational families [mean family size 67; mean age 43 years; mean body mass index (BMI) 28 kg/m2].
After removing the variation attributable to significant covariates, heritabilities of inflammation markers [C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α)] ranged from 33% (TNFα) to 40% (CRP); all P<0.01. Higher CRP, IL-6, and TNF-α were associated with lower subcutaneous AT around skeletal muscle (r=−0.13 to −0.19, P<0.05). Higher CRP was additionally associated with lower skeletal muscle density, indicative of greater intramuscular AT (r=−0.10, P<0.05), hyperinsulinemia (r=0.12, P<0.05), and increased homeostasis model assessment of insulin resistance (HOMA-IR) (r=0.17, P<0.01).
Our findings suggest that heredity may play a significant role in the determination of several markers of inflammation in African ancestry individuals. Higher concentrations of CRP appear to be associated with greater skeletal muscle AT infiltration, lower subcutaneous AT, hyperinsulinemia, and insulin resistance. Longitudinal studies are needed to further evaluate the relationship between inflammation with changes in skeletal muscle AT distribution with aging and the incidence of T2DM.
Two F2 functional polymorphisms, rs1799963 (G20210A) and rs3136516 (A19911G), are known to be associated with elevated prothrombin (encoded by F2) levels/activity and thrombosis risk. Since systemic lupus erythematosus (SLE) patients have high risk of thrombosis and accelerated atherosclerosis and also high prevalence of anti-prothrombin antibodies, we hypothesized that these two F2 polymorphisms could affect SLE risk.
We investigated these polymorphisms in 627 women with SLE (84% Caucasian Americans, 16% African Americans) and 657 female controls (78% Caucasian Americans, 22% African Americans).
While the rs1799963 A allele was almost absent in African Americans, it was present at ~2% frequency in Caucasian Americans and showed no significant association with SLE. The rs3136516 G allele frequency was significantly higher in Caucasian SLE cases than controls (48.4% vs. 43.7%) with a covariate-adjusted odds ratio (OR) of 1.22 (95%CI: 1.03–1.46; P = 0.023). The association was replicated in African Americans (rs3136516 G allele frequency: 91.2% in cases vs. 82.2% in controls) with an adjusted OR of 1.96 (95%CI: 1.08–3.58; P = 0.022). Stratification of Caucasian SLE patients based on the presence or absence of cardiac and vascular events (CVE) revealed stronger association with the CVE-positive SLE subgroup than the CVE-negative SLE subgroup (OR: 1.42 vs. 1.20). Prothrombin activity measurements in a subset of SLE cases demonstrated higher activity in the carriers of the rs3136516 G allele.
Our results suggest a potential role for prothrombin and the crosstalk between hemostatic and immune/inflammatory systems in SLE and SLE-associated cardiovascular events, which warrant further investigation in independent samples.
lupus; prothrombin; F2; polymorphism; A19911G; G20210A
Identification of gene variants that contribute to exceptional survival may provide critical biologic information that informs optimal health across the life span.
As part of phenotype development efforts for the Long Life Family Study, endophenotypes that represent exceptional survival were identified and heritability estimates were calculated. Principal components (PCs) analysis was carried out using 28 physiologic measurements from five trait domains (cardiovascular, cognition, physical function, pulmonary, and metabolic).
The five most dominant PCs accounted for 50% of underlying trait variance. The first PC (PC1), which consisted primarily of poor pulmonary and physical function, represented 14.3% of the total variance and had an estimated heritability of 39%. PC2 consisted of measures of good metabolic and cardiovascular function with an estimated heritability of 27%. PC3 was made up of cognitive measures (h2 = 36%). PC4 and PC5 contained measures of blood pressure and cholesterol, respectively (h2 = 25% and 16%).
These PCs analysis–derived endophenotypes may be used in genetic association studies to help identify underlying genetic mechanisms that drive exceptional survival in this and other populations.
Heritability; Longevity; Endophenotypes
We previously detected strong evidence for linkage of forearm bone mineral density (BMD) to chromosome 4p (lod = 4.3) in a set of 29 large Mexican American families. Fibroblast growth factor binding protein 1 (FGFBP1) is a strong candidate gene for bone homeostasis in this region. We sequenced the coding region of FGFBP1 in a subset of our Mexican American study population and performed association studies with BMD on SNPs genotyped in the entire cohort. We then attempted to replicate these findings in an independent study cohort and performed invitro functional studies on replicated, potentially functional polymorphisms using a luciferase reporter construct to evaluate influence on gene expression. Several SNPs spanning the gene, all in one large block of linkage disequilibrium, were significantly associated with BMD at various skeletal sites (n=872, p = 0.001-0.04). The associations were then replicated in an independent population of European ancestry (n = 972; p = 0.02-0.04). Sex-stratified association analyses in both study populations suggest this association is much stronger in men. Subsequent luciferase reporter gene assays revealed marked differences in FGFBP1 expression among the three common haplotypes. Further experiments revealed that a promoter polymorphism, rs12503796, results in decreased expression of FGFBP1 and inhibits upregulation of the gene by testosterone in vitro. Collectively, these findings suggest that sequence variation in FGFBP1 may contribute to variation in BMD, possibly influencing osteoporosis risk.
FGFBP1; polymorphisms; bone mineral density; osteoporosis; testosterone
Little is known about the progression of bone loss during young adulthood and whether it differs between men and women. As part of the San Antonio Family Osteoporosis Study we tested whether bone mineral density (BMD) changed over time in men or women, and whether the rate of BMD change differed between the sexes. BMD of the proximal femur, spine, radius, and whole body was measured in 115 men and 202 pre-menopausal women (ages 25 to 45 years; Mexican American ancestry) by dual-energy x-ray absorptiometry at two time points (5.6 years apart), from which annual percent change-in-BMD was calculated. Likelihood-based methods were used to test whether change-in-BMD differs from zero or differs between men and women. In men, percent change-in-BMD was significantly greater than zero for the 1/3 radius (i.e. indicating a gain of BMD; Bonferroni-adjusted p < 0.01), less than zero for the femoral neck, lumbar spine, ultradistal radius, and whole body (i.e. indicating a loss of BMD; p < 0.01 for all), and not different than zero for the total hip (p = 0.24). In women, percent change-in-BMD was greater than zero for the total hip, 1/3 radius, and whole body (p < 0.01 for all), less than zero for the ultradistal radius (p < 0.01), and not significantly different than zero for the femoral neck and lumbar spine (p = 1.0 for both). For all skeletal sites, men experienced greater decrease in BMD (or less increase in BMD) than women; this result was observed both with and without adjustment for age, BMI, and change-in-BMI (p < 0.05 for all). These results suggest that significant bone loss occurs at some skeletal sites in young men and women, and that loss of BMD is occurring significantly faster, or gain of BMD is occurring significantly slower, in young men compared to young women.
bone mineral density; bone loss; osteoporosis; sex differences; dual-energy x-ray absorptiometry
Principal component analysis (PCA) and factor analysis (FA) are often used to uncover genetic factors that contribute to complex disease phenotypes. The purpose of such an analysis is to distill a genetic signal from a large number of correlated phenotype measurements. That signal can then be used in genetic analyses (e.g. linkage analysis), presumably leading to greater success at finding genes than one would achieve with any one raw trait. Although both PCA and FA have been used this way, there has been no comparison of their performance in the literature. We compared the ability of these two procedures to extract unobserved underlying genetic components from complex simulated data on nuclear families. We first simulated 7 underlying genetic and environmentally determined traits. Then we derived two sets of 50 complex (observed) traits using algebraic combinations of the underlying components. We next performed PCA and FA on the complex traits. We assessed two aspects of the performance of the methods: 1) ability to detect the underlying genetic components; 2) whether the methods worked better when applied to raw traits or to residuals (after regressing out significant environmental covariates). Our results indicate that both methods behave similarly in most cases, although FA generally produced factors that had stronger correlations with the underlying traits. We also found that using residuals in PCA or FA analyses greatly increased the probability that the PCs or factors detected common genetic components instead of common environmental factors, except if there was statistical interaction between genetic and environmental factors.
multivariate analysis; PCA; factor analysis; quantitative traits
This study characterized the human apolipoprotein H (APOH, a.k.a. β2-glycoprotein I) promoter and its variants by in vitro functional experiments and investigated their relation with human plasma β2GPI levels. We examined the individual effects of 12 APOH promoter SNPs in the 5' flanking region of APOH (~1.4 kb) on luciferase activity in COS-1 cells and HepG2 cells and their impact on plasma β2GPI levels in 799 U.S. Whites, the DNA-binding properties of APOH promoter using electrophoretic mobility shift assay (EMSA) in HepG2 cells, the effects of serial deletion analysis of APOH 5' flanking region in COS-1 and HepG2 cells, and cross-species conservation of the APOH promoter sequence. The variant alleles of three SNPs (−1219G>A, −643T>C and −32C>A) showed significantly lower luciferase expression (51%, 40% and 37%, respectively) as compared to the wild-type allele. EMSA demonstrated that these three variants specifically bind with protein(s) from HepG2 cell nuclear extracts. Three-site haplotype analysis (−1219G>A, −643T>C, and −32C>A) revealed one haplotype carrying −32A (allele frequency = 0.075) to be significantly associated with decreased plasma β2GPI levels (P < 0.001). Deletion analysis localized the core APOH promoter to ~160 bp upstream of ATG codon with the presence of critical cis-acting elements between −166 and −65. Cross-species conservation analysis of the APOH promoters of 7 species indicated that basic promoter elements are highly conserved across species. In conclusion, we have characterized the functional promoter of APOH and identified functional variants that affect the transcriptional activity of the APOH promoter.
APOH; β2-glycoprotein I; promoter; polymorphisms; association
In contrast to conventional dual-energy X-ray absorptiometry, quantitative computed tomography separately measures trabecular and cortical volumetric bone mineral density (vBMD). Little is known about the genetic variants associated with trabecular and cortical vBMD in humans, although both may be important for determining bone strength and osteoporotic risk. In the current analysis, we tested the hypothesis that there are genetic variants associated with trabecular and cortical vBMD at the femoral neck by genotyping 4608 tagging and potentially functional single-nucleotide polymorphisms (SNPs) in 383 bone metabolism candidate genes in 822 Caucasian men aged 65 years or older from the Osteoporotic Fractures in Men Study (MrOS). Promising SNP associations then were tested for replication in an additional 1155 men from the same study. We identified SNPs in five genes (IFNAR2, NFATC1, SMAD1, HOXA, and KLF10) that were robustly associated with cortical vBMD and SNPs in nine genes (APC, ATF2, BMP3, BMP7, FGF18, FLT1, TGFB3, THRB, and RUNX1) that were robustly associated with trabecular vBMD. There was no overlap between genes associated with cortical vBMD and trabecular vBMD. These findings identify novel genetic variants for cortical and trabecular vBMD and raise the possibility that some genetic loci may be unique for each bone compartment. © 2010 American Society for Bone and Mineral Research
osteoporosis; Genetics; BMD; men; qCT
Adiponectin, an adipose-specific protein, is negatively associated with adiposity, insulin sensitivity, and diabetes. Very few studies have examined the role of heredity in the regulation of adiponectin and its association with body fat among individuals of African heritage. Thus, we measured fasting serum adiponectin levels by radioimmunoassay and body composition by dual-energy x-ray absorptiometry (DEXA) in 402 individuals aged 18 to 103 years belonging to 7 multigenerational families of African heritage in the relatively homogeneous island population of Tobago. Heritability of adiponectin was 33.2% (P < .01), and age, sex, and body mass index explained 23.4% of the variance in adiponectin. Sex-specific heritability was significant in men (heritability, 34%; P < .05), but not in women. The inverse associations between body mass index and percentage of body fat and adiponectin, independent of age and height, were much stronger in women (all P values <.001) than in men. However, percentage of trunk fat was consistently strongly associated with adiponectin in both men (r = −0.40, P < .001) and women (r = −0.44, P < .001), independent of age and height. This study suggests that genetic factors are a significant source of interindividual differences in circulating adiponectin among Afro-Caribbeans. Adiponectin may serve as a promising quantitative intermediate trait in studies designed to map the genes underlying diabetes and obesity in this population.
Increased fat infiltration in skeletal muscle has been associated with diabetes. Quantitative computed tomography (QCT) can be used to measure muscle density, which reflects the lipid content of skeletal muscle such that greater fat infiltration in skeletal muscle is associated with lower muscle density. The relative contribution of genetic and environmental factors to fat infiltration in skeletal muscle has not been assessed. Therefore, our aim is to determine genetic and environmental contributions to measures of skeletal muscle composition, and describe their associations with type 2 diabetes in multigenerational families of African ancestry.
Methods and Procedures
Peripheral QCT (pQCT) measures of skeletal muscle density were obtained for the calf in 471 individuals (60% women; mean 43 years) belonging to eight large, multigenerational Afro-Caribbean families (mean family size 51 individuals; 3,535 relative pairs).
The proportion of variance in muscle density due to additive genetic effects (residual heritability) was 35.0% (P < 0.001) and significant covariates (age, gender, BMI, and parity) explained 55.0% of the total phenotypic variation in muscle density. Muscle density was lower (P < 0.001) in 62 diabetics (69.5 mg/cm3) than in 339 nondiabetics (74.3 mg/cm3) and remained significant after adjusting for age, gender, and BMI (P = 0.005) or age, gender, and waist circumference (P = 0.01).
Our results provide new evidence that ectopic lipid deposition in skeletal muscle is a heritable trait and is associated with diabetes, independent of overall and central obesity in families of African heritage. Genome-wide screens and candidate gene studies are warranted to identify the genetic factors contributing to ectopic deposition of skeletal muscle fat.
Bone loss occurs as early as the third decade and its cumulative effect throughout adulthood may impact risk for osteoporosis in later life, however the genes and environmental factors influencing early bone loss are largely unknown. We investigated the role of genes in the change in bone mineral density (BMD) in participants of the San Antonio Family Osteoporosis Study.
Materials and Methods
BMD change in 327 Mexican Americans (ages 25–45 years) from 32 extended pedigrees was calculated from DXA measurements at baseline and follow-up (3.5 to 8.9 years later). Family-based likelihood methods were used to estimate heritability (h2) and perform autosome-wide linkage analysis for BMD change of the proximal femur and forearm, and estimate heritability for BMD change of lumbar spine.
BMD change was significantly heritable for total hip, ultradistal radius and 33% radius (h2 = 0.34, 0.34, 0.27, respectively, p < 0.03 for all), modestly heritable for femoral neck (h2 = 0.22, p = 0.06) and not heritable for spine BMD. Covariates associated with BMD change included age, sex, baseline BMD, menopause, body mass index, and interim BMI change, and accounted for 6% to 24% of phenotype variation. A significant quantitative trait locus (LOD = 3.6) for femoral neck BMD change was observed on chromosome 1q23.
We observed that change in BMD in young adults is heritable, and performed one of the first linkage studies for BMD change. Linkage to chromosome 1q23 suggests this region may harbor one or more genes involved in regulating early BMD change of the femoral neck.
Bone Mineral Density; Bone Loss; Genetics; Linkage; Heritability
Although several studies have quantified costs of cancer care; none to date have examined how cancer costs impact family caregivers’ emotional health. This study was designed to evaluate how perceptions of economic hardship influence burden, depressive symptoms, and anxiety in family caregivers of persons with a primary malignant brain tumor. Caregiver (CG)/patient dyads (n = 33) were recruited at the time of diagnosis; data were collected at diagnosis and 4 months, and linear regression determined the impact of economic hardship on caregivers’ emotional health. Economic hardship did not predict CG burden-schedule at diagnosis or 4 months. Economic hardship predicted burden-abandonment at diagnosis (P < 0.01), but not 4 months. There was a trend for economic hardship to predict CG depressive symptoms at 4 months (P = 0.09), but not at diagnosis. Economic hardship predicted CG anxiety at 4 months (P = 0.06), but not diagnosis. Results suggest caregivers’ economic hardship is an important and dynamic aspect of the emotional health of neuro-oncology family caregivers.
Brain tumor; Caregiver; Emotional health; Economic hardship; Cancer cost
Sodium lithium countertransport (SLC) activity, an intermediate phenotype of essential hypertension, has been linked to a region of baboon chromosome 5, homologous to human chromosome 4p. Human SLC34A2, located at chromosome 4p15.1-p15.3, is a positional candidate gene for SLC. The specific aim of this study was to identify genetic variants of the SLC34A2 gene in both baboon and human, and to examine the relationship of these polymorphisms with SLC activity and blood pressure.
Single nucleotide polymorphism (SNP) was identified by sequencing the SLC34A2 gene in 24 baboon founders and 94 unrelated individuals. All tag SNPs in SLC34A2 were genotyped in 1856 individuals from 252 pedigrees of mixed European ancestry. Three SNPs in baboon were genotyped in 634 baboons comprising 11 pedigrees.
In human, one SNP (rs12501856) was found to be significantly associated with SLC individually, though it did not pass multiple testing correction; however haplotype 2 containing allele C of SNP rs12501856 showed strong evidence of association with SLC (p=0.0037) after multiple comparison adjustment. This haplotype was also marginally associated with diastolic blood pressure and systolic blood pressure. This finding was confirmed in baboons, where a highly significant association was detected between SLC and baboon SNP Asn136Asn (p=0.0001). However, the associated SNP did not account for the linkage signal on baboon chromosome 5.
Consistent results in two different species imply that SLC34A2 is associated with SLC activity and blood pressure.
The genetic contribution to age-related bone loss is not well understood. We estimated that genes accounted for 25–45% of variation in 5-year change in bone mineral density in men and women. An autosome-wide linkage scan yielded no significant evidence for chromosal regions implicated in bone loss.
The contribution of genetics to acquisition of peak bone mass is well documented, but little is know about the influence of genes on subsequent bone loss with age. We therefore measured 5-year change in bone mineral density (BMD) in 300 Mexican Americans (>45 years of age) from the San Antonio Family Osteoporosis Study to identify genetic factors influencing bone loss.
Annualized change in BMD was calculated from measurements taken 5.5 years apart. Heritability (h2) of BMD change was estimated using variance components methods and autosome-wide linkage analysis was carried out using 460 microsatellite markers at a mean 7.6 cM interval density.
Rate of BMD change was heritable at the forearm (h2=0.31, p=0.021), hip (h2 =0.44, p=0.017), spine (h2=0.42, p=0.005), but not whole body (h2=0.18, p=0.123). Covariates associated with rapid bone loss (advanced age, baseline BMD, female sex, low baseline weight, postmenopausal status, and interim weight loss) accounted for 10% to 28% of trait variation. No significant evidence of linkage was observed at any skeletal site.
This is one of the first studies to report significant heritability of BMD change for weight-bearing and non-weight-bearing bones in an unselected population and the first linkage scan for change in BMD.
Bone Loss; Bone Mineral Density; Heritability; Osteoporosis; Quantitative trait locus (QTL)
Very few studies have comprehensively defined the genetic and environmental influences on body fat storage in the arms and legs and their association with diabetes, especially in families of African heritage.
We analyzed body fat distribution by dual-energy X-ray absorptiometry (DXA; percent total fat, percent trunk fat, percent arm fat, and percent leg fat), and fasting serum glucose in 471 individuals (mean age 43 yrs) from 8 multigenerational Afro-Caribbean families (mean family size=51; 3535 relative pairs).
Diabetes was inversely associated with percent leg fat (P=0.009) and to some extent positively associated with percent arm fat, independent of age, gender, and body size (P=0.08), but not with anthropometric or DXA measures of total and central adiposity. Furthermore, percent leg fat was inversely, whereas percent arm fat was positively associated with BMI, waist circumference and serum glucose (p<0.01). Residual heritability (h2r) for arm and leg fat was significant (P<0.01) and high: 62% (for percent arm fat) and 40% (for percent leg fat). Moreover, gender-specific h2r for leg fat was considerably higher (P=0.02) in women than in men (h2r values 58% vs. 17%, respectively). Genetic correlation (ρg) between arm and leg fat was −0.61 (p<0.01), suggesting that only 37% of the co-variation between these two adipose tissue depots may be due to shared genetic influences.
This study provides new evidence for a strong genetic and gender contribution to upper and lower body fat, with relatively little co-variation between these traits due to shared genes. Our findings also suggest that in this population leg fat is associated with diabetes independent of overall adiposity.
Body Fat; African; DXA; Heritability; Family Study; Diabetes
In addition to genetic effects on disease risk, age-at-onset (AAO) of Alzheimer’s disease (AD) is also genetically controlled. Using AAO as a covariate, a linkage signal for AD has been detected on chromosome 14q32 near the a1-antichymotrypsin (ACT) gene. Previously, a signal peptide polymorphism (codon -17A>T) in the ACT gene has been suggested to affect AD risk, but with inconsistent findings. Given that a linkage signal for AAO has been detected near ACT, we hypothesized that ACT genetic variation affects AAO rather than disease risk and this may explain the previous inconsistent findings between ACT genetic variation and AD risk. We examined the impact of the ACT signal peptide polymorphism on mean AAO in 909 AD cases. The ACT polymorphism was significantly associated with AAO and this effect was independent of the APOE polymorphism. Mean AAO among ACT/AA homozygotes was significantly lower than that in the combined AT+TT genotype group (p=0.019) and this difference was confined to male AD patients (p=0.002). Among male AD patients, the ACT/AA genotype was also associated with shorter disease duration before death as compared to the ACT/AT + TT genotypes (p=0.012). These data suggest that the ACT gene may affect AAO and disease duration of AD.
There is considerable interest in understanding genetic determinants of critical illness to improve current risk stratification models, provide individualized therapies, and improve our current understanding of disease mechanisms. This review provides a broad overview of genetic nomenclature, different study designs, and problems unique to each of these study designs in critical illnesses. Well designed genetic studies with careful attention to these issues during the planning phase, use of rigorous statistical methods during analysis, and replication of these results in different cohorts will lead to more robust results and improved understanding of genetics of critical care.
Bone mineral density (BMD) is the most important predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and East Asian ancestry. We tested the top-associated BMD markers for replication in 50,933 independent subjects and for risk of low-trauma fracture in 31,016 cases and 102,444 controls. We identified 56 loci (32 novel)associated with BMD atgenome-wide significant level (P<5×10−8). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal-stem-cell differentiation, endochondral ossification and the Wnt signalling pathways. However, we also discovered loci containing genes not known to play a role in bone biology. Fourteen BMD loci were also associated with fracture risk (P<5×10−4, Bonferroni corrected), of which six reached P<5×10−8 including: 18p11.21 (C18orf19), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
Low serum paraoxonase (PON) activity is associated with the risk of coronary artery disease, diabetes and systemic lupus erythematosus (SLE). Our prior studies have shown that the PON1/rs662 (p.Gln192Arg), PON1/rs854560 (p.Leu55Met), PON3/rs17884563 and PON3/rs740264 SNPs (single nucleotide polymorphisms) significantly affect serum PON activity. Since PON1, PON2 and PON3 share high degree of structural and functional properties, in this study, we examined the role of PON2 genetic variation on serum PON activity, risk of SLE and SLE-related clinical manifestations in a Caucasian case-control sample.
PON2 SNPs were selected from HapMap and SeattleSNPs databases by including at least one tagSNP from each bin defined in these resources. A total of nineteen PON2 SNPs were successfully genotyped in 411 SLE cases and 511 healthy controls using pyrosequencing, restriction fragment length polymorphism (RFLP) or TaqMan allelic discrimination methods.
Our pair-wise linkage disequilibrium (LD) analysis, using an r2 cutoff of 0.7, identified 14 PON2 tagSNPs that captured all 19 PON2 variants in our sample, 12 of which were not in high LD with known PON1 and PON3 SNP modifiers of PON activity. Stepwise regression analysis of PON activity, including the known modifiers, identified five PON2 SNPs [rs6954345 (p.Ser311Cys), rs13306702, rs987539, rs11982486, and rs4729189; P = 0.005 to 2.1 × 10-6] that were significantly associated with PON activity. We found no association of PON2 SNPs with SLE risk but modest associations were observed with lupus nephritis (rs11981433, rs17876205, rs17876183) and immunologic disorder (rs11981433) in SLE patients (P = 0.013 to 0.042).
Our data indicate that PON2 genetic variants significantly affect variation in serum PON activity and have modest effects on risk of lupus nephritis and SLE-related immunologic disorder.
Sequence variation in gene promoters is often associated with disease risk. In this study, we tested the hypothesis that common promoter variation in the APOH gene (encoding for β2-glycoprotein I) is associated with systemic lupus erythematosus (SLE) risk and SLE-related clinical phenotypes in a Caucasian cohort.
We used a case-control design and genotyped 345 SLE women and 454 healthy control women for 8 APOH promoter single nucleotide polymorphisms (SNPs) (−1284C>G, −1219G>A, −1190G>C, −759 A>G, − 700C>A, −643T>C, −38G>A, and −32C>A). Association analyses were performed on single SNPs and haplotypes. Haplotype analyses were performed using EH (Estimate Haplotype-frequencies) and Haploview programs. In vitro reporter gene assay was performed in COS-1 cells. Electrophoretic mobility shift assay (EMSA) was performed using HepG2 nuclear cells.
Overall haplotype distribution of the APOH promoter SNPs was significantly different between cases and controls (P = 0.009). The −643C allele was found to be protective against carotid plaque formation (adjusted OR = 0.37, P = 0.013) among SLE patients. The −643C allele was associated with a ~ 2-fold decrease in promoter activity as compared to wild-type −643T allele (mean ± standard deviation: 3.94 ± 0.05 vs. 6.99 ± 0.68, P = 0.016). EMSA showed that the −643T>C SNP harbors a binding site for a nuclear factor. The −1219G>A SNP showed a significant association with the risk of lupus nephritis (age-adjusted OR = 0.36, P = 0.016).
Our data indicate that APOH promoter variants may be involved in the etiology of SLE, especially the risk for autoimmune-mediated cardiovascular disease.
APOH; β2-glycoprotein I; promoter; SLE; lupus; polymorphism