Comprehensive review and annotation of susceptibility SNPs associated with obesity-related traits.

We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non-coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non-coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity-related pathways directly or through gene-gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.

Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues.

BACKGROUND: With the growing evidence that other tissues, apart from adipose, could have strong relevance to obesity, it is necessary to comprehensively understand the relationship between obesity and other tissues, and to point out the most relevant tissues. METHODS: There were 549 participants with 20 different tissue types involved in this study. We firstly employed both Spearman's correlation test and WGCNA (weighted correlation network analysis) to identify body mass index (BMI)-related genes. Subsequently, we performed enrichment analyses with obesity genes and pathways to see the different regulation patterns among tissues. In addition, we compared obesity genes identified by genome-wide association studies (GWAS) with BMI-related genes to find the overlapping proportion in each tissue. Finally, we integrated preceding results to identify six strong obesity relevant tissues and indicate three categories to represent different obesity relevant tissues. RESULTS: Statistical analyses revealed diverse BMI-related genes and tissue-specific enrichment patterns among tissues. Comparison between BMI-related genes and GWAS findings showed tissue-specific expression changes of GWAS genes. Ultimately, six tissues that showed predominant performance in enrichment analyses and significantly embraced GWAS genes were referred to as strong obesity relevant tissues, including adipose, esophagus, nerve, pancreas, pituitary and skin. We also proposed three categories to represent different obesity relevant tissues. CONCLUSIONS: We performed the first study to investigate the BMI-related gene expression changes across 20 tissues at the same time. With valid data analyses and comparison with GWAS findings, our study provides a holistic view of how different tissues correlate with obesity, and proposes target tissues for obesity pathogenesis investigation.

CIRBP protects H9C2 cells against myocardial ischemia through inhibition of NF-kappaB pathway

Myocardial ischemia is a major cause of death and remains a disease with extremely deficient clinical therapies and a major problem worldwide. Cold inducible RNA-binding protein (CIRBP) is reported to be involved in multiple pathological processes, including myocardial ischemia. However, the molecular mechanisms of myocardial ischemia remain elusive. Here, we first overexpressed CIRBP by transfection of pc-CIRBP (pcDNA3.1 containing coding sequenced for CIRBP) and silenced CIRBP by transfection of small interfering RNA targeting CIRBP (siCIRBP). pcDNA3.1 and the negative control of siCIRBP (siNC) were transfected into H9C2 cells to act as controls. We then constructed a cell model of myocardial ischemia through culturing cells in serum-free medium with hypoxia in H9C2 cells. Subsequently, AlamarBlue assay, flow cytometry and western blot analysis were used, respectively, to assess cell viability, reactive oxygen species (ROS) level and apoptosis, and expression levels of IκBα, p65 and Bcl-3. We demonstrated that CIRBP overexpression promoted cell proliferation (P<0.001), inhibited cell apoptosis (P<0.05), reduced ROS level (P<0.001), down-regulated phosphorylated levels of IκBα and p65 (P<0.01 or P<0.001), and up-regulated expression of Bcl-3 (P<0.001) in H9C2 cells with myocardial ischemia. The influence of CIRBP knockdown yielded opposite results. Our study revealed that CIRBP could protect H9C2 cells against myocardial ischemia through inhibition of NF-κB pathway.

Epigenomic elements analyses for promoters identify ESRRG as a new susceptibility gene for obesity-related traits.

OBJECTIVES: With ENCODE epigenomic data and results from published genome-wide association studies (GWASs), we aimed to find regulatory signatures of obesity genes and discover novel susceptibility genes. METHODS: Obesity genes were obtained from public GWAS databases and their promoters were annotated based on the regulatory element information. Significantly enriched or depleted epigenomic elements in the promoters of obesity genes were evaluated and all human genes were then prioritized according to the existence of the selected elements to predict new candidate genes. Top-ranked genes were subsequently applied to validate their associations with obesity-related traits in three independent in-house GWAS samples. RESULTS: We identified RAD21 and EZH2 as over-represented, and STAT2 (signal transducer and activator of transcription 2) and IRF3 (interferon regulatory transcription factor 3) as depleted transcription factors. Histone modification of H3K9me3 and chromatin state segmentation of 'poised promoter' and 'repressed' were over-represented. All genes were prioritized and we selected the top five genes for validation at the population level. Combining results from the three GWAS samples, rs7522101 in ESRRG (estrogen-related receptor-γ) remained significantly associated with body mass index after multiple testing corrections (P=7.25 × 10(-5)). It was also associated with ß-cell function (P=1.99 × 10(-3)) and fasting glucose level (P<0.05) in the meta-analyses of glucose and insulin-related traits consortium (MAGIC) data set.Cnoclusions:In summary, we identified epigenomic characteristics for obesity genes and suggested ESRRG as a novel obesity-susceptibility gene.

Late Permian marine ecosystem collapse began in deeper waters: evidence from brachiopod diversity and body size changes.

Analysis of Permian-Triassic brachiopod diversity and body size changes from different water depths spanning the continental shelf to basinal facies in South China provides insights into the process of environmental deterioration. Comparison of the temporal changes of brachiopod diversity between deepwater and shallow-water facies demonstrates that deepwater brachiopods disappeared earlier than shallow-water brachiopods. This indicates that high environmental stress commenced first in deepwater settings and later extended to shallow waters. This environmental stress is attributed to major volcanic eruptions, which first led to formation of a stratified ocean and a chemocline in the outer shelf and deeper water environments, causing the disappearance of deep marine benthos including brachiopods. The chemocline then rapidly migrated upward and extended to shallow waters, causing widespread mass extinction of shallow marine benthos. We predict that the spatial and temporal patterns of earlier onset of disappearance/extinction and ecological crisis in deeper water ecosystems will be recorded during other episodes of rapid global warming.

Functional analyses reveal the essential role of SOX6 and RUNX2 in the communication of chondrocyte and osteoblast.

SUMMARY: This study provides novel evidence that sex determining region Y (SRY)-box (SOX6) and runt-related transcription factor 2 (RUNX2) play essential roles in the communication of chondrocyte and osteoblast. Our findings open a new avenue to the limited understanding of the coordination effect between chondrogenesis and osteogenesis. INTRODUCTION: Sox6 and Runx2 are two new susceptibility genes for osteoporosis identified by genome-wide association studies, but the functions of these genes in osteogenesis remain unclear. Both genes are essential transcription factors in chondrogenesis, which reminds us that SOX6 and RUNX2 might be involved in the coordination of chondrogenesis and osteogenesis. Therefore, this study aimed to investigate the functions of SOX6 and RUNX2 in the coupling regulation of chondrogenesis and osteogenesis. METHODS: We established a chondrogenic differentiation model of ATDC5 cell and profiled the expression of SOX6 and RUNX2 during chondroblast differentiation. We co-cultured osteoblast cells with ATDC5 cells in different differentiation stages and examined the proliferation, cell cycle progression, apoptosis, and differentiation of osteoblast cells. SOX6 or RUNX2 was knocked down using specific siRNA and the effect was examined. RESULTS: During chondrogenic differentiation, SOX6 and RUNX2 expressed sequentially in the proliferating and hypertrophic stages. Proliferative ATDC5 cells stimulated the multiplication of osteoblasts and promoted more osteoblasts to enter S-phase. Hypertrophic ATDC5 cells enhanced the differentiation of osteoblasts. Yet, the apoptosis of osteoblasts was neither affected by proliferating nor hypertrophic ATDC5 cells. Knockdown of SOX6 in proliferating ATDC5 cells significantly repressed the stimulation of osteoblast multiplication, whereas depletion of RUNX2 in hypertrophic ATDC5 cells retarded the expression of osteoblastic markers. CONCLUSIONS: Our study first reveals that SOX6 and RUNX2 play important roles in the chondrogenesis-osteogenesis coordination. This finding enriches the limited understanding about this coordination and unravels the novel function of SOX6 and RUNX2 in the endochondral ossification.

Ethnic differentiation of copy number variation on chromosome 16p12.3 for association with obesity phenotypes in European and Chinese populations.

OBJECTIVE: Genomic copy number variations (CNVs) have been strongly implicated as important genetic factors for obesity. A recent genome-wide association study identified a novel variant, rs12444979, which is in high linkage disequilibrium with CNV 16p12.3, for association with obesity in Europeans. The aim of this study was to directly examine the relationship between the CNV 16p12.3 and obesity phenotypes, including body mass index (BMI) and body fat mass. SUBJECTS: Subjects were a multi-ethnic sample, including 2286 unrelated subjects from a European population and 1627 unrelated Han subjects from a Chinese population. Body fat mass was measured using dual energy X-ray absorptiometry. RESULTS: Using Affymetrix Genome-Wide Human SNP Array 6.0, we directly detected CNV 16p12.3, with the deletion frequency of 27.26 and 0.8% in the European and Chinese populations, respectively. We confirmed the significant association between this CNV and obesity (BMI: P=1.38 × 10(-2); body fat mass: P=2.13 × 10(-3)) in the European population. Less copy numbers were associated with lower BMI and body fat mass, and the effect size was estimated to be 0.62 (BMI) and 1.41 (body fat mass), respectively. However, for the Chinese population, we did not observe significant association signal, and the frequencies of this deletion CNV are quite different between the European and Chinese populations (P<0.001). CONCLUSION: Our findings first suggest that CNV 16p12.3 might be ethnic specific and cause ethnic phenotypic diversity, which may provide some new clues into the understanding of the genetic architecture of obesity.

A family-based association study identified CYP17 as a candidate gene for obesity susceptibility in Caucasians.

The cytochrome P450c17α gene (CYP17) encodes a key biosynthesis enzyme of estrogen, which is critical in regulating adipogenesis and adipocyte development in humans. We therefore hypothesized that CYP17 is a candidate gene for predicting obesity. In order to test this hypothesis, we performed a family-based association test to investigate the relationship between the CYP17 gene and obesity phenotypes in a large sample comprising 1873 subjects from 405 Caucasian nuclear families of European origin recruited by the Osteoporosis Research Center of Creighton University, USA. Both single SNPs and haplotypes were tested for associations with obesity-related phenotypes, including body mass index (BMI) and fat mass. We identified three SNPs to be significantly associated with BMI, including rs3740397, rs6163, and rs619824. We further characterized the linkage disequilibrium structure for CYP17 and found that the whole CYP17 gene was located in a single-linkage disequilibrium block. This block was observed to be significantly associated with BMI. A major haplotype in this block was significantly associated with both BMI and fat mass. In conclusion, we suggest that the CYP17 gene has an effect on obesity in the Caucasian population. Further independent studies will be needed to confirm our findings.

Are bone mineral density loci associated with hip osteoporotic fractures? A validation study on previously reported genome-wide association loci in a Chinese population.

Osteoporosis is a heritable disease characterized mainly by low bone mineral density (BMD) and/or osteoporotic fractures (OF). Most genome-wide association studies on osteoporosis have focused on BMD, whereas little effort has been expended to identify genetic variants directly linked to OF. To determine whether BMD-loci are also associated with OF risk, we performed a validation study to examine 23 BMD-loci reported by recent genome-wide association studies for association with hip OF risk. Our sample consisted of 700 elderly Chinese Han subjects, 350 with hip OF and 350 healthy matched controls. We identified four BMD-loci that were significantly associated with hip OF in this Chinese population, including 7q21 (FLJ42280, P = 1.17 × 10(-4) for rs4729260; P = 0.008 for rs7781370), 6p21 (MHC, P = 0.004 for rs3130340), 13q14 (TNFSF11, P = 0.012 for rs9533090; P = 0.018 for rs9594759; P = 0.020 for rs9594738; P = 0.044 for rs9594751), and 18q21 (TNFRSF11A, P = 0.015 for rs884205). The SNP rs4729260 at 7q21 remained significantly associated, even after conservative Bonferroni's correction. Our results further highlight the importance of these loci in the pathogenesis of osteoporosis, and demonstrate that it is feasible and useful to use OF as the direct phenotype to conduct genetic studies, to enhance our understanding of the genetic architecture of osteoporosis.

Genetic variants in the SOX6 gene are associated with bone mineral density in both Caucasian and Chinese populations.

SUMMARY: Given the biological function of SOX6 and recent genome-wide association finding, we performed a fine-mapping association analyses to investigate the relationship between SOX6 and BMD both in Caucasian and Chinese populations. We identified many single-nucleotide polymorphisms (SNPs) within or near the SOX6 gene to be significantly associated with hip bone mineral density (BMD). INTRODUCTION: SOX6 gene is an essential transcription factor in chondrogenesis and cartilage formation. Recent genome-wide association studies (GWAS) detected a SNP (rs7117858) located at the downstream of SOX6 significantly associated with hip BMD. METHODS: Given the biological function of SOX6 and the GWAS finding, we considered SOX6 as a new candidate for BMD and osteoporosis. Therefore, in this study, we performed a fine-mapping association analyses to investigate the relationship between SNPs within and near the SOX6 gene and BMD at both hip and spine. A total of 301 SNPs were tested in two independent US Caucasian populations (2,286 and 1,000 unrelated subjects, respectively) and a Chinese population (1,627 unrelated Han subjects). RESULTS: We confirmed that the previously reported rs7117858-A was associated with reduced hip BMD, with combined P value of 2.45 × 10(-4). Besides this SNP, we identified another 19 SNPs within or near the SOX6 gene to be significantly associated with hip BMD after false discovery rate adjustment. The most significant SNP was rs1347677 located at the intron 3 (P = 3.15 × 10(-7)). Seven additional SNPs in high linkage disequilibrium with rs1347677 were also significantly associated with hip BMD. SNPs in SOX6 showed significant skeletal site specificity since no SNP was detected to be associated with spine BMD. CONCLUSION: Our study identified many SNPs in the SOX6 gene associated with hip BMD even across different ethnicities, which further highlighted the importance of the SOX6 gene influencing BMD variation and provided more information to the understanding of the genetic architecture of osteoporosis.

A follow-up association study of two genetic variants for bone mineral density variation in Caucasians.

SUMMARY: We tested whether two genetic variants were associated with BMD at multiple clinically relevant skeletal sites in Caucasians. We found that variant rs7776725 is consistently associated with hip, spine, wrist and whole-body BMD, which highlights the potential importance of this variant or linked variants for osteoporosis. INTRODUCTION: A recent genome-wide association study identified two single nucleotide polymorphisms (SNPs), rs7776725 and rs1721400, that were associated with bone mineral density (BMD) variation at the radius, tibia and calcaneus in a Korean population. In this study, we aimed to test whether the association of these two genetic variants can be replicated in Caucasians and whether their association with BMD can be extended to other clinically relevant skeletal sites. METHODS: We performed this study in two large cohorts of unrelated US Caucasians. Area BMD at the hip, spine, wrist (ultra-distal radius) and whole body were measured with Hologic dual-energy X-ray absorptiometer. SNPs were genotyped with Affymetrix human genome-wide genotyping arrays. Association analyses were performed using PLINK. RESULTS: We detected highly significant association (combined p = 1.42 × 10(-16)) of rs7776725 with wrist BMD but only borderline association signal (combined p = 0.017) for rs1721400 with wrist BMD. In addition, we found that rs7776725 was associated with BMD at the hip, spine and whole body. At the FAM3C gene locus where rs7776725 was located, we identified several other SNPs (rs4727922, rs1803389, rs718766 and rs7793554) that were also associated with BMD. CONCLUSIONS: This is the first follow-up association study of rs7776725 and rs1721400 with BMD. The rs7776725 showed consistent association with BMD at multiple clinically important skeletal sites, which highlighted the potential importance of rs7776725 or linked SNPs for risk of osteoporosis. Further in-depth re-sequencing studies and functional assays are necessary to elucidate the underlying mechanisms.

Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians.

UNLABELLED: Osteoporotic fracture (OF) is a serious outcome of osteoporosis. Important risk factors for OF include reduced bone mineral density and unstable bone structure. This genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians. INTRODUCTION: Bone mineral density (BMD) and femoral neck cross-sectional geometric parameters (FNCSGPs) are under strong genetic control. DNA copy number variation (CNV) is an important source of genetic diversity for human diseases. This study aims to identify CNVs associated with BMD and FNCSGPs. METHODS: Genome-wide CNV association analyses were conducted in 1,000 unrelated Caucasian subjects for BMD at the spine, hip, femoral neck, and for three FNCSGPs -cortical thickness (CT), cross-section area (CSA), and buckling ratio (BR). BMD was measured by dual energy X-ray absorptiometry (DEXA). CT, CSA, and BR were estimated using DEXA measurements. Affymetrix 500K arrays and copy number analysis tool was used to identify CNVs. RESULTS: A CNV in VPS13B gene was significantly associated with spine, hip and FN BMDs, and CT, CSA, and BR (p < 0.05). Compared to subjects with two copies of the CNV, carriers of one copy had an average of 14.6%, 12.4%, and 13.6% higher spine, hip, and FN BMD, 20.0% thicker CT, 10.6% larger CSA, and 12.4% lower BR. Thus, a decrease of the CNV consistently produced stronger bone, thereby reducing osteoporotic fracture risk. CONCLUSIONS: VPS13B gene, via affecting BMD and FNCSGPs, is a novel osteoporosis risk gene.

Genomewide linkage scan for combined obesity phenotypes using principal component analysis.

Traditional whole genome linkage scans for obesity were usually performed for a number of correlated obesity related phenotypes separately without considering their correlations. The purpose of this study was to identify quantitative trait loci (QTLs) underlying variations in multiple correlated obesity phenotypes. We performed principal component analysis (PCA) for four highly correlated obesity phenotypes (body mass index [BMI], fat mass, percentage of fat mass [PFM], and lean mass) in a sample of 427 pedigrees (comprising 3,273 individuals) and generated two independent principal components (PC1 and PC2). A whole genome linkage scan (WGS) was then conducted for PC1 and PC2. For PC1, the strongest linkage signal was identified on chromosome 20p12 (LOD = 2.67). For PC2, two suggestive linkages were found on 5q35 (LOD = 2.03) and 7p22 (LOD = 2.18). This study provided evidence supporting several previously identified linkage regions for obesity (e.g., 1p36, 6p23 and 7q34). In addition, our approach by linear combination of highly correlated obesity phenotypes identified several novel QTLs which were not found in genome linkage scans for individual phenotypes.

Mechanism for blockade of angiotensin subtype 1 receptors to lower plasma glucose in streptozotocin-induced diabetic rats.

AIMS: We investigated the mechanism(s) by which valsartan, a selective antagonist of angiotensin subtype 1 (AT(1)) receptor, decreased plasma glucose in streptozotocin (STZ)-induced diabetic rats. METHODS: The plasma glucose concentration was assessed by the glucose oxidase method. The concentration of beta-endorphin in plasma or medium incubating adrenal medulla was measured using an enzyme-linked immunosorbent assay. The mRNA levels of the subtype 4 form of glucose transporter (GLUT4) in soleus muscle and phosphoenolpyruvate carboxykinase (PEPCK) in the liver were detected by Northern blotting analysis, while the protein levels of GLUT4 in isolated soleus muscle and hepatic PEPCK were investigated using Western blotting analysis. RESULTS: A single intravenous injection of valsartan dose-dependently increased plasma beta-endorphin-like immunoreactivity (BER) in parallel with the lowering of plasma glucose concentration in STZ-induced diabetic rats. Naloxone and naloxonazine inhibited the plasma glucose-lowering action of valsartan at doses sufficient to block opioid micro-receptors. In contrast to its action in wild-type diabetic mice, valsartan failed to modify plasma glucose in opioid micro-receptor knockout diabetic mice. Bilateral adrenalectomy in STZ-induced diabetic rats eliminated both the plasma glucose-lowering action and the plasma BER-elevating action of valsartan. In the isolated adrenal medulla of STZ-induced diabetic rats, angiotensin II (Ang II) or valsartan did not affect spontaneous BER secretion. Activation of cholinergic receptors by 1.0 micromol/l acetylcholine (ACh) enhanced BER secretion from the isolated adrenal medulla of STZ-induced diabetic rats, but not in the presence of 1.0 nmol/l Ang II, while valsartan reversed this inhibition by Ang II in a concentration-dependent manner. Treatment of STZ-induced diabetic rats with valsartan (0.2 mg/kg) three times daily for 3 days resulted in an increase in gene expression of GLUT4 in soleus muscle and impeded the reduction of elevated mRNA or protein level of hepatic PEPCK. Both of these effects were blocked by opioid micro-receptor antagonist. CONCLUSIONS: The results suggest that blockade of AT(1) receptor by valsartan may enhance the adrenal beta-endorphin secretion induced by ACh, activating the opioid micro-receptors to increase glucose utilization and/or to decrease hepatic gluconeogenesis, resulting in the reduction of plasma glucose in STZ-induced diabetic rats.

Genetic and environmental correlations of bone mineral density at different skeletal sites in females and males.

Bone mineral density (BMD) is a complex trait having genetic and environmental determination. There are gender-specific differences in BMD measurements, and the rate of BMD changes with age and lifestyle. Previous studies have shown that the genetic loci underlying BMD variation are gender-specific in mice and humans. Our study aimed to investigate correlations between BMD at the spine, hip, and ultradistal radius (UD) and degree of shared genetic and environmental factors among them in females and males, separately. For a large sample of 4,489 subjects containing 2,667 females and 1,822 males from 512 Caucasian pedigrees, we performed bivariate variance decomposition analyses. Our results showed that the genetic correlations (rhoG), environmental correlations (rhoE), and phenotypical correlations (rhoP) were all significant and positive. Strong genetic correlations were observed in both female and male groups, ranging 0.590-0.738 and 0.583-0.773, respectively. Genetic correlations of BMD at the spine, hip, and UD were generally higher than environmental correlations. In summary, we are the first to test the genetic and environmental correlations in females and males, separately. It is suggested that the phenotypic correlations of BMDs at the three different sites may have more genetic than environmental components. BMDs at the spine and hip may share more environmental components in females than males. We did not detect gender-specific difference in spine/UD and hip/UD. It is also indicated that the environmental factors that preserve or increase BMD at one skeletal site may have similar beneficial effects on some other skeletal sites and vice versa.

Large cell neuroendocrine carcinoma of the ampulla of Vater with glandular differentiation.

Large cell neuroendocrine carcinoma of the ampulla of Vater is extremely rare. A 55 year old woman presented with an ampullary tumour causing pancreaticobiliary obstruction and a pancreaticoduodenectomy was performed. Microscopically, the tumour was diagnosed as a CD117 positive large cell neuroendocrine carcinoma with glandular differentiation. Four months later the patient developed a general recurrence. The metastatic tumours showed CD117 negativity and pure neuroendocrine features. The patient died of disease six months after diagnosis. It is postulated that the two components originated from a common multipotential stem cell. The clinical behaviour of ampullary large cell neuroendocrine carcinomas appears to be highly aggressive, with early metastases and a fatal outcome.