Molecular genetics of supernumerary tooth formation

Despite advances in the knowledge of tooth morphogenesis and differentiation, relatively little is known about the aetiology and molecular mechanisms underlying supernumerary tooth formation. A small number of supernumerary teeth may be a common developmental dental anomaly, while multiple supernumerary teeth usually have a genetic component and they are sometimes thought to represent a partial third dentition in humans. Mice, which are commonly used for studying tooth development, only exhibit one dentition, with very few mouse models exhibiting supernumerary teeth similar to those in humans. Inactivation of Apc or forced activation of Wnt/β(catenin signalling results in multiple supernumerary tooth formation in both humans and in mice, but the key genes in these pathways are not very clear. Analysis of other model systems with continuous tooth replacement or secondary tooth formation, such as fish, snake, lizard, and ferret, is providing insights into the molecular and cellular mechanisms underlying succesional tooth development, and will assist in the studies on supernumerary tooth formation in humans. This information, together with the advances in stem cell biology and tissue engineering, will pave ways for the tooth regeneration and tooth bioengineering.

Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients

BACKGROUND

Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstructive CAD likelihood would have diagnostic utility.

RESULTS

Microarray analysis of RNA samples from a 195 patient Duke CATHGEN registry case:control cohort yielded 2,438 genes with significant CAD association (p < 0.05), and identified the clinical/demographic factors with the largest effects on gene expression as age, sex, and diabetic status. RT-PCR analysis of 88 CAD classifier genes confirmed that diabetic status was the largest clinical factor affecting CAD associated gene expression changes. A second microarray cohort analysis limited to non-diabetics from the multi-center PREDICT study (198 patients; 99 case: control pairs matched for age and sex) evaluated gene expression, clinical, and cell population predictors of CAD and yielded 5,935 CAD genes (p < 0.05) with an intersection of 655 genes with the CATHGEN results. Biological pathway (gene ontology and literature) and statistical analyses (hierarchical clustering and logistic regression) were used in combination to select 113 genes for RT-PCR analysis including CAD classifiers, cell-type specific markers, and normalization genes.RT-PCR analysis of these 113 genes in a PREDICT cohort of 640 non-diabetic subject samples was used for algorithm development. Gene expression correlations identified clusters of CAD classifier genes which were reduced to meta-genes using LASSO. The final classifier for assessment of obstructive CAD was derived by Ridge Regression and contained sex-specific age functions and 6 meta-gene terms, comprising 23 genes. This algorithm showed a cross-validated estimated AUC = 0.77 (95% CI 0.73-0.81) in ROC analysis.

CONCLUSIONS

We have developed a whole blood classifier based on gene expression, age and sex for the assessment of obstructive CAD in non-diabetic patients from a combination of microarray and RT-PCR data derived from studies of patients clinically indicated for invasive angiography.

CLINICAL TRIAL REGISTRATION INFORMATION

PREDICT, Personalized Risk Evaluation and Diagnosis in the Coronary Tree, http://www.clinicaltrials.gov, NCT00500617.

Quantitative proteomic analysis of A549 cells infected with human respiratory syncytial virus subgroup B using SILAC coupled to LC-MS/MS

Human respiratory syncytial virus (HRSV) is a leading cause of serious lower respiratory tract infections in infants. The virus has two subgroups A and B, which differ in prevalence and (nucleotide) sequence. The interaction of subgroup A viruses with the host cell is relatively well characterized, whereas for subgroup B viruses it is not. Therefore quantitative proteomics was used to investigate the interaction of subgroup B viruses with A549 cells, a respiratory cell line. Changes in the cellular proteome and potential canonical pathways were determined using SILAC coupled to LC‐MS/MS and Ingenuity Pathway Analysis. To reduce sample complexity and investigate potential trafficking both nuclear and cytoplasmic fractions were analyzed. A total of 904 cellular and six viral proteins were identified and quantified, of which 112 cellular proteins showed a twofold or more change in HRSV‐infected cells. Data sets were validated using indirect immunofluorescence confocal microscopy on independent samples. Major changes were observed in constituents of mitochondria including components of the electron transport chain complexes and channels, as well as increases in the abundance of the products of interferon‐stimulated genes. This is the first quantitative proteomic analysis of cells infected with HRSV‐subgroup B.

Allelic expression imbalance of TP53 mutated and polymorphic alleles in head and neck tumors

TP53 is the most widely mutated gene across all cancer types. In head and neck cancer, approximately half of the tumors are found to contain TP53 mutations, which are correlated to an increased risk for locoregional recurrence and poor outcomes. In this study a mutational profiling of TP53 exons 5-8 was performed on tumor, peritumor and normal tissues from 57 HNSCC patients by direct sequencing of genomic DNA and cDNA. Cloning/sequencing in tumors carrying multiple TP53 mutations and semiquantitative SNaPShot mutation assay was performed in order to assess eventual allelic expression imbalances (AEI). We identified 24 out of 57 HNSCC patients (42%) carrying TP53 mutations and 5 patients carrying the R213R polymorphism. Cloning of the genomic DNA encompassing TP53 exons 5-8 from tumors with multiple TP53 mutations revealed that alleles carrying different types of TP53 mutations are present in these tumors. TP53 missense and nonsense mutations exhibit higher and lower TP53 transcript abundance compared to wild-type TP53 allele, respectively. Interestingly, three out of four patients with the R213R polymorphism analyzed were found positive for TP53 loss of heterozygosity (LOH) and also presented higher transcript abundance than the wild-type counterpart, specifically, in the tumor tissue and not in peritumor or normal tissues. HNSCC tumors present heterogenic cell populations carrying different TP53 mutations. All HNSCC samples analyzed show an alteration in the expression of mutated TP53 mRNA compared to the wild-type allele, most likely independently from the TP53 hemizygous status. The higher expression of R213R TP53 polymorphic allele in cancer tissue compared to normal tissue demonstrates a noninherited variation in allelic expression, independently from its mutation status for exons 5-8, suggesting a potential contribution to TP53 expression in HNSCC disease.

Developmental roles for Srf, cortical cytoskeleton and cell shape in epidermal spindle orientation

During development, a polarized epidermal sheet undergoes stratification and differentiation to produce the skin barrier. Through mechanisms that are poorly understood, the process involves actin dynamics, spindle reorientation and Notch signalling. To elucidate how epidermal embryogenesis is governed, we conditionally targeted serum response factor (Srf), a transcription factor that is essential for epidermal differentiation. Unexpectedly, previously ascribed causative defects are not responsible for profoundly perturbed embryonic epidermis. Seeking the mechanism for this, we identified actins and their regulators that were downregulated after ablation. Without Srf, cells exhibit a diminished cortical network and in mitosis, they fail to round up, features we recapitulate with low-dose actin inhibitors in vivo and shRNA-knockdown in vitro. Altered concomitantly are phosphorylated ERM and cortical myosin-IIA, shown in vitro to establish a rigid cortical actomyosin network and elicit critical shape changes. We provide a link between these features and Srf loss, and we show that the process is physiologically relevant in skin, as reflected by defects in spindle orientation, asymmetric cell divisions, stratification and differentiation.

Respiratory syncytial virus represses glucocorticoid receptor-mediated gene activation

Respiratory syncytial virus (RSV) is a common cause of bronchiolitis in infants. Although antiinflammatory in nature, glucocorticoids have been shown to be ineffective in the treatment of RSV-induced bronchiolitis and wheezing. In addition, the effectiveness of glucocorticoids at inhibiting RSV-induced proinflammatory cytokine production in cell culture has been questioned. In this study, we have investigated the effect of RSV infection on glucocorticoid-induced gene activation in lung epithelium-derived cells. We show that RSV infection inhibits dexamethasone induction of three glucocorticoid receptor (GR)-regulated genes (glucocorticoid-inducible leucine zipper, FK506 binding protein, and MAPK phosphatase 1) in A549, BEAS-2B cells, and primary small airway epithelial cells. UV irradiation of the virus prevents this repression, suggesting that viral replication is required. RSV is known to activate the nuclear factor κB (NFκB) pathway, which is mutually antagonistic towards the GR pathway. However, specific inhibition of NFκB had no effect on the repression of GR-induced genes by RSV infection, indicating that RSV repression of GR is independent of NFκB. RSV infection of A549 cells does not alter GR protein levels or GR nuclear translocation but does reduce GR binding to the promoters of the glucocorticoid responsive genes analyzed in this study. Repression of GR by RSV infection may account for the apparent clinical ineffectiveness of glucocorticoids in RSV bronchiolitis therapy. In addition, this data adds to our previously published data suggesting that GR may be a general target for infectious agents. Identifying the mechanisms through which this suppression occurs may lead to the development of novel therapeutics.

Are ACEI/ARBs associated with the decreased peritoneal protein clearance in long-term PD patients?

Objective. Peritoneal protein clearance (PrC) is recognized as a new marker of systemic endothelial dysfunction and predictor of mortality in patients on peritoneal dialysis (PD). Given that angiotensin-converting enzyme inhibitors (ACEI)/angiotensin II receptor blockers (ARBs) could improve endothelial dysfunction in the general population, we aim to explore whether this benefit is present in the PD population.

METHODS

We analysed data from a PD cohort with data prospectively collected. The PrC, defined daily doses (DDDs) of ACEI/ARBs, as well as other clinical variables were recorded at baseline and then repeatedly measured at 3- to 6-month intervals till to death or censoring. A total of 156 patients were treated with ACEI/ARBs with 0.60 of median time-averaged DDDs, the untreated group consisted of 149 patients who received none of the above drugs during the follow-up.

RESULTS

The baseline and time-averaged PrC were 69.9 ± 34.7 mL/day and 75.2 ± 28.3 mL/day, respectively. Time-averaged PrC was an independent predictor of mortality adjusted for recognized confounders in a multivariate Cox regression model (P = 0.037). There were no significant differences in the time course of PrC (P = 0.82) and peritoneal protein loss (P = 0.83) between the ACEI/ARBs group and the untreated group after adjustment for age, gender, diabetes, baseline C-reactive protein, mean blood pressure and baseline PrC or baseline peritoneal protein loss in the generalized linear mixed model.

CONCLUSIONS

We conclude that ACEI/ARBs did not correlate with a decreased PrC in this observational study. The effect of higher doses of ACEI/ARBs needs to be determined in future interventional studys.

Findings from a community education needs assessment to facilitate the integration of genomic medicine into primary care

PURPOSE

To assess the lay public's knowledge of, and beliefs about, genetics and genetic testing to create an educational initiative that promotes acceptance and utilization of genomic medicine in primary health care.

METHODS

A telephone survey of English-speaking adults in Guilford County, North Carolina was conducted in 2006 to identify community members' educational needs regarding genetics and genetic testing.

RESULTS

Most respondents recognized the connection between family history and disease risk. A majority did not appear to know about: (1) basic principles of inheritance, (2) laws prohibiting genetic discrimination, and (3) the availability and limitations of genetic tests. About 25% thought that they could not reduce their risk if they have a genetic predisposition for disease. Knowledge level was affected by education, experience, age, and race.

CONCLUSION

If primary care providers use family history as a risk assessment tool, community education programs must address (1) the collection of family health history, (2) legislation regarding genetic nondiscrimination, (3) benefits and limitations of existing genetic tests, and (4) genetic determinism. Programs emphasizing practical, "how to" information can be targeted to individuals likely to collect family history information and address misperceptions about discrimination, testing, and determinism.

Up-regulation of TNF-alpha secretion by cigarette smoke is mediated by Egr-1 in HaCaT human keratinocytes

Many epidemiologic studies have pointed to a significant association between cigarette smoking and inflammatory skin disease such as psoriasis. Cigarette smoke induces expression of regulators of inflammation such as interleukin (IL)-1, IL-6, IL-8 and tumor necrosis factor (TNF)-alpha. It was recently demonstrated that early growth response-1 (Egr-1) transcription factor is significantly up-regulated in the skin lesions of patients with psoriasis. The mechanism by which cigarette smoke extract (CSE) regulates inflammatory cytokine expression in keratinocyte was still unknown. The aim of this study was to investigate the signalling of CSE-induced Egr-1 expression and the role for Egr-1 in CSE-induced TNF-alpha expression. Cytotoxicity of CSE in HaCaT cells was measured by thiazolyl blue tetrazolium bromide (MTT) assay. CSE-induced Egr-1 expression was investigated by western blot, luciferase reporter assay and confocal microscopy. TNF-alpha expression was measured by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay. Involvement of Egr-1 in CSE-induced TNF-alpha secretion was determined by using Egr-1 specific siRNA. CSE increases the Egr-1 expression, promoter activity and its nuclear translocation in human HaCaT keratinocytes. CSE activates mitogen-activated protein kinase (MAPK) pathways including extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK). Up-regulation of Egr-1 expression by CSE stimulation was found to be inhibited by an ERK and JNK but not p38 inhibitor. CSE increases TNF-alpha expression and secretion. This increase is mediated by CSE-induced Egr-1 expression. Our results showed that CSE induces Egr-1 expression via MAPK pathway in human keratinocytes and TNF-alpha expression by Egr-1. This pathway may contribute to the development of inflammatory disease such as psoriasis.

In silico searching for disease-associated functional DNA variants

Experimental analyses of disease-associated DNA variants have provided significant insights into the functional implications of sequence variation. However, such experiment-based approaches for identifying functional DNA variants from a pool with a large number of neutral variants are challenging. Computational biology has the opportunity to play an important role in the identification of functional DNA variants in large-scale genotyping studies, ultimately yielding new drug targets and biomarkers. This chapter outlines in silico methods to predict disease-associated functional DNA variants so that the number of DNA variants screened for association with disease can be reduced to those that are most likely to alter gene function. To explore possible relationships between genetic mutations and phenotypic variation, different computational methods like Sorting Intolerant from Tolerant (SIFT, an evolutionary-based approach), Polymorphism Phenotyping (PolyPhen, a structure-based approach) and PupaSuite are discussed for prioritization of high-risk DNA variants. The PupaSuite tool aims to predict the phenotypic effect of DNA variants on the structure and function of the affected protein as well as the effect of variants in the non-coding regions of the same genes. To further investigate the possible causes of disease at the molecular level, deleterious nonsynonymous variants can be mapped to 3D protein structures. An analysis of solvent accessibility and secondary structure can also be performed to understand the impact of a mutation on protein function and stability. This chapter demonstrates a 'real-world' application of some existing bioinformatics tools for DNA variant analysis.

Evaluation of the disease liability of CFTR variants

Over 1600 novel sequence variants in the CFTR gene have been reported to the CF Mutation Database (http://www.genet.sickkids.on.ca/cftr/Home.html). While about 25 mutations are well characterized by clinical studies and functional assays, the disease liability of most of the remaining mutations is either unclear or unknown. This gap in knowledge has implications for diagnosis, therapy selection, and counseling for patients and families carrying an uncharacterized CFTR mutation. This chapter will describe a critical approach to assessing the disease implications of CFTR mutations utilizing clinical data, literature review, functional testing, and bioinformatic in silico methods.

Data standards for Omics data: the basis of data sharing and reuse

To facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards. Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.

Molecular signature for early detection and prediction of polycyclic aromatic hydrocarbons in peripheral blood

Whole blood is one of the most easily accessible biofluids, and circulating leukocytes would include informative transcripts as a first line of immune defense for many disease processes. To demonstrate that transcriptomic responses of circulating blood cells reflect the exposure to environmental toxicants and the characteristic molecular signatures can discriminate and predict the type of toxicant at an early exposure time, we identified and validated characteristic gene expression profiles of rat whole blood after exposure to polycyclic aromatic hydrocarbons (PAHs). At an early exposure time point, conventional toxicological analysis including changes in the body and organ weight, histopathological examination, and blood biochemical analysis did not reflect any toxicant stresses. However, unsupervised gene expression analysis of blood cells resulted in a characteristic molecular signature for each toxicant. Further analysis of multiclassification suggested 220 genes as early detective and surrogate markers for predicting each PAH with 100% accuracy. These findings suggest that the blood expression signature could be used as a predictable and discernible surrogate marker for detection and prediction of PAHs, and the use of these molecular markers may be more widely implemented in combination with more traditional techniques for assessment and prediction of toxicity exposure to PAHs from an environmental aspect.

Nutrigenomics and nutrigenetics

The nutrients are able to interact with molecular mechanisms and modulate the physiological functions in the body. The Nutritional Genomics focuses on the interaction between bioactive food components and the genome, which includes Nutrigenetics and Nutrigenomics. The influence of nutrients on f genes expression is called Nutrigenomics, while the heterogeneous response of gene variants to nutrients, dietary components and developing nutraceticals is called Nutrigenetics. Genetic variation is known to affect food tolerances among human subpopulations and may also influence dietary requirements and raising the possibility of individualizing nutritional intake for optimal health and disease prevention on the basis of an individual's genome. Nutrigenomics provides a genetic understanding for how common dietary components affect the balance between health and disease by altering the expression and/or structure of an individual's genetic makeup. Nutrigenetics describes that the genetic profile have impact on the response of body to bioactive food components by influencing their absorption, metabolism, and site of action.In this way, considering different aspects of gene-nutrient interaction and designing appropriate diet for every specific genotype that optimize individual health, diagnosis and nutritional treatment of genome instability, we could prevent and control conversion of healthy phenotype to diseases.

Prolonged application of high fluid shear to chondrocytes recapitulates gene expression profiles associated with osteoarthritis

Background

Excessive mechanical loading of articular cartilage producing hydrostatic stress, tensile strain and fluid flow leads to irreversible cartilage erosion and osteoarthritic (OA) disease. Since application of high fluid shear to chondrocytes recapitulates some of the earmarks of OA, we aimed to screen the gene expression profiles of shear-activated chondrocytes and assess potential similarities with OA chondrocytes.

Methodology/Principal Findings

Using a cDNA microarray technology, we screened the differentially-regulated genes in human T/C-28a2 chondrocytes subjected to high fluid shear (20 dyn/cm²) for 48 h and 72 h relative to static controls. Confirmation of the expression patterns of select genes was obtained by qRT-PCR. Using significance analysis of microarrays with a 5% false discovery rate, 71 and 60 non-redundant transcripts were identified to be ≥2-fold up-regulated and ≤0.6-fold down-regulated, respectively, in sheared chondrocytes. Published data sets indicate that 42 of these genes, which are related to extracellular matrix/degradation, cell proliferation/differentiation, inflammation and cell survival/death, are differentially-regulated in OA chondrocytes. In view of the pivotal role of cyclooxygenase-2 (COX-2) in the pathogenesis and/or progression of OA in vivo and regulation of shear-induced inflammation and apoptosis in vitro, we identified a collection of genes that are either up- or down-regulated by shear-induced COX-2. COX-2 and L-prostaglandin D synthase (L-PGDS) induce reactive oxygen species production, and negatively regulate genes of the histone and cell cycle families, which may play a critical role in chondrocyte death.

Conclusions/Significance

Prolonged application of high fluid shear stress to chondrocytes recapitulates gene expression profiles associated with osteoarthritis. Our data suggest a potential link between exposure of chondrocytes/cartilage to abnormal mechanical loading and the pathogenesis/progression of OA.

Cancer-associated p53 tetramerization domain mutants: quantitative analysis reveals a low threshold for tumor suppressor inactivation

The tumor suppressor p53, a 393-amino acid transcription factor, induces cell cycle arrest and apoptosis in response to genotoxic stress. Its inactivation via the mutation of its gene is a key step in tumor progression, and tetramer formation is critical for p53 post-translational modification and its ability to activate or repress the transcription of target genes vital in inhibiting tumor growth. About 50% of human tumors have TP53 gene mutations; most are missense ones that presumably lower the tumor suppressor activity of p53. In this study, we explored the effects of known tumor-derived missense mutations on the stability and oligomeric structure of p53; our comprehensive, quantitative analyses encompassed the tetramerization domain peptides representing 49 such substitutions in humans. Their effects on tetrameric structure were broad, and the stability of the mutant peptides varied widely (ΔT(m) = 4.8 ∼ -46.8 °C). Because formation of a tetrameric structure is critical for protein-protein interactions, DNA binding, and the post-translational modification of p53, a small destabilization of the tetrameric structure could result in dysfunction of tumor suppressor activity. We suggest that the threshold for loss of tumor suppressor activity in terms of the disruption of the tetrameric structure of p53 could be extremely low. However, other properties of the tetramerization domain, such as electrostatic surface potential and its ability to bind partner proteins, also may be important.

Translating genomic analyses into improved management of coronary artery disease

Human genetic variation can modulate pathophysiologic processes that alter susceptibility to complex disease. Recent genomic analyses have sought to identify how common genetic variation alters susceptibility to coronary artery disease (CAD). From genome-wide association studies (GWAS), common genetic variants in several novel chromosomal loci have been associated with CAD. GWAS identified the 9p21 locus as the strongest independent genetic CAD risk factor, along with 11 additional loci that harbor common genetic variants associated with increased CAD risk. A thorough understanding of human genetic variation and genomic analyses will be crucial to understand how GWAS-identified loci increase susceptibility to CAD. This article outlines the relevance of genetic variation in the elucidation of novel CAD risk factors and the clinical utility of genetic variants in the management and treatment of CAD.

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks

BACKGROUND

Alzheimer's disease (AD) is a progressive neurodegenerative disorder involving variations in the transcriptome of many genes. AD does not affect all brain regions simultaneously. Identifying the differences among the affected regions may shed more light onto the disease progression. We developed a novel method involving the differential topology of gene coexpression networks to understand the association among affected regions and disease severity.

METHODS

We analysed microarray data of four regions--entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC) and middle temporal gyrus (MTG) from AD affected and normal subjects. A coexpression network was built for each region and the topological overlap between them was examined. Genes with zero topological overlap between two region-specific networks were used to characterise the differences between the two regions.

RESULTS AND CONCLUSION

Results indicate that MTG shows early AD pathology compared to the other regions. We postulate that if the MTG gets affected later in the disease, post-mortem analyses of individuals with end-stage AD will show signs of early AD in the MTG, while the EC, HIP and PCC will have severe pathology. Such knowledge is useful for data collection in clinical studies where sample selection is a limiting factor as well as highlighting the underlying biology of disease progression.

Preferences for genetic and behavioral health information: the impact of risk factors and disease attributions

Increased availability of genetic risk information may lead the public to give precedence to genetic causation over behavioral/environmental factors, decreasing motivation for behavior change. Few population-based data inform these concerns. We assess the association of family history, behavioral risks, and causal attributions for diseases and the perceived value of pursuing information emphasizing health habits or genes. 1,959 healthy adults completed a survey that assessed behavioral risk factors, family history, causal attributions of eight diseases, and health information preferences. Participants' causal beliefs favored health behaviors over genetics. Interest in behavioral information was higher than in genetic information. As behavioral risk factors increased, inclination toward genetic explanations increased; interest in how health habits affect disease risk decreased. Those at greatest need for behavior change may hold attributions that diminish interest in information for behavior change. Enhancing understanding of gene-environment influences could be explored to increase engagement with health information.

Association of an INSIG2 obesity allele with cardiovascular phenotypes is gender and age dependent

Background

The INSIG2 gene has been implicated in cholesterol metabolism and a single nucleotide polymorphism (SNP) near INSIG2 has been shown to be associated with obesity. We sought to determine the relationship of the INSIG2 SNP to cardiovascular disease (CVD) related phenotypes.

Methods and Results

Nine hundred forty six patients undergoing percutaneous coronary intervention (PCI) in wave 5 of the multicenter NHLBI Dynamic Registry were genotyped using RT-PCR/TaqMan/allelic discrimination for the rs7566605 SNP near the INSIG2 gene. Clinical variables analyzed include demographics, medical history, and procedural details. The prevalence of peripheral vascular disease (PVD) was significantly higher in older men (≥65 years) who were either homozygous or carriers of the obesity/lipid risk allele ("C") compared to non-carriers (odds ratio 3.4, p = 0.013) using a logistic regression model incorporating history of hypercholesterolemia, history of hypertension, cerebrovascular disease, history of diabetes, and BMI. A similar relationship with cerebrovascular disease was found in older (>65) women (odds ratio 3.4, p = 0.013). The INSIG2 SNP was not associated with BMI, nor with other clinical variables.

Conclusion

Age and gender may influence the association of the INSIG2 obesity SNP with PVD and cerebrovascular disease in patients with pre-existing CVD.

Etiological analysis of neurodevelopmental disabilities: single-center eight-year clinical experience in south China

Etiology determination of neurodevelopmental disabilities (NDDs) currently remains a worldwide common challenge on child health. We herein reported the etiology distribution feature in a cohort of 285 Chinese patients with NDDs. Although concrete NDD etiologies in 48.4% of the total patients could not be identified, genetic diseases (with the proportion of 35.8% in the total cases) including inborn errors of metabolism (IEM) and congenital dysmorphic diseases, constituted the commonest etiology category for NDDs in this study. The two key experimental technologies in pediatric metabolomics, gas chromatography-mass spectrometry (GC-MS), and tandem mass spectrometry (MS-MS), proved to be substantially helpful for the exploration of the NDD etiologies in this clinical investigation. The findings in this paper provided latest epidemiologic information on the etiology distribution of NDDs in Chinese, and the syndromic NDDs caused by citrin deficiency and the novel chromosomal karyotype, respectively, further expanded the etiology spectrum of NDDs.

cDNA targets improve whole blood gene expression profiling and enhance detection of pharmocodynamic biomarkers: a quantitative platform analysis

Background

Genome-wide gene expression profiling of whole blood is an attractive method for discovery of biomarkers due to its non-invasiveness, simple clinical site processing and rich biological content. Except for a few successes, this technology has not yet matured enough to reach its full potential of identifying biomarkers useful for clinical prognostic and diagnostic applications or in monitoring patient response to therapeutic intervention. A variety of technical problems have hampered efforts to utilize this technology for identification of biomarkers. One significant hurdle has been the high and variable concentrations of globin transcripts in whole blood total RNA potentially resulting in non-specific probe binding and high background. In this study, we investigated and quantified the power of three whole blood profiling approaches to detect meaningful biological expression patterns.

Methods

To compare and quantify the impact of different mitigation technologies, we used a globin transcript spike-in strategy to synthetically generate a globin-induced signature and then mitigate it with the three different technologies. Biological differences, in globin transcript spiked samples, were modeled by supplementing with either 1% of liver or 1% brain total RNA. In order to demonstrate the biological utility of a robust globin artifact mitigation strategy in biomarker discovery, we treated whole blood ex vivo with suberoylanilide hydroxamic acid (SAHA) and compared the overlap between the obtained signatures and signatures of a known biomarker derived from SAHA-treated cell lines and PBMCs of SAHA-treated patients.

Results

We found cDNA hybridization targets detect at least 20 times more specific differentially expressed signatures (2597) between 1% liver and 1% brain in globin-supplemented samples than the PNA (117) or no treatment (97) method at FDR = 10% and p-value < 3x10-3. In addition, we found that the ex vivo derived gene expression profile was highly concordant with that of the previously identified SAHA pharmacodynamic biomarkers.

Conclusions

We conclude that an amplification method for gene expression profiling employing cDNA targets effectively mitigates the negative impact on data of abundant globin transcripts and greatly improves the ability to identify relevant gene expression based pharmacodynamic biomarkers from whole blood.

Thiopurine S-methyltransferase (TPMT) assessment prior to starting thiopurine drug treatment; a pharmacogenomic test whose time has come

Thiopurine S-methyltransferase (TPMT) is involved in the metabolism of thiopurine drugs. Patients that due to genetic variation lack this enzyme or have lower levels than normal, can be adversely affected if normal doses of thiopurines are prescribed. The evidence for measuring TPMT prior to starting patients on thiopurine drug therapy has been reviewed and the various approaches to establishing a service considered. Until recently clinical guidelines on the use of the TPMT varied by medical specialty. This has now changed, with clear guidance encouraging clinicians to use the TPMT test prior to starting any patient on thiopurine therapy. The TPMT test is the first pharmacogenomic test that has crossed from research to routine use. Several analytical approaches can be taken to assess TPMT status. The use of phenotyping supported with genotyping on selected samples has emerged as the analytical model that has enabled national referral services to be developed to a high level in the UK. The National Health Service now has access to cost-effective and timely TPMT assay services, with two laboratories undertaking the majority of the work at national level and with several local services developing. There appears to be adequate capacity and an appropriate internal market to ensure that TPMT assay services are commensurate with the clinical demand.

Only connect: personal genomics and the future of American medicine

Access to one's own complete genome was unheard of just a few years ago. At present we have a smattering of identifiable complete human genomes, but the coming months and years will undoubtedly bring thousands more. What will this mean for the practice of medicine in the US? No one knows, but given the remarkable drop in the cost of DNA sequencing over the last few years, it seems a safe bet that within the next decade, primary care physicians will order patients' whole genome sequences with no more fanfare than they would a complete blood count. But the challenges of transforming that easily accessible information into cost savings and better health outcomes will be daunting. Obviously, we lack interpretive abilities and phenotypic information commensurate with our skill in amassing DNA sequences. Worse, we have exacerbated these problems by failing to embrace the increasing ubiquity of genomic information, the populace's interest in it, and its relevance to virtually every medical specialty. The success of personal genomics will require a profound cultural shift by every entity with a stake in human health.

Fault diagnosis engineering in molecular signaling networks: an overview and applications in target discovery

Fault diagnosis engineering is a key component of modern industrial facilities and complex systems, and has gone through considerable developments in the past few decades. In this paper, the principles and concepts of molecular fault diagnosis engineering are reviewed. In this area, molecular intracellular networks are considered as complex systems that may fail to function, due to the presence of some faulty molecules. Dysfunction of the system due to the presence of a single or multiple molecules can ultimately lead to the transition from the normal state to the disease state. It is the goal of molecular fault diagnosis engineering to identify the critical components of molecular networks, i.e., those whose dysfunction can interrupt the function of the entire network. The results of the fault analysis of several signaling networks are discussed, and possible connections of the findings with some complex human diseases are examined. Implications of molecular fault diagnosis engineering for target discovery and drug development are outlined as well.

Pharmacogenomics instruction in US and Canadian medical schools: implications for personalized medicine

Aims: To determine the extent of pharmacogenomics instruction at US and Canadian medical schools, characterize perceptions of curricular coverage, identify curricular resources and compare responses with similar studies conducted in US pharmacy schools and British medical schools. Materials & methods: A survey was sent to the pharmacology department chairs of US and Canadian medical schools accredited by the Liaison Committee on Medical Education or the American Osteopathic Association’s Commission on Osteopathic College Accreditation. Data were collected from July 2009 to February 2010. Results: A total of 56% of eligible medical schools responded (90 out of 160). Of these schools, 82% (74 out of 90) incorporated pharmacogenomics into their curriculum. However, only 28% (21 out of 74) had more than 4 h of the required didactic pharmacogenomic coursework, and only 29% (22 out of 75) were planning to increase the number of pharmacogenomic coursework hours in the next 3 years. Pharmacogenomics coursework was most often contained within a required pharmacology course (66%; 49 out of 74) taught in the second professional year (72%; 53 out of 74). A total of 57% (44 out of 77) considered pharmacogenomics instruction at their own school as ‘poor’ or ‘not at all adequate’ while 76% (54 out of 71) considered it ‘poor’ or ‘not at all adequate’ at most medical schools. Conclusion: Most US and Canadian medical schools have begun to incorporate pharmacogenomics material into their curriculum; however, the extent of instruction is less than that of US pharmacy schools. To adequately prepare physicians to practice in the era of personalized medicine, medical schools should be encouraged to incorporate greater pharmacogenomic material in their curriculum.

Axenfeld-Rieger Syndrome Associated with Congenital Glaucoma and Cytochrome P4501B1 Gene Mutations

Developmental anomalies of the ocular anterior chamber angle may lead to an incomplete development of the structures that form the conventional aqueous outflow pathway. Thus, disorders that present with such dysfunction tend to be associated with glaucoma. Among them, Axenfeld-Rieger (ARS) malformation is a rare clinical entity with an estimated prevalence of one in every 200,000 individuals. The changes in eye morphogenesis in ARS are highly penetrant and are associated with 50% risk of development of glaucoma. Mutations in the cytochrome P4501B1 (CYP1B1) gene have been reported to be associated with primary congenital glaucoma and other forms of glaucoma and mutations in pituitary homeobox 2 (PITX2) gene have been identified in ARS in various studies. This case was negative for PITX2 mutations and compound heterozygote for CYP1B1 mutations. Clinical manifestations of this patient include bilateral elevated intraocular pressure (>40 mmHg) with increased corneal diameter (>14 mm) and corneal opacity. Patient also had iridocorneal adhesions, anteriorly displaced Schwalbe line, anterior insertion of iris, broad nasal bridge and protruding umbilicus. This is the first study from north India reporting CYP1B1 mutations in Axenfeld-Rieger syndrome with bilateral buphthalmos and early onset glaucoma. Result of this study supports the role of CYP1B1 as a causative gene in ASD disorders and its role in oculogenesis.

Impact of common variants of PPARG, KCNJ11, TCF7L2, SLC30A8, HHEX, CDKN2A, IGF2BP2, and CDKAL1 on the risk of type 2 diabetes in 5,164 Indians

OBJECTIVE

Common variants in PPARG, KCNJ11, TCF7L2, SLC30A8, HHEX, CDKN2A, IGF2BP2, and CDKAL1 genes have been shown to be associated with type 2 diabetes in European populations by genome-wide association studies. We have studied the association of common variants in these eight genes with type 2 diabetes and related traits in Indians by combining the data from two independent case-control studies.

RESEARCH DESIGN AND METHODS

We genotyped eight single nucleotide polymorphisms (PPARG-rs1801282, KCNJ11-rs5219, TCF7L2-rs7903146, SLC30A8-rs13266634, HHEX-rs1111875, CDKN2A-rs10811661, IGF2BP2-rs4402960, and CDKAL1-rs10946398) in 5,164 unrelated Indians of Indo-European ethnicity, including 2,486 type 2 diabetic patients and 2,678 ethnically matched control subjects.

RESULTS

We confirmed the association of all eight loci with type 2 diabetes with odds ratio (OR) ranging from 1.18 to 1.89 (P = 1.6 x 10(-3) to 4.6 x 10(-34)). The strongest association with the highest effect size was observed for TCF7L2 (OR 1.89 [95% CI 1.71-2.09], P = 4.6 x 10(-34)). We also found significant association of PPARG and TCF7L2 with homeostasis model assessment of beta-cell function (P = 6.9 x 10(-8) and 3 x 10(-4), respectively), which looked consistent with recessive and under-dominant models, respectively.

CONCLUSIONS

Our study replicates the association of well-established common variants with type 2 diabetes in Indians and shows larger effect size for most of them than those reported in Europeans.

Realities and expectations of pharmacogenomics and personalized medicine: impact of translating genetic knowledge into clinical practice

The implementation of genetic data for a better prediction of response to medications and adverse drug reactions is becoming a reality in some clinical fields. However, to be successful, personalized medicine should take advantage of an informational structured framework of genetic, phenotypic and environmental factors in order to provide the healthcare system with useful tools that can optimize the effectiveness of specific treatment. The impact of personalized medicine is potentially enormous, but the results that have so far been gathered are often difficult to translate into clinical practice. In this article we have summarized the most relevant applications of pharmacogenomics on diseases to which they have already been applied and fields in which they are currently emerging. The article provides an overview of the opportunities and shortcomings of the implementation of genetic information into personalized medicine and its full adoption in the clinic. In the second instance, it provides readers from different fields of expertise with an accessible interpretation to the barriers and opportunities in the use/adoption of pharmacogenomic testing between the different clinical areas.

Gene expression profiling in whole blood of patients with coronary artery disease

Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10⁻¹⁶). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease.

Gene expression differences in lungs of mice during secondary immune responses to respiratory syncytial virus infection

Vaccine-induced immunity has been shown to alter the course of a respiratory syncytial virus (RSV) infection both in murine models and in humans. To elucidate which mechanisms underlie the effect of vaccine-induced immunity on the course of RSV infection, transcription profiles in the lungs of RSV-infected mice were examined by microarray analysis. Three models were used: RSV reinfection as a model for natural immunity, RSV challenge after formalin-inactivated RSV vaccination as a model for vaccine-enhanced disease, and RSV challenge following vaccination with recombinant RSV virus lacking the G gene (DeltaG-RSV) as a model for vaccine-induced immunity. Gene transcription profiles, histopathology, and viral loads were analyzed at 1, 2, and 5 days after RSV challenge. On the first 2 days after challenge, all mice displayed an expression pattern in the lung similar of that found in primary infection, showing a strong innate immune response. On day 5 after RSV reinfection or after challenge following DeltaG-RSV vaccination, the innate immune response was waning. In contrast, in mice with vaccine-enhanced disease, the innate immune response 5 days after RSV challenge was still present even though viral replication was diminished. In addition, only in this group was Th2 gene expression induced. These findings support a hypothesis that vaccine-enhanced disease is mediated by prolonged innate immune responses and Th2 polarization in the absence of viral replication.

A comprehensive in silico analysis of the functional and structural impact of SNPs in the IGF1R gene

Insulin-like growth factor 1 receptor (IGF1R) acts as a critical mediator of cell proliferation and survival. Many single nucleotide polymorphisms (SNPs) found in the IGF1R gene have been associated with various diseases, including both breast and prostate cancer. The genetics of these diseases could be better understood by knowing the functions of these SNPs. In this study, we performed a comprehensive analysis of the functional and structural impact of all known SNPs in this gene using publicly available computational prediction tools. Out of a total of 2412 SNPs in IGF1R retrieved from dbSNP, we found 32 nsSNPs, 58 sSNPs, 83 mRNA 3' UTR SNPs, and 2225 intronic SNPs. Among the nsSNPs, a total of six missense nsSNPs were found to be damaging by both a sequence homology-based tool (SIFT) and a structural homology-based method (PolyPhen), and one nonsense nsSNP was found. Further, we modeled mutant proteins and compared the total energy values with the native IGF1R protein, and showed that a mutation from arginine to cysteine at position 1216 (rs61740868) on the surface of the protein caused the greatest impact on stability. Also, the FASTSNP tool suggested that 31 sSNPs and 3 intronic SNPs might affect splicing regulation. Based on our investigation, we report potential candidate SNPs for future studies on IGF1R mutations.

Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets

Background

Chronic inflammatory diseases including inflammatory bowel disease (IBD; Crohn's disease and ulcerative colitis), psoriasis and rheumatoid arthritis (RA) afflict millions of people worldwide, but their pathogenesis is still not well understood.

It is also not well known if distinct changes in gene expression characterize these diseases and if these patterns can discriminate between diseased and control patients and/or stratify the disease. The main focus of our work was the identification of novel markers that overlap among the 3 diseases or discriminate them from each other.

Methods

Diseased (n = 13, n = 15 and n = 12 in IBD, psoriasis and RA respectively) and healthy patients (n = 18) were recruited based on strict inclusion and exclusion criteria; peripheral blood samples were collected by clinicians (30 ml) in Venous Blood Vacuum Collection Tubes containing EDTA and peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. RNA was extracted using Trizol reagent. Gene expression data was obtained using TaqMan Low Density Array (TLDA) containing 96 genes that were selected by an algorithm and the statistical analyses were performed in Prism by using non-parametric Mann-Whitney U test (P-values < 0.05).

Results

Here we show that using a panel of 96 disease associated genes and measuring mRNA expression levels in peripheral blood derived mononuclear cells; we could identify disease-specific gene panels that separate each disease from healthy controls. In addition, a panel of five genes such as ADM, AQP9, CXCL2, IL10 and NAMPT discriminates between all samples from patients with chronic inflammation and healthy controls. We also found genes that stratify the diseases and separate different subtypes or different states of prognosis in each condition.

Conclusions

These findings and the identification of five universal markers of chronic inflammation suggest that these diseases have a common background in pathomechanism, but still can be separated by peripheral blood gene expression. Importantly, the identified genes can be associated with overlapping biological processes including changed inflammatory response. Gene panels based on such markers can play a major role in the development of personalized medicine, in monitoring disease progression and can lead to the identification of new potential drug targets in chronic inflammation.

Pharmacogenetics education: 10 years of experience at Tel Aviv University

Lack of knowledge among clinicians regarding pharmacogenetics is often cited as one of the barriers delaying its clinical uptake, albeit there are many other, more crucial aspects that impede the implementation of pharmacogenetics into routine medical practice. Pharmacogenetics has been incorporated to the MD teaching curriculum at the Tel Aviv University Faculty of Medicine (Tel Aviv, Israel) since 2001 and offered as an elective class for graduate students since 2003. I share here my pharmacogenetics teaching experience over the past decade and look forward to 2020 when – hopefully – the use of pharmacogenetics tools will have become more established in routine clinical care.

Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance

BACKGROUND

Several studies have demonstrated that array comparative genomic hybridisation (CGH) for genome-wide imbalance provides a substantial increase in diagnostic yield for patients traditionally referred for karyotyping by G-banded chromosome analysis. The purpose of this study was to demonstrate the feasibility of and strategies for, the use of array CGH in place of karyotyping for genome imbalance, and to report on the results of the implementation of this approach.

RESULTS

Following a validation period, an oligoarray platform was chosen. In order to minimise costs and increase efficiency, a patient/patient hybridisation strategy was used, and analysis criteria were set to optimise detection of pathogenic imbalance. A customised database application with direct links to a number of online resources was developed to allow efficient management and tracking of patient samples and facilitate interpretation of results. Following introduction into our routine diagnostic service for patients with suspected genome imbalance, array CGH as a follow-on test for patients with normal karyotypes (n = 1245) and as a first-line test (n = 1169) gave imbalance detection rates of 26% and 22% respectively (excluding common, benign variants). At least 89% of the abnormalities detected by first line testing would not have been detected by standard karyotype analysis. The average reporting time for first-line tests was 25 days from receipt of sample.

CONCLUSIONS

Array CGH can be used in a diagnostic service setting in place of G-banded chromosome analysis, providing a more comprehensive and objective test for patients with suspected genome imbalance. The increase in consumable costs can be minimised by employing appropriate hybridisation strategies; the use of robotics and a customised database application to process multiple samples reduces staffing costs and streamlines analysis, interpretation and reporting of results. Array CGH provides a substantially higher diagnostic yield than G-banded chromosome analysis, thereby alleviating the burden of further clinical investigations.

Myocardial gene expression alterations in peripheral blood mononuclear cells of patients with idiopathic dilated cardiomyopathy

AIMS

To assess cardiac gene expression in peripheral blood cells of patients with idiopathic dilated cardiomyopathy (IDCM) and its relationship to echocardiographic left ventricular (LV) function.

METHODS AND RESULTS

A complete echocardiographic study and blood sampling were performed in 65 consecutive stable IDCM patients with LV ejection fraction (LVEF) 31.76 +/- 10.07% and chronic mild to moderate heart failure (NYHA functional class II to III) for > or =9 months. Blood samples from 19 healthy individuals were included for comparison. Transcript levels of myocardin, GATA4, alpha- and beta-myosin heavy chain (MHC), sarcoplasmic reticulum calcium ATPase 2 (SERCA2), and phospholamban were determined by quantitative real-time reverse transcription-polymerase chain reaction. Myocardin (24.88 +/- 4.93 vs. 3.98 +/- 1.12, P = 0.0048) and GATA4 (17.85 +/- 4.85 vs. 0.45 +/- 0.15, P = 0.0069 x 10(-5)) were upregulated in IDCM patients compared with controls, whereas SERCA2 (5.11 +/- 0.42 vs. 8.93 +/- 1.07, P = 0.001) was downregulated. In IDCM patients, myocardin (r = 0.279, P = 0.025), GATA4 (r = 0.314, P = 0.011), beta-MHC (r = 0.444, P=0.0002), and alpha-MHC (r = 0.272, P = 0.034) showed positive correlations, whereas SERCA2 (r = -0.264, P = 0.034) exhibited a negative correlation with LVEF. Patients with elevated LV filling pressures had lower myocardin (15.06 +/- 3.10 vs. 43.12 +/- 12.03, P = 0.048), GATA4 (8.96 +/- 2.17 vs. 34.38 +/- 12.60, P = 0.026), beta-MHC (10.59 +/- 4.05 vs. 16.43 +/- 4.91, P = 0.013), and alpha-MHC (0.27 +/- 0.08 vs. 0.79 +/- 0.20, P = 0.033) and higher SERCA2 (5.65 +/- 0.54 vs. 3.90 +/- 0.61, P = 0.037) levels. Patients with atrial fibrillation (AF) had higher SERCA2 levels compared with sinus rhythm patients (6.75 +/- 0.84 vs. 4.54 +/- 0.45, P = 0.017).

CONCLUSION

Our data indicate that cardiac gene expression alterations in peripheral blood cells of IDCM patients may reflect alterations in LV function, whereas the presence of AF may be associated with increased SERCA2 levels in these patients.

Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record

Large-scale DNA databanks linked to electronic medical record (EMR) systems have been proposed as an approach for rapidly generating large, diverse cohorts for discovery and replication of genotype-phenotype associations. However, the extent to which such resources are capable of delivering on this promise is unknown. We studied whether an EMR-linked DNA biorepository can be used to detect known genotype-phenotype associations for five diseases. Twenty-one SNPs previously implicated as common variants predisposing to atrial fibrillation, Crohn disease, multiple sclerosis, rheumatoid arthritis, or type 2 diabetes were successfully genotyped in 9483 samples accrued over 4 mo into BioVU, the Vanderbilt University Medical Center DNA biobank. Previously reported odds ratios (OR(PR)) ranged from 1.14 to 2.36. For each phenotype, natural language processing techniques and billing-code queries were used to identify cases (n = 70-698) and controls (n = 808-3818) from deidentified health records. Each of the 21 tests of association yielded point estimates in the expected direction. Previous genotype-phenotype associations were replicated (p < 0.05) in 8/14 cases when the OR(PR) was > 1.25, and in 0/7 with lower OR(PR). Statistically significant associations were detected in all analyses that were adequately powered. In each of the five diseases studied, at least one previously reported association was replicated. These data demonstrate that phenotypes representing clinical diagnoses can be extracted from EMR systems, and they support the use of DNA resources coupled to EMR systems as tools for rapid generation of large data sets required for replication of associations found in research cohorts and for discovery in genome science.

Severe cleidocranial dysplasia and hypophosphatasia in a child with microdeletion of the C-terminal region of RUNX2

Cleidocranial dysplasia (CCD) is a rare autosomal dominant skeletal dysplasia due to mutations causing haploinsufficiency of RUNX2, an osteoblast transcription factor specific for bone and cartilage. The classic form of CCD is characterized by delayed closure of the fontanels, hypoplastic or aplastic clavicles and dental anomalies. Clinical reports suggest that a subset of patients with CCD have skeletal changes which mimic hypophosphatasia (HPP). Mutations in RUNX2 are detected in approximately 65% of cases of CCD, and microdeletions occur in 13%. We present clinical and radiological features in a 6-year-old child with severe CCD manifested by absence of the clavicles marked calvarial hypomineralization, osteoporosis and progressive kyphoscoliosis. HPP features included Bowdler spurs, severe osteopenia, and low alkaline phosphatase. Following negative mutation analysis of RUNX2, comparative genomic hybridization (CGH) microarray was performed. The result revealed a microdeletion in RUNX2, disrupting the C-terminal part of the gene.

A FTO variant and risk of acute coronary syndrome

BACKGROUND

The FTO gene plays an important role in the determination of body weight and BMI and it has been suspected of being associated with all-case mortality.

METHODS

We have analyzed the FTO rs17817449 variant in consecutive 1092 male patients with acute coronary syndrome (ACS) and in 1191 randomly selected Caucasian individuals (population controls).

RESULTS

The FTO variant was significantly associated with BMI both in controls (P<0.02) and ACS patients (P<0.01). In both groups, BMI was highest in GG homozygotes and lowest in TT homozygotes. There was a significant difference between the ACS patients and controls in the frequency of the FTO genotype GG (21.4% vs. 15.9%, P<0.005). FTO GG homozygotes had a significantly increased risk of ACS, compared with TT homozygotes which was independent of age and BMI (odds ratio 1.49, 95% confidence interval 1.16-1.93). The odds ratio of ACS patients for the GG genotype remained significant even after the exclusion of diabetics (100 controls and 339 ACS patients), with OR 1.32 (95% CI 1.01-1.72).

CONCLUSIONS

This study provides an evidence of an association between the FTO variant and risk of ACS in Caucasian males.

Two neighboring microdeletions of 5q13.2 in a child with oculo-auriculo-vertebral spectrum

We describe a patient with multiple congenital anomalies, including hemifacial microsomia, asymmetric macrostomia, dysplastic mandible, multiple preauricular tags, atresia of the external auricular canal, and vertebral anomalies, which coincide with oculo-auriculo-vertebral spectrum. G-banding ( approximately 850 band level) showed a normal 46, XY karyotype. A genome-wide screen for copy number variations (CNVs) using single nucleotide polymorphism (SNP) arrays revealed a 1Mb and a 167 kb deletion both on chromosome 5q13.2, which were absent in the parents and in 27 controls. Sixteen genes were located in the deleted region, including BIR1C and OCLN, which are involved in apoptosis. Haploinsufficiency of these genes may be contributing to the phenotype in this patient. To our knowledge, there are no previous reports of this 5q13.2 deletion in a patient with oculo-auriculo-vertebral spectrum.

Distribution of methionine between cells and incubation medium in suspension of rat hepatocytes

Methionine is an essential amino acid involved in many significant intracellular processes. Aberrations in methionine metabolism are associated with a number of complex pathologies. Liver plays a key role in regulation of blood methionine level. Investigation of methionine distribution between hepatocytes and medium is crucial for understanding the mechanisms of this regulation. For the first time, we analyzed the distribution of methionine between hepatocytes and incubation medium using direct measurements of methionine concentrations. Our results revealed a fast and reversible transport of methionine through the cell membrane that provides almost uniform distribution of methionine between hepatocytes and incubation medium. The steady-state ratio between intracellular and extracellular methionine concentrations was established within a few minutes. This ratio was found to be 1.06±0.38, 0.89±0.26, 0.67±0.16 and 0.82±0.06 at methionine concentrations in the medium of 64±19, 152±39, 413±55, and 1,204±104 μmol/L, respectively. The fast and uniform distribution of methionine between hepatocytes and extracellular compartments provides a possibility for effective regulation of blood methionine levels due to methionine metabolism in hepatocytes.

Mitochondrial DNA analysis in primary congenital glaucoma

PURPOSE

To screen mitochondrial DNA (mtDNA) for nucleotide variations in primary congenital glaucoma (PCG).

METHODS

The entire coding region of the mitochondrial genome was amplified by polymerase chain reaction from 35 PCG patients and 40 controls. The full mtDNA genome except the D-loop was sequenced. All sequences were analyzed against mitochondrial reference sequence NC_012920.

RESULTS

MtDNA sequencing revealed a total of 132 and 58 nucleotide variations in PCG and controls, respectively. Of 132 nucleotide variations, 42 (31.81%) were non-synonymous and 82 (62.12%) were synonymous changes, and 8 were in RNA genes. The highest number of nucleotide variations were recorded in complex I followed by complex IV, then complex V. Eight patients (22.85%) had potentially pathogenic mtDNA nucleotide changes and twenty (57.14%) had mtDNA sequence changes associated with elevated reactive oxygen species (ROS) production. Mitochondria not only constitute the energy-generating system in the cell, but are also critically involved in calcium signaling and apoptosis. Mitochondrial function can be affected by mutations in mitochondrial and nuclear DNA, chemical insults to components of the electron transport chain, and a lack of substrates such as oxygen. Mitochondrial dysfunction results in an excessive generation of free radicals and reduced mitochondrial respiration. Developing trabecular meshwork (TM) is deficient in antioxidant enzymes, and thus is more susceptible to oxidative stress (OS) induced damage. Previous studies have documented certain mtDNA sequence variations associated with elevated ROS levels and OS. Three such changes (G10398A, A12308G, and G13708A) were present in our patients. Elevated ROS may cause OS. This OS may further damage mtDNA and may cause decreased mitochondrial respiration. This may lead to impaired growth, development and differentiation of TM and consequently trabecular-dysgenesis, which is a characteristic feature of PCG. OS affects both TM and retinal ganglion cells (RGCs) and may be involved in the neuronal death affecting the optic nerve in glaucoma. There are several studies which point to mitochondrial dysfunction in different types of glaucoma and critically participate in RGC death. Recent studies also implicate mitochondrial dysfunction-associated OS as a risk factor for glaucoma patients. It has been reported that elevated hydrostatic pressure causes breakdown of the mitochondrial network by mitochondrial fission and induce cristae depletion and cellular ATP reduction in differentiated RGC-5 cells in vitro as well as in vivo.

CONCLUSIONS

A total of 44 novel mtDNA variations were identified in this study. Non-synonymous mtDNA variations may adversely affect respiratory chain, impair OXPHOS pathway result in low ATP production, high ROS production and impair growth, development and differentiation of TM lead to trabecular-dysgenesis and consequently RGC's death. Such cases with mtDNA variations and consequent OS may benefit by early diagnosis and prompt management by antioxidant therapy. This may delay OS induced injury to TM and RGCs and hence improve visual prognosis.

Biobank governance in the post-genomic age

Biobank governance is about the regulation of the relationship between individual citizens, society and biobanks. Its key agenda is to link society, citizens and biobanks with respect to issues of consent, privacy, ownership, access and benefit sharing. With the transformation of biobank research from local/national activities towards transnational projects and the emergence of post-genomic medical research, biobanks need to establish novel governance structures. We consider governance solutions that focus on ‘bioethical–theoretical’ arguments to be of only limited value in this context. By contrast, we think the key lies in developing participatory arrangements that are responsive to the views of patients and ‘lay people’, and also operate on a transnational level. The social–political and communicative competence of biobank infrastructures must be improved, thereby assuring the long-term legitimacy and commitment to these often highly expensive projects from a large variety of different stakeholders over the decades.

Evaluation of DOK5 as a susceptibility gene for type 2 diabetes and obesity in North Indian population

BACKGROUND

Type 2 diabetes is a complex metabolic disorder with obesity being a major contributing factor in its development. Susceptibility loci for type 2 diabetes and obesity have been localized on different chromosomal regions by various genome-wide linkage scans. Of these chromosomal regions, 20q13 is one of the strongest linked regions for type 2 diabetes as well as obesity. On 20q13 lies DOK5 that seems to be a strong functional and positional candidate for type 2 diabetes and obesity because of its involvement in insulin signaling and immune responses. Hence, for the first time, we explored DOK5 as a potential type 2 diabetes and obesity susceptibility gene.

METHODS

We sequenced 43 subjects for polymorphisms in functionally relevant regions of DOK5. A total of 10 SNPs that included 5 that were identified by sequencing and 5 additional SNPs from NCBI Variation Database were genotyped in 2,115 participants comprising of 1,073 patients with type 2 diabetes and 1,042 controls of Indo-European ethnicity from North India.

RESULTS

We identified a novel variant in intron 7 referred to as DK176673. We found nominal association of three SNPs-rs6064099 (OR = 0.75, P = 0.019), rs873079 (OR = 0.76, P = 0.036) and DK176673 (OR = 1.55, P = 0.037) with type 2 diabetes among normal-weight subjects [BMI < 23 kg/m2]. The haplotype GGC harboring rs6068916, rs6064099 and rs873079 showed strong association with type 2 diabetes among normal-weight subjects (OR = 1.37, P/Pperm = 5.8 x 10-3/0.037). Association analysis with obesity revealed that rs6064099 is associated with reduced susceptibility for obesity (OR = 0.48, P = 6.8 x 10-3). Also, haplotype GGC conferred increased susceptibility for obesity (OR = 1.27, P/Pperm = 9.0 x 10-3/0.039). Also, rs6064099 was significantly associated with reduced BMI [median(IQR) = 24.0(20.7-27.1) vs 23.9(20.2-26.8) vs 21.8(19.2-24.7) for GG vs GC vs CC, P = 7.0 x 10-3].

CONCLUSIONS

We identified DOK5 as a novel susceptibility gene for obesity and type 2 diabetes in North Indian subjects. Association of DOK5 variants both with obesity and type 2 diabetes suggests that these variants might modulate type 2 diabetes susceptibility through obesity.