Showing papers by "Simon G. Gregory published in 2009"

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.

Abstract: Background: Autism comprises a spectrum of behavioral and cognitive disturbances of childhood development and is known to be highly heritable. Although numerous approaches have been used to identify genes implicated in the development of autism, less than 10% of autism cases have been attributed to single gene disorders. Methods: We describe the use of high-resolution genome-wide tilepath microarrays and comparative genomic hybridization to identify copy number variants within 119 probands from multiplex autism families. We next carried out DNA methylation analysis by bisulfite sequencing in a proband and his family, expanding this analysis to methylation analysis of peripheral blood and temporal cortex DNA of autism cases and matched controls from independent datasets. We also assessed oxytocin receptor (OXTR) gene expression within the temporal cortex tissue by quantitative real-time polymerase chain reaction (PCR). Results: Our analysis revealed a genomic deletion containing the oxytocin receptor gene, OXTR (MIM accession no.: 167055), previously implicated in autism, was present in an autism proband and his mother who exhibits symptoms of obsessive-compulsive disorder. The proband's affected sibling did not harbor this deletion but instead may exhibit epigenetic misregulation of this gene through aberrant gene silencing by DNA methylation. Further DNA methylation analysis of the CpG island known to regulate OXTR expression identified several CpG dinucleotides that show

Neuropeptide Y gene polymorphisms confer risk of early-onset atherosclerosis.

Abstract: Neuropeptide Y (NPY) is a strong candidate gene for coronary artery disease (CAD). We have previously identified genetic linkage to familial CAD in the genomic region of NPY. We performed follow-up genetic, biostatistical, and functional analysis of NPY in early-onset CAD. In familial CAD (GENECARD, N = 420 families), we found increased microsatellite linkage to chromosome 7p14 (OSA LOD = 4.2, p = 0.004) in 97 earliest age-of-onset families. Tagged NPY SNPs demonstrated linkage to CAD of a 6-SNP block (LOD = 1.58-2.72), family-based association of this block with CAD (p = 0.02), and stronger linkage to CAD in the earliest age-of-onset families. Association of this 6-SNP block with CAD was validated in: (a) 556 non-familial early-onset CAD cases and 256 controls (OR 1.46-1.65, p = 0.01-0.05), showing stronger association in youngest cases (OR 1.84-2.20, p = 0.0004-0.09); and (b) GENECARD probands versus non-familial controls (OR 1.79-2.06, p = 0.003-0.02). A promoter SNP (rs16147) within this 6-SNP block was associated with higher plasma NPY levels (p = 0.04). To assess a causal role of NPY in atherosclerosis, we applied the NPY1-receptor-antagonist BIBP-3226 adventitially to endothelium-denuded carotid arteries of apolipoprotein E-deficient mice; treatment reduced atherosclerotic neointimal area by 50% (p = 0.03). Thus, NPY variants associate with atherosclerosis in two independent datasets (with strong age-of-onset effects) and show allele-specific expression with NPY levels, while NPY receptor antagonism reduces atherosclerosis in mice. We conclude that NPY contributes to atherosclerosis pathogenesis.

Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis.

Abstract: Leukotrienes are arachidonic acid derivatives long known for their inflammatory properties and their involvement with a number of human diseases, most particularly asthma. Recently, leukotriene-based inflammation has also been shown to play an important role in atherosclerosis: ALOX5AP and LTA4H, both genes in the leukotriene biosynthesis pathway, have individually been shown to be associated with various cardiovascular disease (CVD) phenotypes. To assess the role of the leukotriene pathway in CVD pathogenesis, we performed genetic association studies of ALOX5AP and LTA4H in a family based study of early onset coronary artery disease (EOCAD) (GENECARD, 1,101 families) and in a non-familial dataset of EOCAD (CATHGEN, 656 cases and 405 controls). We found weak to moderate association between single nucleotide polymorphisms (SNPs) in ALOX5AP and LTA4H with EOCAD. The previously reported four-SNP haplotype (HapA) in ALOX5AP showed association with EOCAD in CATHGEN (P = 0.02), while controlling for age, race and CVD risk factors. HapK, the previously reported ten-SNP haplotype in LTA4H was associated with EOCAD in CATHGEN (P = 0.04). Another previously reported four-SNP haplotype in ALOX5AP (HapB) was not significant in our sample (P = 0.39). The overall lack of (or weak) association of single SNPs as compared with the haplotype results demonstrates the need for analyzing multiple SNPs within each gene in such studies. Interestingly, we detected an association of SNPs in ALOX5 (P < 0.05), the target of ALOX5AP, with CVD. Using a pathway-based approach, we also detected statistical evidence for interactions among ALOX5, ALOX5AP and LTA4H using RNA expression data from a collection of freshly harvested human aortas with varying degrees of atherosclerosis. The GENECARD families did not demonstrate evidence for linkage or association with ALOX5, ALOX5AP or LTA4H. Our results support a modest role for the leukotriene pathway in atherosclerosis pathogenesis, reveal important genomic interactions within the pathway, and suggest the importance of using pathway-based modeling for evaluating the genomics of atherosclerosis susceptibility.

Genome-wide Linkage Scan in Fuchs Endothelial Corneal Dystrophy

Abstract: Fuchs endothelial corneal dystrophy (FECD) is a common progressive disorder of the corneal endothelium that becomes symptomatic with aging.1 It appears as guttae progressively form on Descemet’s membrane along with corneal edema and stromal clouding leading to impaired vision. FECD has been one of the main indications for corneal transplantation in many countries, including the United States,2 with the main treatment modality being a penetrating keratoplasty, until the advent of various types of endothelial keratoplasty. FECD typically becomes symptomatic during the fifth or sixth decade of life and predominantly affects women, who comprise three of four affected individuals.3 The pathogenesis of FECD remains unknown, but the corneal endothelial cells are arrested in the G1 phase of the cell cycle and do not undergo mitosis.4 During a normal state, the cornea is kept in a state of deturgescence by endothelial cell Na+/K+ ATPases that remove fluid from the stroma and by tight junctions between endothelial cells that limit fluid entry.1 This maintains the stroma’s ordered arrangement of collagen and with it, the transparency of the cornea. In states of low endothelial cell density, the loss of the endothelium’s barrier function causes corneal edema. Damage to the endothelial cell layer therefore results in irreparable tissue damage that necessitates endothelial or penetrating keratoplasty.1 It is well established that FECD can affect multiple family members and that several genetic factors underlie the development of the disorder.5 However, the use of genetic approaches to identify the genes underlying the development of FECD is complicated by the late onset of the disease, so that parents and even siblings of the proband are often unavailable for study. In addition, younger individuals in a family may not clinically exhibit the disease because they may not be old enough to manifest the disorder. The first progress toward identifying gene mutations associated with familial FECD was provided by a rare subtype of FECD characterized by onset in early childhood. Early-onset FECD was found to be caused by a missense mutation, Q455K, in the COL8A2 gene (MIM: 120252), which encodes for the α2 subtype of collagen VIII, a major component of Descemet’s membrane. Three other missense mutations within COL8A2—R155Q, R304Q, and R434H—were found in patients with late-onset FECD, but their role remains uncertain, as R155Q has the same frequency in normal controls.6 Another mutation in COL8A2, L450W, that is believed to be pathogenic has been detected in a family with atypical FECD.7,8 Although mutations in COL8A2 have been linked to early-onset FECD, to date, mutations in the COL8A2 gene have not been associated with the much more common late-onset FECD.9–11 Heterozygous single nucleotide polymorphisms in the SLC4A11 gene on chromosome 20 (20p13) have recently been detected in four Chinese and Indian patients with the common phenotype of FECD,12 but they contribute to only ∼5% of the genetic burden of the disease. Family-based studies have mapped late-onset FECD susceptibility loci to 13ptel-13q12.1313 and 18q21.2-q21.32,14 in one and three large multigenerational FECD families, respectively. However, to date, there have been no FECD genetic linkage studies involving a large number of affected families. In this study, we performed the first whole-genome linkage scan for late-onset FECD in 22 families (linkage panel IV; Illumina, Inc., San Diego, CA).

A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease

Abstract: Transcription factors are key mediators of human complex disease processes. Identifying the target genes of transcription factors will increase our understanding of the biological network leading to disease risk. The prediction of transcription factor binding sites (TFBSs) is one method to identify these target genes; however, current prediction methods need improvement. We chose the transcription factor upstream stimulatory factor l (USF1) to evaluate the performance of our novel TFBS prediction method because of its known genetic association with coronary artery disease (CAD) and the recent availability of USF1 chromatin immunoprecipitation microarray (ChIP-chip) results. The specific goals of our study were to develop a novel and accurate genome-scale method for predicting USF1 binding sites and associated target genes to aid in the study of CAD. Previously published USF1 ChIP-chip data for 1 per cent of the genome were used to develop and evaluate several kernel logistic regression prediction models. A combination of genomic features (phylogenetic conservation, regulatory potential, presence of a CpG island and DNaseI hypersensitivity), as well as position weight matrix (PWM) scores, were used as variables for these models. Our most accurate predictor achieved an area under the receiver operator characteristic curve of 0.827 during cross-validation experiments, significantly outperforming standard PWM-based prediction methods. When applied to the whole human genome, we predicted 24,010 USF1 binding sites within 5 kilobases upstream of the transcription start site of 9,721 genes. These predictions included 16 of 20 genes with strong evidence of USF1 regulation. Finally, in the spirit of genomic convergence, we integrated independent experimental CAD data with these USF1 binding site prediction results to develop a prioritised set of candidate genes for future CAD studies. We have shown that our novel prediction method, which employs genomic features related to the presence of regulatory elements, enables more accurate and efficient prediction of USF1 binding sites. This method can be extended to other transcription factors identified in human disease studies to help further our understanding of the biology of complex disease.

Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis

Abstract: Multiple sclerosis (MS) is a debilitating neuroimmunological and neurodegenerative disease affecting >4,00,000 individuals in the United States. Population and family-based studies have suggested that there is a strong genetic component. Numerous genomic linkage screens have identified regions of interest for MS loci. Our own second-generation genome-wide linkage study identified a handful of non-major histocompatibility complex regions with suggestive linkage. Several of these regions were further examined using single-nucleotide polymorphisms (SNPs) with average spacing between SNPs of approximately 1.0 Mb in a dataset of 173 multiplex families. The results of that study provided further evidence for the involvement of the chromosome 1q43 region. This region is of particular interest given linkage evidence in studies of other autoimmune and inflammatory diseases including rheumatoid arthritis and systemic lupus erythematosus. In this follow-up study, we saturated the region with approximately 700 SNPs (average spacing of 10 kb per SNP) in search of disease-associated variation within this region. We found preliminary evidence to suggest that common variation within the RGS7 locus may be involved in disease susceptibility.