Genome-wide analysis points to roles for extracellular matrix remodeling, the visual cycle, and neuronal development in myopia

Myopia, or nearsightedness, is the most common eye disorder, resulting primarily from excess elongation of the eye. The etiology of myopia, although known to be complex, is poorly understood. Here we report the largest ever genome-wide association study (43,360 participants) on myopia in Europeans. We performed a survival analysis on age of myopia onset and identified 19 significant associations (p < 5e-8), two of which are replications of earlier associations with refractive error. These 19 associations in total explain 2.7% of the variance in myopia age of onset, and point towards a number of different mechanisms behind the development of myopia. One association is in the gene PRSS56, which has previously been linked to abnormally small eyes; one is in a gene that forms part of the extracellular matrix (LAMA2); two are in or near genes involved in the regeneration of 11-cis-retinal (RGR and RDH5); two are near genes known to be involved in the growth and guidance of retinal ganglion cells (ZIC2, SFRP1); and five are in or near genes involved in neuronal signaling or development. These novel findings point towards multiple genetic factors involved in the development of myopia and suggest that complex interactions between extracellular matrix remodeling, neuronal development, and visual signals from the retina may underlie the development of myopia in humans

Neonatal Maternal Deprivation Response and Developmental Changes in Gene Expression Revealed by Hypothalamic Gene Expression Profiling in Mice

Neonatal feeding problems are observed in several genetic diseases including Prader-Willi syndrome (PWS). Later in life, individuals with PWS develop hyperphagia and obesity due to lack of appetite control. We hypothesized that failure to thrive in infancy and later-onset hyperphagia are related and could be due to a defect in the hypothalamus. In this study, we performed gene expression microarray analysis of the hypothalamic response to maternal deprivation in neonatal wild-type and Snord116del mice, a mouse model for PWS in which a cluster of imprinted C/D box snoRNAs is deleted. The neonatal starvation response in both strains was dramatically different from that reported in adult rodents. Genes that are affected by adult starvation showed no expression change in the hypothalamus of 5 day-old pups after 6 hours of maternal deprivation. Unlike in adult rodents, expression levels of Nanos2 and Pdk4 were increased, and those of Pgpep1, Ndp, Brms1l, Mett10d, and Snx1 were decreased after neonatal deprivation. In addition, we compared hypothalamic gene expression profiles at postnatal days 5 and 13 and observed significant developmental changes. Notably, the gene expression profiles of Snord116del deletion mice and wild-type littermates were very similar at all time points and conditions, arguing against a role of Snord116 in feeding regulation in the neonatal period

Efficient Replication of Over 180 Genetic Associations with Self-Reported Medical Data

While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for amassing large amounts of medical information in a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and excluding a set of associations with contradictory published evidence). Altogether we replicated over 180 previously reported associations, including many for type 2 diabetes, prostate cancer, cholesterol levels, and multiple sclerosis. We found significant variation across categories of conditions in the percentage of expected associations that we were able to replicate, which may reflect systematic inflation of the effects in some initial reports, or differences across diseases in the likelihood of misdiagnosis or misreport. We also demonstrated that we could improve replication success by taking advantage of our recontactable cohort, offering more in-depth questions to refine self-reported diagnoses. Our data suggests that online collection of self-reported data in a recontactable cohort may be a viable method for both broad and deep phenotyping in large populations

Normal histone modifications on the inactive X chromosome in ICF and Rett syndrome cells: implications for methyl-CpG binding proteins

BACKGROUND: In mammals, there is evidence suggesting that methyl-CpG binding proteins may play a significant role in histone modification through their association with modification complexes that can deacetylate and/or methylate nucleosomes in the proximity of methylated DNA. We examined this idea for the X chromosome by studying histone modifications on the X chromosome in normal cells and in cells from patients with ICF syndrome (Immune deficiency, Centromeric region instability, and Facial anomalies syndrome). In normal cells the inactive X has characteristic silencing type histone modification patterns and the CpG islands of genes subject to X inactivation are hypermethylated. In ICF cells, however, genes subject to X inactivation are hypomethylated on the inactive X due to mutations in the DNA methyltransferase (DNMT3B) genes. Therefore, if DNA methylation is upstream of histone modification, the histones on the inactive X in ICF cells should not be modified to a silent form. In addition, we determined whether a specific methyl-CpG binding protein, MeCP2, is necessary for the inactive X histone modification pattern by studying Rett syndrome cells which are deficient in MeCP2 function. RESULTS: We show here that the inactive X in ICF cells, which appears to be hypomethylated at all CpG islands, exhibits normal histone modification patterns. In addition, in Rett cells with no functional MeCP2 methyl-CpG binding protein, the inactive X also exhibits normal histone modification patterns. CONCLUSIONS: These data suggest that DNA methylation and the associated methyl-DNA binding proteins may not play a critical role in determining histone modification patterns on the mammalian inactive X chromosome at the sites analyzed

Autosomal recessive neuromuscular disorder in a transgenic line of mice

We have generated a line of transgenic mice that when homozygous for the transgene develop a severe, adult-onset neuromuscular disorder. This mutation is likely the result of the insertional inactivation of an endogenous gene by the transgene integration. The mutant mice have a gait abnormality with stiffened and/or splayed hind legs, and adopt a hunched posture with some exhibiting kyphosis of the thoracic spine. These symptoms progress gradually to severe motor dysfunction. Pathologic changes were found in skeletal muscle and peripheral nerve of the mutant animals. In young mice the muscles from both upper and lower extremities show necrosis and phagocytosis. In older mice, regeneration with muscle fiber splitting, internally located nuclei, and variable fiber size are conspicuous features. Interactions between Schwann cells and axons also appear disrupted in these animals. Although many peripheral axons are well myelinated, the nerve and nerve roots contain very large bundles of juxtaposed, bare axons, reminiscent of Schwann cell-axon interactions in early development. Within these bundles there are axons large enough to be myelinated. The relationship between the pathologic changes in the muscles and nerves is not clear. The phenotypic abnormalities of these animals resemble those that occur in the spontaneous mouse mutants dystrophia muscularis and myodystrophy. Nevertheless, the chromosomal position of the transgene integration site, which was mapped by fluorescent in situ hybridization to chromosome 11, indicates that this disorder represents a new neuromuscular mutation

Mapping of human and murine genes for latent TGF-β binding protein-2 (LTBP2)

A novel gene, isolated because of structural similarities to fibrillin, was called LTBP2 when its 4.6-kb transcript was found to encode a protein sequence related to the latent TGF-β binding protein (LTBP1), which is encoded on human chromosome (Chr) 2, region p12-q22. We have assigned the human and murine LTBP2 loci to regions of conserved synteny on human Chr 11 and mouse Chr 19. By PCR analysis of somatic cell hybrid DNA and fluorescence in situ hybridization, LTBP2 was mapped to human Chr band 11q12 and Ltbp2 to mouse Chr band 19B. Differences between inbred strains were discovered by single-strand conformation analysis of PCR products from the 3′ untranslated region. Analysis of BXD and AKXL recombinant inbred strains have placed Ltbp2 between D19Rp19 and Ly10 on proximal mouse Chr 19.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47013/1/335_2004_Article_BF00350892.pd

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

<p>Abstract</p> <p>Background</p> <p>Marfan syndrome (MFS) is a heritable connective tissue disorder caused by mutations in the fibrillin-1 gene. This syndrome constitutes a significant identifiable subtype of aortic aneurysmal disease, accounting for over 5% of ascending and thoracic aortic aneurysms.</p> <p>Results</p> <p>We used spotted membrane DNA macroarrays to identify genes whose altered expression levels may contribute to the phenotype of the disease. Our analysis of 4132 genes identified a subset with significant expression differences between skin fibroblast cultures from unaffected controls versus cultures from affected individuals with known fibrillin-1 mutations. Subsequently, 10 genes were chosen for validation by quantitative RT-PCR.</p> <p>Conclusion</p> <p>Differential expression of many of the validated genes was associated with MFS samples when an additional group of unaffected and MFS affected subjects were analyzed (p-value < 3 × 10^-6under the null hypothesis that expression levels in cultured fibroblasts are unaffected by MFS status). An unexpected observation was the range of individual gene expression. In unaffected control subjects, expression ranges exceeding 10 fold were seen in many of the genes selected for qRT-PCR validation. The variation in expression in the MFS affected subjects was even greater.</p

Fibrillin genes map to regions of conserved mouse/human syntenyon mouse chromosomes 2 and 18

Fibrillin proteins are major structural components of the 10-nm microfibrils found in elastic and nonelastic connective tissues. Previous studies have mapped the human genes for two fibrillins to chromosome bands 15q21 (FBN1) and 5823-q31 (FBN2) and have demonstrated that FBN1 mutations are associated with Marfan syndrome, while FBN2 is linked to the gene for congenital contractural arachnodactyly. Here, we report the isolation of genomic clones of the corresponding mouse fibrillin genes (Fbn-1 and Fbn-2). By analyzing a mapping panel of mouse &#x00d7; rodent somatic hybrid cell lines, we have assigned the Fbn-1 gene to mouse chromosome 2 and the Fbn-2 gene to mouse chromosome 18. We then sublocalized the fibrillin genes to bands 2F (Fbn-1) and 18D-E1 (Fbn-2) by fluorescence in situ hybridization. These regions are known to exhibit conserved synteny with the regions on human chromosomes 15 and 5 that carry the homologous human fibrillin genes. In addition, the Fbn-1 gene maps in the vicinity of the gene for a connective tissue disorder on mouse chromosome 2 called Tight-skin (Tsk).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30422/1/0000043.pd

Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson's Disease

Although the causes of Parkinson's disease (PD) are thought to be primarily environmental, recent studies suggest that a number of genes influence susceptibility. Using targeted case recruitment and online survey instruments, we conducted the largest case-control genome-wide association study (GWAS) of PD based on a single collection of individuals to date (3,426 cases and 29,624 controls). We discovered two novel, genome-wide significant associations with PD–rs6812193 near SCARB2 (, ) and rs11868035 near SREBF1/RAI1 (, )—both replicated in an independent cohort. We also replicated 20 previously discovered genetic associations (including LRRK2, GBA, SNCA, MAPT, GAK, and the HLA region), providing support for our novel study design. Relying on a recently proposed method based on genome-wide sharing estimates between distantly related individuals, we estimated the heritability of PD to be at least 0.27. Finally, using sparse regression techniques, we constructed predictive models that account for 6%–7% of the total variance in liability and that suggest the presence of true associations just beyond genome-wide significance, as confirmed through both internal and external cross-validation. These results indicate a substantial, but by no means total, contribution of genetics underlying susceptibility to both early-onset and late-onset PD, suggesting that, despite the novel associations discovered here and elsewhere, the majority of the genetic component for Parkinson's disease remains to be discovered