23 research outputs found
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Genetic Analysis of Macular Telangiectasia
Macular telangiectasia type 2, or MacTel, is an adult onset retinal disease that causes progressive loss of central vision, usually beginning between the 5th and 7th decades of life. Macular degenerative diseases comprise a large portion of the blinding diseases affecting people over the age of 50. The collective burden of vision loss and low vision includes the impact on patients in loss of independence and decline of self-reported quality of life, as well as significant resource allocation in medical and supportive care. There are no cures for macular diseases; currently available treatments may slow the progression in some cases, but patients remain at risk of losing their eyesight and the independence that vision affords. While macular telangiectasia is not as prevalent as other macular degenerative diseases, such as age-related macular degeneration, elucidating the causes of MacTel may reveal mechanisms that are common to other macular diseases, providing clues to guide research into possible treatment targets. In this work, I have assembled the first cohort of MacTel patients and their family members in collaboration with the MacTel Project, an international consortium of researchers and clinicians dedicated to studying this disease. I have identified and analyzed families with multiple affected relatives in which MacTel appears to be an inherited disease. The goal of this work has been to identify a genetic cause for the disease in these families. To that end, I used genotyping data from approximately 900,000 single nucleotide polymorphism per individual to create sets of genetic markers for linkage analysis. I analyzed these markers using two-point and multipoint linkage algorithms to search for a region of the genome that was inherited in conjunction with the phenotype more often than would be expected by chance alone, with the goal of finding a causative genetic variant. This analysis resulted in the identification of a region of chromosome 1 spanning approximately 15 million bases that is significantly linked to the MacTel phenotype. I analyzed recombination breakpoints in this region, as well as across the genome, to map chromosomal segments inherited identical by descent in siblings that express the MacTel phenotype. This approach provided a profile for each set of siblings of regions of the genome incompatible with inherited genetic disease by virtue of the fact that no alleles were shared identical by descent. I then compared these regions across families under the hypothesis that if MacTel is caused by the same gene in all families, the chromosomal region harboring a causative variant would fail to be excluded in any family. This analysis excluded much of the genome and refined the boundaries of the linkage interval on chromosome 1, but did not appreciably narrow the region of interest. In parallel with analysis of linkage in families, I sequenced 40 genes of interest as possible functional candidates, using Sanger sequencing in the probands of families with multiple affected relatives. I selected candidate genes based on gene function and expression, choosing genes with a plausible connection to the phenotype based on information in the literature. Thirteen of these genes were selected based on their location in the region of the maximum linkage score. I was unable to identify any variant that was consistent with being a causative variant for inherited MacTel
Analysis of candidate genes for macular telangiectasia type 2
Purpose: To find the gene(s) responsible for macular telangiectasia type 2 (MacTel) by a candidate-gene screening approach.Methods: Candidate genes were selected based on the following criteria: those known to cause or be associated with diseases with phenotypes similar to MacTel, genes with known function in the retinal vasculature or macular pigment transport, genes that emerged from expression microarray data from mouse models designed to mimic MacTel phenotype characteristics, and genes expressed in the retina that are also related to diabetes or hypertension, which have increased prevalence in MacTel patients. Probands from eight families with at least two affected individuals were screened by direct sequencing of 27 candidate genes. Identified nonsynonymous variants were analyzed to determine whether they cosegregate with the disease in families. Allele frequencies were determined by TaqMan analysis of the large MacTel and control cohorts.Results: We identified 23 nonsynonymous variants in 27 candidate genes in at least one proband. Of these, eight were known single nucleotide polymorphisms (SNPs) with allele frequencies of >0.05; these variants were excluded from further analyses. Three previously unidentified missense variants, three missense variants with reported disease association, and five rare variants were analyzed for segregation and/or allele frequencies. No variant fulfilled the criteria of being causal for MacTel. A missense mutation, p.Pro33Ser in frizzled homolog (Drosophila) 4 (FZD4), previously suggested as a disease-causing variant in familial exudative vitreoretinopathy, was determined to be a rare benign polymorphism.Conclusions: We have ruled out the exons and flanking intronic regions in 27 candidate genes as harboring causal mutations for MacTel
Gene-Wise Association of Variants in Four Lysosomal Storage Disorder Genes in Neuropathologically Confirmed Lewy Body Disease
Objective
Variants in GBA are associated with Lewy Body (LB) pathology. We investigated whether variants in other lysosomal storage disorder (LSD) genes also contribute to disease pathogenesis.
Methods
We performed a genetic analysis of four LSD genes including GBA, HEXA, SMPD1, and MCOLN1 in 231 brain autopsies. Brain autopsies included neuropathologically defined LBD without Alzheimer Disease (AD) changes (n = 59), AD without significant LB pathology (n = 71), Alzheimer disease and lewy body variant (ADLBV) (n = 68), and control brains without LB or AD neuropathology (n = 33). Sequencing of HEXA, SMPD1, MCOLN1 and GBA followed by ‘gene wise’ genetic association analysis was performed. To determine the functional effect, a biochemical analysis of GBA in a subset of brains was also performed. GCase activity was measured in a subset of brain samples (n = 64) that included LBD brains, with or without GBA mutations, and control brains. A lipidomic analysis was also performed in brain autopsies (n = 67) which included LBD (n = 34), ADLBV (n = 3), AD (n = 4), PD (n = 9) and control brains (n = 17), comparing GBA mutation carriers to non-carriers.
Results
In a ‘gene-wise’ analysis, variants in GBA, SMPD1 and MCOLN1 were significantly associated with LB pathology (p range: 0.03–4.14 x10-5). Overall, the mean levels of GCase activity were significantly lower in GBA mutation carriers compared to non-carriers (p<0.001). A significant increase and accumulation of several species for the lipid classes, ceramides and sphingolipids, was observed in LBD brains carrying GBA mutations compared to controls (p range: p<0.05-p<0.01).
Interpretation
Our study indicates that variants in GBA, SMPD1 and MCOLN1 are associated with LB pathology. Biochemical data comparing GBA mutation carrier to non-carriers support these findings, which have important implications for biomarker development and therapeutic strategies
Untangling the Manganese-α-synuclein Web
Neurodegenerative diseases affect a significant portion of the aging population. Several lines of evidence suggest a positive association between environmental exposures, which are common and cumulative in a lifetime, and development of neurodegenerative diseases. Environmental or occupational exposure to manganese (Mn) has been implicated in neurodegeneration due to its ability to induce mitochondrial dysfunction, oxidative stress and α-synuclein (α-Syn) aggregation. The role of the α-Syn protein vis-a-vis Mn is controversial, as it seemingly plays a duplicitous role in neuroprotection and neurodegeneration. α-Syn has low affinity for Mn, however an indirect interaction cannot be ruled out. In this review we will examine the current knowledge surrounding the interaction of α-Syn and Mn in neurodegenerative process
Four families with multiple relatives affected with MacTel.
<p>Black shaded symbols represent affected; dark gray shading represents possibly affected; light gray shading represents probably not affected; unshaded symbols represent unaffected or unexamined relatives. Numbered individuals were enrolled and examined.</p
LOD, HLOD, and NPL scores for chromosome 1 in 17 families.
<p>The 1-LOD support interval around the maximum LOD of 3.45 is shaded in gray.</p
Segregating haplotypes and IBD allele sharing.
<p>Putative risk haplotypes (shown in red and designated with a star) are shown for two families where the parents in both families were genotyped and the phased haplotypes were resolved. Allele sharing identical by descent is shown for six additional families (five ASPs and one affected sibling trio). Phased haplotypes were not resolved in families where parental genotypes were missing. Regions with one allele shared IBD are shown in dark blue; regions with two alleles shared IBD are shown in purple.</p
NPL scores indicating IBD allele sharing on chromosome 1 in 8 families.
<p>Recombinations were mapped by determining IBD allele sharing in 8 families. Regions where at least one allele is shared IBD are marked in green; regions excluded by virtue of no alleles shared IBD are marked in red. Gray bars represent the 1-LOD support interval. For ASPs with parental genotypes missing, 0.3 = 2 alleles shared, 0 = 1 allele shared, −0.3 = 0 alleles shared. For ASPs with parents genotyped and one parent affected, 0.3 = 2 alleles shared, 0.12 = 1 allele shared from the affected parent, −0.12 = 1 allele shared from the unaffected parent, −0.3 = 0 alleles shared. For the affected sib trio, 0.6 = 2 alleles shared between all sibs, 0.3 = 1 allele shared between all sibs, and −.12 = 0 alleles shared between all sibs.</p