Nucleotide methylation and neurocognitive phenotypes

Epigenetic modifications are under increasing scrutiny in research of health and disease states. The most commonly researched epigenetic modification, DNA methylation, is associated with familial forms of dementia, developmental delay syndromes, and disparate cognitive phenotypes. This thesis investigates the relationship between nucleotide methylation and brain disease using three distinct approaches. The majority of the thesis focuses on a genetic variant located within a DNA methyltransferase, DNMT3L R278G, which had previously been associated with intelligence scores in a Scottish birth cohort. Data was utilised from the Oxford Project To Investigate Memory and Aging, specifically the VITACOG cohort of individuals who have mild cognitive impairment and who received B vitamin treatment over a two-year period. It was discovered that minor allele carriers of the R278G variant who received B vitamin treatment showed improved visuospatial associative memory, but diminished verbal semantic memory. These effects were reflected in rates of brain atrophy for these individuals over the course of the two-year study. In silico modelling suggests that the R278G variant disrupts the DNMT3A-3L complex required for de novo methylation. Investigation of genetic variants in methylation genes was by examining next-generation sequencing data from the UK10K project for multiple intellectual disability and autism spectrum disorder cohorts. Thirty DNA and RNA methylation genes were investigated to identify rare coding variants these cohorts. Case-control analysis of these intellectual disability and autism cohorts compared to the TwinsUK general population controls identified four rare missense variants associated with risk for disease. As these variants were found only in individuals with intellectual disability comorbid with psychiatric disease, the findings suggest that these variants contribute to disease risk for a specific clinical population. DNA methylation is a dynamic process where demethylation of 5mC results in the formation of further methylation marks including 5hmC and 5caC. An optimised immunohistochemical method was used to detect 5hmC and 5caC modifications in multiple regions of human brain tissue. Initial characterisation confirmed the near-ubiquitous presence of 5hmC in the human brain. Further, substantial 5caC staining was recorded in the human cerebellum that was absent in all other brain regions, signifying an as-of-yet unidentified relationship between this methylation mark and cerebellar function. Taken together, the different strands of investigation carried out in this thesis have substantiated the importance of nucleotide methylation in dementia progression, intellectual disability, and healthy brain function. Our use of well-curated cohort studies provides the basis for further investigation into methylation patterns and their role in the pathogenesis of multiple brain diseases

Damaging coding variants within kainate receptor channel genes are enriched in individuals with schizophrenia, autism and intellectual disabilities

Schizophrenia (Scz), autism spectrum disorder (ASD) and intellectual disability are common complex neurodevelopmental disorders. Kainate receptors (KARs) are ionotropic glutamate ion channels involved in synaptic plasticity which are modulated by auxiliary NETO proteins. Using UK10K exome sequencing data, we interrogated the coding regions of KAR and NETO genes in individuals with Scz, ASD or intellectual disability and population controls; performed follow-up genetic replication studies; and, conducted in silico and in vitro functional studies. We found an excess of Loss-of-Function and missense variants in individuals with Scz compared with control individuals (p = 1.8 x 10-10), and identified a significant burden of functional variants for Scz (p < 1.6 x 10-11) and ASD (p = 6.9 x 10-18). Single allele associations for 6 damaging missense variants were significantly replicated (p < 5.0 x 10-15) and confirmed GRIK3 S310A as a protective genetic factor. Functional studies demonstrated that three missense variants located within GluK2 and GluK4, GluK2 (K525E) and GluK4 (Y555N, L825W), affect agonist sensitivity and current decay rates. These findings establish that genetic variation in KAR receptor ion channels confers risk for schizophrenia, autism and intellectual disability and provide new genetic and pharmacogenetic biomarkers for neurodevelopmental diseas

Vitamin intake is associated with improved visuospatial and verbal semantic memory in middle-aged individuals

Objectives: Factors maintaining cognitive health are still largely unknown. In particular, the cognitive benefits associated with vitamin intake and vitamin supplementation are disputed. We investigated self-reported vitamin intake and serum vitamin levels with performance in cognitive factors sensitive to dementia progression in two large middle-aged general population cohorts. Methods: Survey data was used to assess regular vitamin intake in 4400 NCDS 1958 and 1177 TwinsUK cohort members, and serum homocysteine and B vitamin levels were measured in 675 individuals from the TwinsUK study. Principal component analysis was applied to cognitive test performance from both cohorts resulting in two dementia-sensitive cognitive factors reflecting visuospatial associative memory and verbal semantic memory. Results: In both cohorts, individuals who reported regular intake of vitamins, particularly B vitamins, showed significantly better performance in visuospatial associative memory and verbal semantic memory (p < 0.001). A significant association was also found between homocysteine levels, vitamin serum concentration and visuospatial associative memory performance which indicated that individuals with high B vitamin and homocysteine levels showed better visuospatial associative memory performance than individuals with low vitamin B levels (p < 0.05). Discussion: The findings demonstrate that early dementia-sensitive cognitive changes can be identified in middle-aged asymptomatic individuals and that regular vitamin intake is associated with improved cognitive performance. These findings reinforce the potential cognitive benefits of regular vitamin intake, which should be considered as an economically viable therapeutic strategy for maintaining cognitive health

Interaction of nutrition and genetics via DNMT3L-mediated DNA methylation determines cognitive decline

Low homocysteine levels and B vitamin treatment are reported to protect against declining cognitive health. Both B vitamins and homocysteine are involved in the production of S-adenosylmethionine, a universal methyl donor essential for the process of DNA methylation. We investigated the effect of a damaging coding variant within the DNA methyltransferase gene, DNMT3L (R278G, A/G) by examining B vitamin intake, homocysteine levels, cognitive performance, and brain atrophy in individuals in the VITACOG study of Mild Cognitive Impairment and the TwinsUK cohort. In the VITACOG study, individuals who received a two- year treatment of B vitamins and carried the G allele, showed better ‘visuospatial associative memory’ and slower rates of brain atrophy. In the TwinsUK study, improved ‘visuospatial associative memory’ was evident in individuals who reported regular vitamin intake and were A/A homozygotes. In silico modelling indicated that R278G disrupts protein interaction between DNMT3L and DNMT3A, affecting the DNMT3A-3L-H3 complex required for DNA methylation. These findings show that vitamin intake and genetic variation within DNMT3L interact to influence cognitive decline

A kainate receptor GluK4 deletion, protective against bipolar disorder, is associated with enhanced cognitive performance across diagnoses in the TwinsUK cohort

Objectives: Cognitive deficits are a common feature of neuropsychiatric disorders. We investigated the relationship between cognitive performance and a deletion allele within GluK4 protective against risk for bipolar disorder, in 1642 individuals from the TwinsUK study. Methods: Cognitive performance was assessed using the National Adult Reading Test, four CANTAB tests (Spatial Working Memory, Paired Associates Learning, Pattern Recognition Memory, and Reaction Time), and two Principal Component Analysis derived factors. Performance in individuals homozygous for the insertion allele was compared to deletion carriers and analysis was adjusted for age of diagnosis, medication and clinical diagnosis. Results: Individuals with the GluK4 protective deletion allele performed significantly better in Spatial Working Memory compared to insertion homozygotes when adjusted for a clinical diagnosis. GluK4 deletion carriers who had a mental health problem (predominately depression) showed better performance in visuo-spatial ability and mental processing speed compared to individuals with mental health problems homozygous for the insertion. Conclusions: These findings of genotype-dependent cognitive enhancement across clinical groups support the potential clinical use of the GluK4 deletion allele in personalized medicine strategies and provide new insight into the relationship between genetic variation and mood disorders

Nucleotide methylation and neurocognitive phenotypes

Epigenetic modifications are under increasing scrutiny in research of health and disease states. The most commonly researched epigenetic modification, DNA methylation, is associated with familial forms of dementia, developmental delay syndromes, and disparate cognitive phenotypes. This thesis investigates the relationship between nucleotide methylation and brain disease using three distinct approaches. The majority of the thesis focuses on a genetic variant located within a DNA methyltransferase, DNMT3L R278G, which had previously been associated with intelligence scores in a Scottish birth cohort. Data was utilised from the Oxford Project To Investigate Memory and Aging, specifically the VITACOG cohort of individuals who have mild cognitive impairment and who received B vitamin treatment over a two-year period. It was discovered that minor allele carriers of the R278G variant who received B vitamin treatment showed improved visuospatial associative memory, but diminished verbal semantic memory. These effects were reflected in rates of brain atrophy for these individuals over the course of the two-year study. In silico modelling suggests that the R278G variant disrupts the DNMT3A-3L complex required for de novo methylation. Investigation of genetic variants in methylation genes was by examining next-generation sequencing data from the UK10K project for multiple intellectual disability and autism spectrum disorder cohorts. Thirty DNA and RNA methylation genes were investigated to identify rare coding variants these cohorts. Case-control analysis of these intellectual disability and autism cohorts compared to the TwinsUK general population controls identified four rare missense variants associated with risk for disease. As these variants were found only in individuals with intellectual disability comorbid with psychiatric disease, the findings suggest that these variants contribute to disease risk for a specific clinical population. DNA methylation is a dynamic process where demethylation of 5mC results in the formation of further methylation marks including 5hmC and 5caC. An optimised immunohistochemical method was used to detect 5hmC and 5caC modifications in multiple regions of human brain tissue. Initial characterisation confirmed the near-ubiquitous presence of 5hmC in the human brain. Further, substantial 5caC staining was recorded in the human cerebellum that was absent in all other brain regions, signifying an as-of-yet unidentified relationship between this methylation mark and cerebellar function. Taken together, the different strands of investigation carried out in this thesis have substantiated the importance of nucleotide methylation in dementia progression, intellectual disability, and healthy brain function. Our use of well-curated cohort studies provides the basis for further investigation into methylation patterns and their role in the pathogenesis of multiple brain diseases