GLS loss of function causes autosomal recessive spastic ataxia and optic atrophy.

We describe a consanguineous family in which two brothers were affected by childhood onset spastic ataxia with optic atrophy and loss of motor and language skills. Through a combination of homozygosity mapping and whole-genome sequencing, we identified a homozygous copy number variant in GLS as the cause. The duplication leads to complete knockout of GLS expression. GLS encodes the brain- and kidney-specific enzyme glutaminase, which hydrolyzes glutamine for the production of glutamate, the most abundant central nervous system neurotransmitter. This is the first report implicating GLS loss of function in human disease

The Friedreich ataxia GAA repeat expansion mutation induces comparable epigenetic changes in human and transgenic mouse brain and heart tissues

Friedreich ataxia (FRDA) is caused by a homozygous GAA repeat expansion mutation within intron 1 of the FXN gene, leading to reduced expression of frataxin protein. Evidence suggests that the mutation may induce epigenetic changes and heterochromatin formation, thereby impeding gene transcription. In particular, studies using FRDA patient blood and lymphoblastoid cell lines have detected increased DNA methylation of specific CpG sites upstream of the GAA repeat and histone modifications in regions flanking the GAA repeat. In this report we show that such epigenetic changes are also present in FRDA patient brain, cerebellum and heart tissues, the primary affected systems of the disorder. Bisulfite sequence analysis of the FXN flanking GAA regions reveals a shift in the FRDA DNA methylation profile, with upstream CpG sites becoming consistently hypermethylated and downstream CpG sites becoming consistently hypomethylated. We also identify differential DNA methylation at three specific CpG sites within the FXN promoter and one CpG site within exon 1. Furthermore, we show by chromatin immunoprecipitation (ChIP) analysis that there is overall decreased histone H3K9 acetylation together with increased H3K9 methylation of FRDA brain tissue. Further studies of brain, cerebellum and heart tissues from our GAA repeat expansion-containing FRDA YAC transgenic mice reveal comparable epigenetic changes to those detected in FRDA patient tissue. We have thus developed a mouse model that will be a valuable resource for future therapeutic studies targeting epigenetic modifications of the FXN gene to increase frataxin expression

Increased brain expression of GPNMB is associated with genome wide significant risk for Parkinson's disease on chromosome 7p15.3

Genome wide association studies (GWAS) for Parkinson's disease (PD) have previously revealed a significant association with a locus on chromosome 7p15.3, initially designated as the glycoprotein non-metastatic melanoma protein B (GPNMB) locus. In this study, the functional consequences of this association on expression were explored in depth by integrating different expression quantitative trait locus (eQTL) datasets (Braineac, CAGEseq, GTEx, and Phenotype-Genotype Integrator (PheGenI)). Top risk SNP rs199347 eQTLs demonstrated increased expressions of GPNMB, KLHL7, and NUPL2 with the major allele (AA) in brain, with most significant eQTLs in cortical regions, followed by putamen. In addition, decreased expression of the antisense RNA KLHL7-AS1 was observed in GTEx. Furthermore, rs199347 is an eQTL with long non-coding RNA (AC005082.12) in human tissues other than brain. Interestingly, transcript-specific eQTLs in immune-related tissues (spleen and lymphoblastoid cells) for NUPL2 and KLHL7-AS1 were observed, which suggests a complex functional role of this eQTL in specific tissues, cell types at specific time points. Significantly increased expression of GPNMB linked to rs199347 was consistent across all datasets, and taken in combination with the risk SNP being located within the GPNMB gene, these results suggest that increased expression of GPNMB is the causative link explaining the association of this locus with PD. However, other transcript eQTLs and subsequent functional roles cannot be excluded. This highlights the importance of further investigations to understand the functional interactions between the coding genes, antisense, and non-coding RNA species considering the tissue and cell-type specificity to understand the underlying biological mechanisms in PD

Quantitative investigations of FXN transcription and epigenetic modifications, including histone acetylation and methylation, in FRDA human and mouse tissues

This thesis was submitted for the degree of Master of Philosophy and awarded by Brunel University.Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder characterized by progressive gait and, limb ataxia, cardiomayopathy, diabetes mellitus, optic atrophy and hearing loss. It is most often caused by homozygous expanded (GAA)∙(TTC)n repeats within intron 1 of the FXN gene, resulting in severely reduced levels of frataxin protein. The exact mechanisms of how the expanded (GAA)∙(TTC)n repeats reduce FXN transcription are not fully understood. However, many studies have suggested that the expanded repeat may induce epigenetic modifications that cause the FXN transcription inhibition to occur. In the past few years, epigenetic modifications have been given considerable attention as an important mechanism that is contributing to the aetiology of FRDA. This thesis investigated histone acetylation and methylation in three different regions of the FXN gene: FXN promoter, upstream GAA and downstream GAA, using chromatin immunoprecipitation (ChIP) and quantitative reverse transcriptase PCR (qRT-PCR) of the human and transgenic mouse brain tissues. Furthermore, the frataxin mRNA levels were investigated in autopsied brain tissues from an FRDA patient and FXN transgenic mouse brain, heart and liver tissues. In addition, a preliminary study that investigated the effect of a histone deacetylase inhibitor (HDACi) on FXN transcription and histone modifications (acetylation) of transgenic mouse brain, heart and liver tissues was conducted. Results showed an overall significant decrease in the acetylation pattern of H3K9ac and H4K16ac residues in all three regions within FXN gene. Moreover, a significant increase in the di- and trimethylation pattern of the H3K9me2 and the H3K9me3 residues was identified in all three regions of the FXN gene. The results were comparable between the FRDA patient and transgenic mouse (YG8, YG22) brain tissues. The FXN mRNA levels showed a significant decrease in all transgenic mouse brain, heart and liver tissues, which is comparable with the FXN mRNA level of the FRDA patient brain and heart tissues.Results for the preliminary HDACi study showed an approximate 20-30 % increase in the FXN mRNA level in different transgenic mouse tissues after 3 days intake at 150mg/kg dose. In addition, there was an increase in the acetylation pattern of the H3K9ac and the H4K12ac in the HDACi treated transgenic mouse brain tissues. These studies will aid the understanding of FXN epigenetic modifications and their contribution to FRDA disease; this is an exciting challenge leading to a new effective FRDA therapeutic pathway

Genetic evidence for a pathogenic role for the vitamin D3 metabolizing enzyme <i>CYP24A1</i> in multiple sclerosis

Background: Multiple sclerosis (MS) is a common disease of the central nervous system and a major cause of disability amongst young adults. Genome-wide association studies have identified many novel susceptibility loci including rs2248359. We hypothesized that genotypes of this locus could increase the risk of MS by regulating expression of neighboring gene, CYP24A1 which encodes the enzyme responsible for initiating degradation of 1,25-dihydroxyvitamin D3. Methods: We investigated this hypothesis using paired gene expression and genotyping data from three independent datasets of neurologically healthy adults of European descent. The UK Brain Expression Consortium (UKBEC) consists of post-mortem samples across 10 brain regions originating from 134 individuals (1231 samples total). The North American Brain Expression Consortium (NABEC) consists of cerebellum and frontal cortex samples from 304 individuals (605 samples total). The brain dataset from Heinzen and colleagues consists of prefrontal cortex samples from 93 individuals. Additionally, we used gene network analysis to analyze UKBEC expression data to understand CYP24A1 function in human brain. Findings: The risk allele, rs2248359-C, is strongly associated with increased expression of CYP24A1 in frontal cortex (p-value=1.45×10−13), but not white matter. This association was replicated using data from NABEC (p-value=7.2×10−6) and Heinzen and colleagues (p-value=1.2×10−4). Network analysis shows a significant enrichment of terms related to immune response in eight out of the 10 brain regions. Interpretation: The known MS risk allele rs2248359-C increases CYP24A1 expression in human brain providing a genetic link between MS and vitamin D metabolism, and predicting that the physiologically active form of vitamin D3 is protective. Vitamin D3's involvement in MS may relate to its immunomodulatory functions in human brain. Finding: Medical Research Council UK; King Faisal Specialist Hospital and Research Centre, Saudi Arabia; Intramural Research Program of the National Institute on Aging, National Institutes of Health, USA

Increased brain expression of GPNMB is associated with genome wide significant risk for Parkinson's disease on chromosome 7p15.3

Genome wide association studies (GWAS) for Parkinson's disease (PD) have previously revealed a significant association with a locus on chromosome 7p15.3, initially designated as the glycoprotein non-metastatic melanoma protein B (GPNMB) locus. In this study, the functional consequences of this association on expression were explored in depth by integrating different expression quantitative trait locus (eQTL) datasets (Braineac, CAGEseq, GTEx, and Phenotype-Genotype Integrator (PheGenI)). Top risk SNP rs199347 eQTLs demonstrated increased expressions of GPNMB, KLHL7, and NUPL2 with the major allele (AA) in brain, with most significant eQTLs in cortical regions, followed by putamen. In addition, decreased expression of the antisense RNA KLHL7-AS1 was observed in GTEx. Furthermore, rs199347 is an eQTL with long non-coding RNA (AC005082.12) in human tissues other than brain. Interestingly, transcript-specific eQTLs in immune-related tissues (spleen and lymphoblastoid cells) for NUPL2 and KLHL7-AS1 were observed, which suggests a complex functional role of this eQTL in specific tissues, cell types at specific time points. Significantly increased expression of GPNMB linked to rs199347 was consistent across all datasets, and taken in combination with the risk SNP being located within the GPNMB gene, these results suggest that increased expression of GPNMB is the causative link explaining the association of this locus with PD. However, other transcript eQTLs and subsequent functional roles cannot be excluded. This highlights the importance of further investigations to understand the functional interactions between the coding genes, antisense, and non-coding RNA species considering the tissue and cell-type specificity to understand the underlying biological mechanisms in PD

Mutations in the autoregulatory domain of β-tubulin 4a cause hereditary dystonia.

Dystonia type 4 (DYT4) was first described in a large family from Heacham in Norfolk with an autosomal dominantly inherited whispering dysphonia, generalized dystonia, and a characteristic hobby horse ataxic gait. We carried out a genetic linkage analysis in the extended DYT4 family that spanned 7 generations from England and Australia, revealing a single LOD score peak of 6.33 on chromosome 19p13.12-13. Exome sequencing in 2 cousins identified a single cosegregating mutation (p.R2G) in the β-tubulin 4a (TUBB4a) gene that was absent in a large number of controls. The mutation is highly conserved in the β-tubulin autoregulatory MREI (methionine-arginine-glutamic acid-isoleucine) domain, highly expressed in the central nervous system, and extensive in vitro work has previously demonstrated that substitutions at residue 2, specifically R2G, disrupt the autoregulatory capability of the wild-type β-tubulin peptide, affirming the role of the cytoskeleton in dystonia pathogenesis

Comparison Between Expression Microarrays and RNA-Sequencing Using UKBEC Dataset Identified a trans-eQTL Associated with MPZ Gene in Substantia Nigra

In recent years, the advantages of RNA-sequencing (RNA-Seq) have made it the platform of choice for measuring gene expression over traditional microarrays. However, RNA-Seq comes with bioinformatical challenges and higher computational costs. Therefore, this study set out to assess whether the increased depth of transcriptomic information facilitated by RNA-Seq is worth the increased computation over microarrays, specifically at three levels: absolute expression levels, differentially expressed genes identification, and expression QTL (eQTL) mapping in regions of the human brain. Using the United Kingdom Brain Expression Consortium (UKBEC) dataset, there is high agreement of gene expression levels measured by microarrays and RNA-seq when quantifying absolute expression levels and when identifying differentially expressed genes. These findings suggest that depending on the aims of a study, the relative ease of working with microarray data may outweigh the computational time and costs of RNA-Seq pipelines. On the other, there was low agreement when mapping eQTLs. However, a number of eQTLs associated with genes that play important roles in the brain were found in both platforms. For example, a trans-eQTL was mapped that is associated with the MPZ gene in the substantia nigra. These eQTLs that we have highlighted are extremely promising candidates that merit further investigation

The role of genetic variations on gene expression and splicing in control human brain: dissection of the aetiology of complex neurological diseases

Over the past two decades there has been a realization of the importance of understanding the underlying molecular mechanism of complex neurological diseases. GWAS studies confirmed a significant association between SNPs and complex neurologic and psychiatric diseases such as Parkinson’s disease and Alzheimer’s disease. In this project, the impact of genetic variations on gene expression and alternative splicing in control post-mortem human brain tissues from twelve different regions were assessed. These are disease associated regions and support different functional roles. They are: frontal cortex, temporal cortex, occipital cortex, white matter, hippocampus, thalamus, hypothalamus, putamen, substantia nigra, medulla, cerebellum and spinal cord. Based on 1231 RNA human exon arrays, genotyped and imputed DNA samples from 137 control human brain, brain transcriptome profiles, gene and exon expression quantitative trait loci (QTL) were identified in multiple brain regions. Significant region-specific exon and gene expression QTLs were reported. Cerebellum and white matter show more unique expression profiles and expression QTLs in comparison with other brain regions. Furthermore, alternative splicing patterns were in a specific group of regions such as the cortical regions. In addition, two neurodegenerative disease related genes were investigated in detail, namely LRRK2 and MAPT. Significant regional differences in expression at mRNA and protein levels were shown. Moreover, exon QTLs correlated with the expression of specific exons located in functional protein domains of LRRK2. Also, an exon QTL has been found that shows a protective effect against Parkinson’s disease with an increase in the inclusion of exon 3 in grey matter for MAPT. This study has yielded novel regional specific expression QTLs and novel insights into the expression, regulation and function of specific genes in different regions of control human brain that are related to neurological diseases. This reference dataset is a valuable resource to complement other datasets for research into the complex genetics of neurological diseases