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(2014) Coupland, Kirsten G; Mellick, George D; Silburn, Peter A; Huang, Yue; Halliday, Glenda; Hallup, Marianne; Woojin, S. Kim; Dobson-Stone, Carol; Kwok, John BJ; Mather, Karen; Armstrong, Nicola J; Sachdev, Perminder; Brodaty, HenryJournal ArticleBackground: Parkinson's disease (PD) is a neurodegenerative disorder for which environmental factors influence disease risk and may act via an epigenetic mechanism. The microtubule-associated protein tau (MAPT) is a susceptibility gene for idiopathic PD. Methods: Methylation levels were determined by pyrosequencing of bisulfite treated DNA in a leukocyte cohort (358 PD and 1084 controls) and two brain cohorts (Brain1 comprising 69 cerebellum controls, Brain2 comprising 3 brain regions from 28 PD and 12 controls). In vitro assays involved the transfection of methylated promoter-luciferase constructs or treatment with an exogenous micronutrient. Results: In normal leukocytes, MAPT H1/H2 diplotype and gender were predictors of MAPT methylation. Haplotype-specific pyrosequencing confirmed H1 haplotype to have higher methylation than H2 in normal leukocyte and brain tissues. MAPT methylation was negatively associated with MAPT expression in Brain1 cohort and transfected cells. Methylation levels differed between three normal brain regions (Brain2, putamen > cerebellum > anterior cingulate cortex). In PD samples, age at onset was positively associated with MAPT methylation in leukocytes. Moreover, there was hypermethylation in the cerebellum and hypomethylation in the putamen of PD patients compared with controls (Brain2 cohort). Finally, leukocyte methylation status was positively associated with blood Vitamin E levels, the effect being more significant in H2 haplotype carriers; this result was confirmed in cells exposed to 100 μM Vitamin E. Conclusions: The significant effects of gender, diplotype and brain region suggest that hypermethylation of the MAPT is neuroprotective by reducing MAPT expression. Vitamin E effect on MAPT represents a possible gene-environment interaction.
(2012) Stevens, Claire H; Rowe, Dominic; Morel-Kopp, Marie-Christine; Orr, Carolyn; Ranola, Madelaine; Ward, Christopher; Halliday, Glenda; Russell, ToniaJournal ArticleGene association with HLA suggests involvement of immune mediated mechanisms in the pathogenesis of Parkinson’s disease (PD). Only a small number of studies have found differences between circulating leukocyte populations in PD patients compared to controls, with conflicting results. To clarify whether there is a circulating leukocyte PD phenotype, we assessed the numbers of T, B and natural killer cells, and monocytes and found a small reduction (15-25%) in CD4+ T and CD19+ B cells in PD. These findings suggest some compromise in immune cells in PD and have potential implications for immune function and the progression of PD.
(2013) Kavanagh, Tomas; Mills, James D; Kim, Woojin S; Halliday, Glenda; Janitz, MichaelJournal ArticlePathway analysis is a powerful method for discerning differentially regulated genes and elucidating their biological importance. It allows for the identification of perturbed or aberrantly expressed genes within a biological context from extensive data sets and offers a simplistic approach for interrogating such datasets. With the growing use of microarrays and RNA-Seq data for genome wide studies is growing at an alarming rate and the use of deep sequencing is revealing elements of the genome previously uncharacterised. Through the employment of pathway analysis, mechanisms in complex diseases may be explored, and novel causatives found primarily through differentially regulated genes. Further, with the implementation of next generation sequencing (NGS) a deeper resolution may be attained, particularly in identification of isoform diversity and SNP’s. Here we look at a broad overview of pathway analysis in the human brain transcriptome and its relevance in teasing out underlying causes of complex diseases. We will outline processes in data gathering and analysis of particular diseases in which these approaches have been successful.
(2012) Wong, Jenny; Garner, Brett; Halliday, Glenda; Sharpe, Laura J; Brown, Andrew JJournal ArticleSelective Alzheimer’s Disease Indicator-1 (Seladin-1) was originally identified by its down-regulation in the brains of Alzheimer’s Disease (AD) patients. Here, we re-examine existing data and present new gene expression data that refutes its role as a selective AD indicator. Furthermore, we caution against the use of the name “Seladin-1” and instead recommend adoption of the approved nomenclature, 3â-hydroxysterol Ä24-reductase (or DHCR24), which describes its catalytic function in cholesterol synthesis. Further work is required to determine what link, if any, exists between DHCR24 and AD.