Whole-methylome sequencing to identify unique epigenetic profiles in Lewy body dementias (R03)

LBD is a prevalent disorder that is characterized by impaired attention and executive function, visual hallucinations, parkinsonian features, sleep difficulty, and worse functional and survival outcomes than Alzheimer’s disease (AD) or Parkinson’s disease (PD). The two clinical entities of LBD, Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB), are heterogeneous. Although they share a common neuropathological finding, namely Lewy pathology, they have variable disease courses and treatment strategies. Yet current diagnostic procedures to distinguish these subtypes are imprecise and this imprecision poses an important challenge for timely clinical diagnosis and for research. We will therefore leverage existing resources (e.g., postmortem brain tissue, DNA samples, genotypes, and methylome data) to advance the discovery of unique peripheral biomarkers for DLB and PDD. Epigenetic modifications have been shown to be capable of altering transcriptional activity across multiple genes and biological pathways. A state-of-the-art technological method known as a whole-genome methylation genotyping array has been used to construct methylome maps for human cells and to provide unbiased interrogation of the approximately 3 million quantifiable CpG sites. The detection of disease-dependent DNA methylation patterns that are unique in the postmortem brain (PMB) tissue of PD suggests that methylation profiles may serve as a readily accessible biomarker for LBD. However, previous methylation studies did not include genome-wide interrogation of methylation sites. We thus propose the following 3 aims to identify unique epigenetic profiles in LBD.

• • • Aim 1. Generate whole-methylome genotypes from the PMBs of LBD subjects using a state-of-the-art genotyping array. We will perform whole-methylome genotyping in frontal cortical samples selected from a well-characterized national LBD consortium and the University of Washington Neuropathology Core.
    • Aim 2. Identify differentially methylated regions (DMRs) in PMBs from Aim 1 that are specifically associated with LBD, including its DLB and PDD subtypes. We will detect unique methylation profiles in LBD, thereby identifying potential methylation alterations in the brain.
    •  Aim 3. Replicate DMRs identified in Aim 2 in PMB samples selected from the Alzheimer’s Disease Research Centers and Neurobiobank. We hypothesize that we will identify unique methylation patterns in the brains of subjects with LBD, and we expect that a subset of these DMRs will be verified in additional samples. These findings will thereby constitute novel sources for biomarker discovery and development in accessible tissue.

• Conduct whole-methylome genotyping in PMBs from the following groups: pure DLB (n=19), DLB + concomitant AD (n=19), PDD (n=19), AD (n=19), and control (n=19) subjects. We will use the illumina methylation genotyping array, which will interrogate over 85,000 methylation sites throughout the entire genome.

• Identify methylated regions and methylation patterns that differ between each subject group.

• Replicate these patterns in additional samples.

• Pursue future studies, including RNA sequencing in the same samples to investigate whether validated DMRs are associated with changes in gene expression.