Title: Epigenome of the brain: gene regulation in health and disease
Funder: Medical Research Council

Abstract: Genetic variants have been identified that increase the risk of aging-associated brain disorders such as Parkinson’s and Alzheimer’s diseases (AD), however, the function of these variants is largely unknown. They often reside in noncoding regions thought to regulate gene expression, called enhancers. Enhancers integrate environmental signals, resulting in gene expression programs that guide cell type-specific responses. The localization of disease-risk variants in enhancers suggest that enhancer function is critical for normal aging and disease. My research vision is to decipher how cell type-specific enhancer function drives brain physiology and aging-related disease. To address this problem, we established a nuclei isolation protocol for specific cell types of the human brain. Utilizing this approach, we generated enhancer-promoter interactome maps for brain cell types using human paediatric cortical tissue. We found that genetic risk variants for AD were enriched in enhancers of brain immune cells and identified their probable target genes. We validated a microglia-specific enhancer that harbours AD-risk variants at the BIN1 locus using CRISPR-mediated DNA editing of pluripotent stem cells. These findings have expanded the gene repertoire influenced by AD-risk variants and revealed the probable cell types in which they function. The promoter-enhancer interactome maps that we generated using paediatric tissue provided a postnatal developmental snapshot of gene regulatory regions, which does not capture all disease-relevant regions. Degenerative diseases like AD are driven predominantly by aging and are likely altered under disease conditions. Thus, enhancers critical for degenerative disorders may become altered at later stages in life. Our group will map the enhancer landscape in specific cell types during aging and in aging-related brain diseases, such as AD and Parkinson’s disease, to identify dysregulated signalling pathways and transcription factors. Hallmarks of aging-related brain disorders are neuronal atrophy, neuroinflammation, white matter myelin loss and astrogliosis, involving dysfunction of the major brain cell types: neurons, microglia, oligodendrocytes and astrocytes respectively. Utilizing the nuclei isolation approach that we developed for the brain, we will examine the epigenome of the major cell types of the aging human brain. Chromatin immunoprecipitation sequencing (ChIP-seq) and ATAC-seq genome-wide approaches will identify enhancers and promoters, and the transcription factor binding sites within these regulatory regions. Integrative analysis with datasets we generated from young individuals, together with genetic data from genome-wide association studies (GWAS) for brain diseases, will be used to define aging-associated disease-risk enhancer regions. The gene targets for these disease-risk enhancers will be determined by genome conformation assays, such as HiChIP and promoter-capture HiC, which identify chromatin loops connecting enhancers to gene promoters. Select candidate enhancers that harbour disease-risk variants will be tested by gene expression analysis of iPSC-derived cell types with these enhancers deleted by CRISPR. Collectively, these datasets will reveal cell type-specific gene networks and transcription factors important for brain aging and highlight candidate targets that are dysregulated in disease.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;NEUROLOGICAL