Understanding the protective and neuroinflammatory role of human brain immune cells in Alzheimer Disease

Alzheimer's disease (AD) affects half the US population over the age of 85 and is characterized by cognitiveimpairment and reduced life expectancy. Despite extensive clinical and genomic studies, the mechanisms ofdevelopment and progression of AD remain elusive. Microglia and other myeloid origin cells (collectively calledhuman brain immune cells, or HBICs) have recently emerged as crucial players in the pathogenesis of AD. Thisis supported through genetic association studies, where many of the common and rare risk loci affect genes thatare preferentially or selectively expressed in HBICs, emphasizing the pivotal role of the innate immune systemin AD. In addition, single cell RNA sequencing analysis in mouse models of AD has identified a microgliasubpopulation that is present at sites of neurodegeneration. It is unclear if HBICs assume a protective ordamaging role, but that might vary depending on the stage and progression of AD. Therefore, further analysis ofmicroglia and other immune cells purified from human brains is needed to understand the state of HBIC activityin human AD at different stages of disease. As HBICs constitute a small proportion of total brain cells,homogenate-based studies in human brain tissue are unlikely to capture the full spectrum of HBIC molecularsignatures, especially in light of the growing appreciation for the diversity of HBICs in the brain. The proposedwork addresses some of the limitations of previous research and is focused on: (1) cell type specific and singlecell studies in immune cells isolated from human brain tissue; and (2) a systematic study of the regulatory effectsof non-coding DNA on gene and protein expression, which is necessary given that the majority of common riskvariants are situated in non-coding regions of the genome. More specifically, our application is uniquely designedto: (1) apply innovative genomic approaches and generate multi-omics data from HBICs isolated from 300 donors,including whole genome sequencing, RNAseq, ATACseq, HiC chromosome conformation capture andproteomics; (2) perform state-of-the-art single cell analysis that will allow us to assess the diversity of HBICsubpopulations, as well as detect those that are associated with AD; (3) connect AD risk loci with changes in theregulatory mechanisms of gene and protein expression in HBICs; and (4) organize HBIC multiscale data infunctional networks and identify key drivers for AD. Our overall hypothesis is that HBIC subpopulations assumea neuroprotective role during aging and early stages of AD, but as disease progresses, specific HBICsubpopulations transform to neuroinflammatory phenotype(s). This conversion is partially driven by AD riskgenetic variants, which affect regulatory mechanisms of genes that are key drivers of neuroinflammatory HBICsubpopulations. Successful completion of the proposed studies will provide: (1) an increased mechanisticunderstanding of dysfunction in AD risk loci; (2) prioritization of significant loci and genes for future mechanisticstudies; and (3) access to large-scale, multidimensional datasets, together with systems level analyses of thesedatasets for transcriptional regulation in HBICs, which is an urgently needed (and currently missing) resource.