Investigating the Effect of APOE Alleles on Neuro-Immunity of Human Brain Borders in Normal Aging and Alzheimer's Disease Using Single-Cell Multi-Omics and In Vitro Organoids - PROJECT SUMMARY Neuroinflammation and innate immune response have emerged as the forefront pathology of Alzheimer’s disease (AD). Accumulated evidence has shown that Apolipoprotein E4 (APOE4), the most significant AD genetic risk factor, confers a pro-inflammatory state in the normal aging and AD brains. However, most studies have centered around the roles of APOE4 in disrupting the homeostatic functions of astrocytes and microglia in brain parenchyma. Recent discoveries of a lymphatic system in the dura meninges and a repertoire of immune cells at brain borders have highlighted the critical role of border immunity in brain aging and AD. APOE is highly expressed in the border-associated macrophages (BAMs), dura lymphatic vessels, and choroid plexus. Thus, those studies raise a critical question on whether APOE4 regulates the border-associated immunity in normal aging and AD. Despite the recent single-cell transcriptomic study on mouse BAMs18, little information exists on cell states of human brain borders related to normal aging and AD, neither the APOE4’s effects on border cell states, immunity, and functions. The overall goal of this application is to investigate the effect of APOE alleles on cell states and functions of human brain borders in normal aging and AD. Our central hypothesis is that AD and APOE4 alter cell states in brain border regions, and APOE4 exacerbates molecular and cellular phenotypes in control and AD isogenic border cell models. We formulated this hypothesis based on literature as mentioned above and our transcriptomic analysis showing distinct cell transcriptomic signature and strong APOE expression in BAMs at human brain borders. We will test this hypothesis by combining single-cell multi-omics profiling of ex vivo human border regions and in vitro border region modeling. Specifically, we will first profile the single-cell transcriptome and chromatin accessibility from the same cells of postmortem meninges and choroid plexus of APOE4 and non-APOE4 carriers from control and AD individuals. This Aim will enable us to reveal cell types, cell states, regional specificity, and intercellular communications at human brain borders and identify upstream master regulators of AD- and APOE4-specific cell states (Aim 1). To study the APOE4’s functions in human brain borders, we will develop multicellular choroid plexus 3D models by introducing iPSC-derived immune cells to choroid plexus organoids. We will then generate control and AD isogenic choroid plexus models carrying either APOE3 or APOE4 alleles to examine the APOE4’s cellular, molecular, and functional effects in both cell-autonomous and non-cell-autonomous manners (Aim 2). Our study will shed significant insights into human border-associated immunity and reveal a novel mechanism underlying AD pathophysiology. The upstream regulators of AD- and APOE4-specific cell states identified in this study will serve as ideal therapeutic targets for modulating the brain border immunity. Our choroid plexus model provides a tractable system to test other genetic targets, extrinsic factors, and candidate drugs, opening a new avenue of targeting the brain borders for AD therapeutic interventions.
