Doo Yeon Kim - US grants

[unreadable] DESCRIPTION (provided by applicant): Abstract Alzheimer's disease (AD) is the most common cause of dementia, and is characterized by progressive decline in memory and cognitive functions. In addition, AD patients frequently show severe personality changes and various psychiatric symptoms, as well as epileptic and myoclonic seizures. Some of these functional disturbances may reflect altered membrane excitability of neuronal cells in AD patients. However, the underlying molecular mechanism is not known. Recently we and others reported that the voltage-gated sodium channel (Nav1) 22-subunit (22) undergoes proteolytic processing mediated by BACE1, ADAM10, and gamma- secretase, similar to the processing of the AD amyloid precursor protein (APP). 22 is essential for maintaining expression, trafficking, and cell surface localization of the Nav1 1-subunits, the major channel-forming subunits regulating membrane excitability in neuronal cells. Our preliminary data indicate that elevated BACE1 activity dramatically decreases sodium current densities by reducing cell surface expression of Nav1 1-subunits through the enhanced processing of 22 in both cell-based and animal model systems. Interestingly, we also found highly elevated 22 processing and altered Nav1 1-subunit levels in brains of AD patients with elevated BACE1 activity. Dysfunctions in Nav1 activity lead to psychiatric symptoms and epileptic seizures. Since BACE1 activities significantly increased in brains of AD patients, enhanced 22 processing and consequent Nav1 dysfunction may lead or contribute to psychiatric symptoms and epileptic seizures that frequently occur in the course of the disease. Based on this reasoning, we propose to test the hypothesis that elevated 22 processing by BACE1 and presenilin/gamma-secretase impairs the normal Nav1 metabolism including trafficking and surface expression of Nav1 1-subunits in brains of AD patients, contributing to AD pathology. To test this hypothesis, we propose the following Aims: In Aim. 1, we will characterize the altered Nav1 metabolism by elevated BACE1 activity and its physiological effects on neuronal cells by using BACE1- transgenic mice, an animal model mimicking the elevated BACE1 activity in AD patients. In an attempt to explore the therapeutic application of our findings, we will test whether BACE1 and/or gamma-secretase inhibitors can restore altered Nav1 metabolism in BACE1-trangenic mice. In addition, we will test whether these inhibitors can affect normal Nav1 metabolism in wild-type mice as well. In Aim. 2, we will study altered Nav1 metabolism in brains of AD patients by using immunohistochemical and biochemical methods. The goal of this proposal is to determine how altered 22 processing and Nav1 metabolism affect the physiology of neurons in AD, leading to dysfunction and selective degeneration observed in the course of the disease. Our study will also suggest potential therapeutic applications of BACE1 inhibitors and sodium channel modulating drugs in treating abnormal neuronal activities in AD patients. PUBLIC HEALTH RELEVANCE: In this proposal, we seek to elucidate the pathogenic contribution of altered voltage-gated sodium channel levels and activity to Alzheimer's disease. Our study will also suggest potential therapeutic applications of BACE1 inhibitors and sodium channel modulating drugs in treating abnormal neuronal activities in AD patients. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Recent genome-wide association studies (GWAS) and whole genome sequencing (WGS) have been successful in identifying novel Alzheimer's disease (AD)-associated risk genes and their functional variants, respectively. Our recent large-scale WGS efforts (Alzheimer's Genome Project, AGP-WGS; N = 1510 samples) have identified dozens of functional genetic variants that tightly co-segregate with familial AD. AD risk genes and their functional variants carry significant potential for unraveling the pathogenic mechanisms underlying AD, as well as provide new drug targets for the prevention and treatment of AD. The major challenge is to now fully characterize the pathogenic effects of AD-linked functional variants. To date, the field has lacked a single disease model system that fully recapitulates the pathogenic cascade of AD in a human neural system. In preliminary studies, we describe the creation of a novel human stem cell-derived 3D neural cell culture model in which familial AD mutations in the amyloid-? precursor protein (APP) and presenilin 1 (PSEN1) that induce extracellular ?-amyloid accumulation, also leads to neurofibrillary tangles. Thus, using this unique model system, we show for the first time that ?-amyloid deposition is sufficient to induce robust tauopathy, including hyperphosphorylated tau and detergent-resistant, silver-positive neurofibrillary tangles in a human neural cell system. No mouse model has previously achieved this without co-expressing both A?- and tau-related gene mutations. We now propose the following aims to employ our novel 3D human neural cell culture model to comprehensively assess novel AD genes and their functional variants for effects on AD pathogenesis. In Aim 1, we will investigate the impact of AD-risk genes and their functional genetic variants, identified b AGP-WGS, on ?-amyloid and tau pathologies, using our unique human 3D neural cell model system. In Aim 2, we will explore changes in gene expression and proteomic profile induced by excess ?-amyloid deposition in the human 3D neural cell model system. Potential interactions between AD risk genes/functional variants and molecular pathways triggered by excess ?-amyloid will also be explored. The overarching goal of the proposed studies is to construct a framework for systematically identifying and characterizing GWAS/WGS AD risk genes and their functional variants using our novel human 3D neural cell culture technology. Our studies should not only enhance our understanding of the etiology and pathology of AD, but also facilitate the discovery of novel AD drug targets for the treatment and prevention of AD.

DESCRIPTION (provided by applicant): While BACE1 has emerged as an effective drug target for the prevention and treatment of Alzheimer's disease (AD); side effects of BACE1 inhibitors are not well characterized. To identify the neuronal surface proteins most affected by lack of BACE1 inhibition, we recently performed an unbiased screen of surface proteins in adult BACE1-null mouse brain slices. This screen and subsequent cell-based studies revealed those two GPI- anchored adhesion molecules, contactin-1 and -2, highly increased in the BACE1-null brain. Interestingly, contactin-1 is known to regulate the surface expression and localization of Nav1.2 channels while contactin-2 modulates Kv1.1/2 channels. Nav and Kv channels almost exclusively carry out the rising and falling phases of action potentials. Previously, we have also shown that BACE1 activity regulates mRNA, protein, and cell- surface levels of the pore-forming Nav1.1 ?-subunit, a major CNS-specific voltage-gated sodium channel (Nav). Contactin-2 is also known to promote APP processing. In vitro analyses confirmed that BACE1 cleaves both contactin-1 and -2. In primary hippocampal/cortical neurons, we found that either BACE1 inhibitor treatment or overexpression of BACE1 dramatically alter surface levels of contactin-1 and -2. Interestingly, contactin-2 levels decrease by ~50% in AD brains with elevated BACE1. Nav1.2 surface levels are increased in BACE1- null neurons and the surface expression of Kv1.2 channels is dramatically modulated by BACE1 activity in brain slices and primary neurons. Importantly, overexpression of contactin-1 rescues impaired Nav channel ?-subunit channel trafficking in neuroblastoma cells expressing BACE1. Therefore, our new findings suggest that BACE1 regulates Nav1.2 and Kv1.2 channel trafficking by modulating the surface expression of contactin-1 and -2. The overarching goals of this application are to explore how contactin-1 and -2 processing by BACE1 regulates ion channel metabolism and to elucidate non-amyloidogenic functions of BACE1 for developing a safe therapeutic protocol to inhibit BACE1 activity in AD patients. To this end, we propose to use an integrated approach of cell biology and in vivo animal models. We will first identify the BACE1 cleavage sites in contactin- 1 and -2, and characterize the effect of these cleavages on APP metabolism. We will then determine the functional role of BACE1-mediated contactin processing in Nav and Kv channel metabolism. We will also explore the effect of BACE1 inhibitors on non-amyloidogenic BACE1 functions, including contactin-regulated ion channels in adult mouse brains, and in 3D cultures of human neural cells. Collectively, the proposed studies will define how BACE1-mediated processing of contactin-1 and -2 regulates Nav1.2 and Kv1.2 channel metabolism and may also provide novel mechanistic insights on contactin-regulated A? generation. Since imbalance in ion channel function may lead to seizures, the overall goal of these experiments is to provide necessary mechanistic and in vivo data for further development of BACE1 inhibitors as a safe therapeutic strategy for AD.

There are no effective drugs to prevent Alzheimer?s disease (AD). We seek to prevent onset or progression of AD by discovering and enhancing the activity of naturally occurring pathways that prevent its occurrence. This natural resilience is significant because it is the only known manner in which Alzheimer?s appears to be controlled. Here, we exploit the fact that a proportion of the aging population appear to remain cognitively intact while controlling or compensating AD related Tau pathology and enjoy a relative natural resistance to cognitive impairment or diagnosis of AD. Using whole genome sequencing (WGS) and transcriptome analysis of a naturally AD-resilient population, we will identify novel drug-sensitive resilience associated (RA) pathways in AD. We will implement a novel, validated technology, the Pathway Drug Network (PDN), constructed from human gene expression data enriched in drug?pathway?gene clusters, to identify drugs that enhance RA pathways. First round screening of the PDN-predicted single or combinations of leads will be tested in our innovative 3D human neural cell culture models of AD, which recapitulate various pathogenic stages of AD including Ab deposition (Ab plaque), Ab-driven tau pathology (neurofibrillary tangles (NFTs), and neuroinflammation and neurodegeneration. Validated leads will then be scored in transgenic AD mouse models for reduction of synaptic loss and cognitive integrity. The approach will establish the basis for a therapeutic intervention that can prevent or reduce cognitive decline related to AD. Intellectual merit: This project will significantly advance the understanding of neuroprotection in aging adult human brains while providing novel insights into the relationships between control of AD related pathology and loss of cognition. Broader impact: AD increasingly affects the aging population and there is no effective intervention. Reduction of its incidence will be of major significance. If successful, the project will allow development of clinical application of novel drugs or repurposed FDA approved drugs while creating a powerful new paradigm for developing successful AD drug combinations. Aim1: Using network analytical techniques, we will generate a molecular systems definition of RA pathways using pathways, genes and network modules from whole genome sequencing data and literature, and post mortem brain transcriptomes that show resilient high or low plaque/tangle, low AD symptoms, but high cognitive scores. Aim 2: Compare RA pathways within PDN to predict drug/pathway combinations that confer resilience. A series of drug-repurposing screens will optimise lists of ranked drugs/combinations and pathway activity. Selected combinations will be validated in multiple 3D human neural cell culture models of AD that mimic various pathogenic stages of AD for their impact on AD pathogenic markers. Aim 3: Validate using proxies of cognition in an AD transgenic APP mouse model. Score for the ability to confer resilience and neuroprotection in AD transgenic mouse models for either Ab deposition, synaptic/cognitive deficits and/or neuroinflammation.

Title: The impact of AD-associated genetic variants in 3D human mixed neural-glial models of AD Project summary A growing number of Alzheimer?s disease (AD)-associated genes are associated with innate immunity and neuroinflammatory pathways. Network-based integrative analyses of AD-related genes have shown that microglial gene networks are strongly associated with AD neuropathology (1,5). We have shown that the protective AD-associated CD33 variant, rs3865444, leads to reduced CD33 expression and lower levels of A?42)(1). Conversely, microglial TREM2 variants, which increase AD risk, reduce microglial clearance of Ab. In addition to AD-linked functional variants in CD33 and TREM2, our AD whole genome sequencing (WGS) and whole exome sequencing (WES) datasets from AD families and case-controls, have revealed functional variants in AD-associated microglial genes linked to innate immunity and neuroinflammation, including CD33, TREM2, MS4A cluster, ABCA7, ABI3, PLGC2, CR1, and others. To test the impact of microglial genetic variants on AD pathogenesis on human genetic background, we developed a novel 3D human neuron- astrocyte-microglia tri-culture AD model using a unique 3D microfluidic system. We demonstrated that human microglial cells are recruited towards 3D AD (Ab-producing) neuron-astrocyte cultures via microglia-specific migration channels, in a chemokine-dependent manner, leading to neuroinflammation and neurodegeneration. Here, we propose to use our extensive collection of AD WGS and WES datasets, together with our 3D human tri-culture AD model, to evaluate the pathogenic effects of functional variants in AD-associated innate immune genes linked to neuroinflammation. In Aim 1, we will identify functional genomic variants and enriched gene networks that are linked to innate immunity and neuroinflammation. We will then examine the pathogenic roles of microglial AD risk or protective genes and their functional variants in 3D human mixed neural-astrocyte- microglial models of AD (Aim 2), explore AD pathogenic pathways that are linked to microglial AD risk genes and their functional variants using integrated multi-omics approaches, and validate selectively blocking these pathway (Aim 3). The overarching goals of this proposal are to comprehensively assess the pathogenic effects of functional variants in innate immune AD-risk genes on AD pathogenesis and explore underlying molecular networks, which will provide novel therapeutic targets for AD patients.

Abstract Alzheimer?s disease (AD) affects more than 50 million people worldwide but there is no clear therapeutic option for the patients. For last two decades, AD research has been focusing on a neuron-centric biochemical process that leads to synaptic deficits and neuronal degeneration. However, recent failures in clinical trials clearly demonstrate a gap in knowledge in our current understanding of AD pathogenesis and call for studies that lead to unbiased and holistic understanding of disease pathways in different types of brain cells. This project aims to tackle this important and urgent issue by combining a computational systems biology platform Single-Cell Resolution Brain Interactome (SCRBI) Explorer, 3D human Alzheimer?s-in-a-dish models, and the publicly available multiple-omics AD databases through NIH-funded AMP-AD portal. We will expand the knowledge base of SCRBI Explorer to handle single cell transcriptomic and multiple omics profiles from 3D cell models and human brain tissues, which can detect on multiple layers of neuron-glia and glia-glia crosstalk pathways via ligand-receptor interactions, cytokine/chemokine signaling, intracellular signaling activities, and transcriptional activation. The central hypothesis is that the combined use of multi-cellular systems biology modeling and 3D human AD cellular models will identify AD-specific neuron-glia and glia-glia crosstalk pathways, which would provide novel therapeutic targets for drug repositioning. We will test this hypothesis by pursuing three specific aims: 1) Develop a multi-cellular crosstalk model to uncover altered neuron-glia and glia-glia crosstalk pathways in AD, 2) identify and validate AD-specific neuron-glia and glia-glia crosstalk pathways that are enriched in 3D human AD cellular models and human AD brain cells, and 3) evaluate the therapeutic potential of neuron-glia and glia-glia crosstalk using 3D human neural cell culture models of AD. The potential impact of this proposal is high because the proposed study, if successful, will provide a unique integrated bioinformatics tool to unbiasedly identify neuron-glia and glia-glia crosstalk pathways in AD and even other neurodegenerative diseases. More importantly, it will provide novel therapeutic targets based on altered neuron-glia interaction pathways in AD and open up a new vista for drug repositioning targeting cell-cell interactions in the brain of AD patients.