Suman Jayadev - US grants

The rising global prevalence of Alzheimer disease (AD) has heightened the urgency to develop effective AD therapeutics. Many lines of evidence support the hypothesis that AD pathogenesis involves dysfunctional innate immune effector cells in both the periphery and central nervous system (CNS). Innate immunity promotes tissue repair, clearance of debris, release of cytokines and chemokines which act to signal appropriate interface with adaptive immune responses. However, dysregulation of CNS innate immune cells, microglia, or of peripheral monocytes, contributes to a neurotoxic environment directly injuring synapses, creating a feed forward loop of neural injury. Recent technological advances have produced powerful tools to survey the molecular regulators of the innate immune network contributing to AD pathogenesis. MicroRNAs, a class of small non-coding RNAs, have emerged as powerful modulators of CNS and peripheral innate immunity, regulating pro-inflammatory activity, phagocytosis and contributing to mechanisms of A? clearance. MiRNA profiles are altered in brain tissue, serum and CSF of patients with AD. In particular, miR146 and miR155, proximal inflammatory modulating miRNAs, are dysregulated in AD implicating miRNAs in the inflammatory arm of AD pathogenesis. Work by our group and others have demonstrated that miR146 and miR155 participate in in the development of age-dependent chronic inflammation in vivo. These data underscore putative pathways by which AD pathogenesis is influenced by inflammatory miRNA regulatory networks. In this multi-PI proposal, we have designed a systems approach to investigate the role of miRNAs in CNS and circulating innate immune cell regulation in the context of AD. MicroRNA profiling, gene co- expression analysis and amyloid-? (A?) clearance studies will be performed in peripheral macrophage and microglia-like cells differentiated from individuals with early symptomatic AD and early or asymptomatic carriers of familial autosomal dominant Alzheimer disease genes (PSEN1, PSEN2 and APP). In parallel, we will employ the murine APP/PS1 and 5XFAD AD models to determine the impact of altered miR146 and miR155 expression in vivo on cognitive deficits, synapse loss, A? clearance and chronic CNS inflammation. By capturing the inflammatory miRNA landscape and inflammatory profile in patients destined to develop dementia of the Alzheimer type and modeling microRNA modulation in vivo, we aim to identify targetable pathways which leverage the bidirectional communication between CNS and peripheral inflammation.

Alzheimer disease (AD) is a complex phenotype influenced by the cumulative impact of many genetic elements. While environmental factors and age certainly contribute to phenotypic expression, we hypothesize that the underlying biological process of AD is driven by the burden of genetic variants influencing risk. Understanding how genetic burden causes disease can inform efforts to develop more effective AD therapeutics. Furthermore, the spectrum of known AD genetic risk variants implicates numerous cell types and thus knowing how variants impact biological networks and in which cell type is critical to directing therapeutic target design. In this proposal we leverage our collaborative and interdisciplinary AD research programs at the University of Washington and SAGE Bionetworks to create a cell-type specific systems biology program in AD. We hypothesize that non-coding variants confer AD risk through disruption of cellular pathways which can be identified by molecular phenotyping of AD patient brain tissue and assayed in vitro. Specifically, we focus on endosome biology given the link between endosome pathways and neural cell function and the known association with endosomal genetic variant risk and AD. Through the use of an endosome pathway specific polygenic risk score we can enrich our AD cohort for those more likely to manifest AD driven by endosomal dysfunction. We will employ single nuclei transcriptomics and functional studies in reprogrammed neural cells derived from the same cohort to investigate the impact of genetic risk in endosomal pathways on AD pathophysiology. We will 1) determine if a high endosome pathway polygenic risk score predicts endosome dysfunction in neurons and 2) determine how high endosome polygenic risk influences microglia function. Through development of these datasets, which will be available as open-source through SAGE Bionetworks, we can begin to identify the cell type specific transcriptomic changes in AD associated with endosomal variant load as well as the concomitant functional cell alterations using induced pluripotent stem cell derived neurons, microglia and transdifferentiated neurons. Our integrated molecular and cell biology phenotyping approach seeks to identify biological pathways by which aggregate endosomal genetic risk may contribute to AD pathogenesis and elucidate the cellular subtypes most directly impacted by endosomal dysfunction. Understanding candidate biological pathways and the cell types in which they are disrupted will provide valuable information for more effective therapeutic targeting in AD.

Abstract The University of Washington (UW) Alzheimer Disease Research Center (ADRC) Clinical Core is a valuable component the center's overall aim of supporting meaningful and innovative ADRD research. Advances in human genetics, pathological and imaging technologies have revealed the biological diversity of ADRD. The UW Clinical Core aims to capture this spectrum of ADRD heterogeneity in its longitudinal cohort to support multi-modal study of participants. Sensitive phenotyping is critical to the interpretation of post-mortem pathology and ante-mortem imaging heterogeneity. To that end, we have expanded our neuropsychological evaluation to identify relative vulnerable and resilient cognitive domains. Acknowledging that effective ADRD therapies for all requires improving study of ADRD in under-represented groups, we have developed a strategy with our Outreach Recruitment and Engagement Core to enhance the diversity of our ADRC. Over the last 5 years the UW ADRC has built a strong collaborative relationship with the Partners for Native Health, led by Dr. Dedra Buchwald. In this cycle we continue this effort through developing consensus algorithms for longitudinal cognitive and clinical data collected by Dr. Buchwald's team. Additionally, we work with the UW ADRC's Native Research and Resource Core (NRRC) to build upon data derived from community based participatory research approaches in the AI/AN population and develop community sensitive uniform ADRD clinical evaluations. The rationale driving the Clinical Core composition is to a) reflect the UW ADRC scientific theme of heterogeneity and resilience b) respond to the scientific needs of the ADRC research community and c) increase the racial, socioeconomic and educational attainment diversity of the Clinical Core. In this cycle, the Clinical Core will 1) Characterize clinically and follow longitudinally persons with normal aging, prodromal and symptomatic ADRD representing the clinical, anatomic and risk heterogeneity of disease, and promote their inclusion into research 2) Promote the inclusion of underrepresented groups in ADRD research and collaborate to establish diagnostic algorithms in AI/AN studies 3) Use modern psychometric approaches to co-calibrate cognitive scores across UDS, pre-enrollment clinical tests, and external studies to integrate pre-enrollment cognitive data and facilitate interoperability across and 4) obtain longitudinal CSF, blood and skin biospecimens from a well-characterized cohort of research participants presenting with normal and pathological aging, prodromal dementia and ADRD.

Project Summary Women have a higher lifetime risk of developing Alzheimer's disease (AD) than men. This increased risk is not fully explained by differences in longevity, hormones or brain structure. Women who carry at least one copy of the APOE?4 allele, the strongest genetic risk factor for late onset AD (LOAD), have accelerated neuropathology. However, some studies suggest a faster decline in men, suggesting that sex bias may differ depending on the stage of the disease. Here, we will investigate how the sex chromosome complement and sex-linked genes influences sex differences in onset and progression of LOAD. Genome-wide association studies have identified genetic and epigenetic risk factors for LOAD, but the sex-chromosomes are often excluded in these studies meaning there is a lack of data on sex-linked genes. Males have unique Y-linked genes and females have higher expression of genes that escape X inactivation. Interestingly, many of the escape genes are related to immune function and neuroinflammation is a hallmark of AD, suggesting that these genes may directly contribute to disease progression. To address the impact of sex-linked genes combined with APOE?4 alleles on neuroinflammation in LOAD we will use unique cellular models and AD tissue for leveraging integrated omics and functional studies. We will evaluate the functional roles of sex chromosomes and sex-linked genes in brain cell types using human induced pluripotent stem cell (hiPSC) models. We have derived isogenic pairs of hiPSCs with a different number of sex chromosomes on the same genetic background (XXY/XY or XXX/X). These new hiPSC lines minimize variability between individuals, as well as environmental or hormonal confounders. We will generate isogenic pairs of these lines with ?3/3 or ?3/4 alleles by gene editing. After differentiation of hiPSC into neurons, microglia, and brain organoids we will employ a combination of `omic' analyses and functional assays focusing on neuroinflammation and neurodegeneration. This approach will identify sex-linked candidate genes, which will be tested for dosage effects by knockdown and overexpression. These in vitro studies will be validated in human tissue collected by the Precision Neuropathology Core from our Alzheimer's Disease Research Center brain bank. Using pathologically characterized AD brains we will employ myeloid-specific single-nucleus RNA sequencing to determine the effects of sex and APOE?4 genotypes on microglial subtypes and neuroimmune gene expression. Our new team combines expertise in hiPSC modeling, sex-linked genes, neuroinflammation, `omic analyses and neuropathology. This integrative study will help understand sex-specific genetic factors and how those factors interact with APOE?4 risk to modulate cellular dysfunction and pathology, thus providing novel insights into how to tailor a more effective treatment for AD.