David A. Bennett, MD, Rush Medical Center - US grants

The goal of the Clinical Core is to provide clinical research resources for clinical, epidemiologic, and clinical-pathoanatomic studies related to Alzheimer's disease (AD). To accomplish this goal, the Core will recruit community-dwelling persons with clinically diagnosed AD and comparable unaffected persons. These persons will be rigorously evaluated at entry and annually thereafter to provide descriptive data regarding change in cognitive function, behavioral disturbance and physical function. Finally, in collaboration with the Neuropathology Core, this Core will assure a high autopsy rate with a short post-mortem interval on persons with clinical data proximate to death. The ability to accomplish these Aims will be enhanced by the infrastructure provided by the Rush Alzheimer's Disease Center (RADC). Specifically, the RADC supplies a steady source of persons to enter into this Core. From January 1, 1988 through December 31, 1990, there have been between 304 and 349 new patient evaluations each year, 429 of them receiving a diagnosis of probable AD by NINCDS/ADRDA criteria. In addition, there have been 83 autopsies on persons evaluated by RADC personnel. The RADC is staffed by skilled neurologists and neuropsychologists with extensive experience in the evaluation of persons with dementia, and a supporting staff skilled in adapting evaluations to the needs of the patients and their families, and obtaining coordination.

The overall goal of the Religious Orders Study Core is to continue to facilitate externally funded high quality research on Alzheimer's disease and related disorders. The Core supports a variety of studies by investigators at Rush and across the country, including studies of the transition from normality to mild cognitive impairment to Alzheimer's disease; studies linking complex post-mortem findings to change in different cognitive abilities over multiple years prior to death; and studies that explore the biologic mechanisms linking risk factors to post-mortem findings to the clinical manifestations of disease proximate to death. Requests for brain tissue from the Core substantially exceeds its availability. The Core will build on its success during the past funding period and continue recruiting and performing annual evaluations on older members of Catholic Religious Communities without dementia with an emphasis on enrolling African American and Hispanic Catholic clergy. Nearly 850 participants have enrolled. The overall follow-up rate exceeds 98% with up to seven evaluations and the autopsy rate is 90% with 130 brain autopsies out of 145 deaths. The Core supported 22 individual funded projects. Brain tissue from nearly 90% of participants has already been distributed to one or more investigators; 65 cases were distributed to between five and nine investigators, and 16 cases were distributed to more than 10 investigators. The proposed Core provides a plan for ongoing enrollment to ensure that the Core remains a renewable source of clinical data and post-mortem tissue for externally funded studies. The continuation of this Core for five more years will result in up to 12 years of data on more than 1000 persons and brain tissue from about 250 persons. Such a rich and diverse resource will allow the Core to continue to support numerous investigators. It will also offer the Alzheimer's disease research community new opportunities to use clinical pathologic studies in novel ways to understand the complex relation between cognitive decline and progression of pathology. Such studies will require post-mortem tissue from persons who died at all stages of disease with all possible trajectories of cognitive decline prior to death.

The goals of the Clinical Core are (1) to recruit and thoroughly evaluate persons with Alzheimer's disease and unaffected individuals, (2) to determine eligibility for and distribute appropriate participants to the two proposed clinical projects, and (3) to follow a subset of these persons who agree to brain autopsy with annual re-evaluations to assure timely assessment of clinical status proximate to death for the three proposed clinical-pathologic projects. The ability of Clinical Core to meet these goals, will be greatly facilitated by the Clinical and Religious orders Study. The ability of Clinical Core to meet these goals, will be greatly facilitated by the Clinical and Religious orders Study (ROS) Cores of the existing Rush ADCC. Specifically, since March 2, 1992, these two cores of the Rush ADCC have evaluated 2217 persons. The clinical evaluations are uniform and structured and the diagnosis of probable AD conforms to the recommendations of the NINCDS/ADRDA Workgroup. The Rush ADCC is staffed by skilled neurologists and neuropsychologists with extensive experience in the evaluation of persons with dementia, and a supporting staff skilled in adapting evaluations to the needs of the patients, their families, and friends, and coordinating multiple studies.

[unreadable] DESCRIPTION (provided by applicant): The past project periods identified several risk factors for incident AD and examined the biologic pathways linking risk factors to clinically diagnosed disease. We quantified AD pathology, cerebral infarctions, and Lewy bodies in brain tissue from 300 persons and found that one or more of these pathologies is present in virtually everyone with clinically diagnosed AD, most people with mild cognitive impairment (MCI), and many without dementia or MCI. Of note, only the genetic risk factor APOE led to clinical disease directly through an association with AD neuropathology, in addition to a small component through cerebral infarctions. Diabetes appeared to lead to disease through cerebral infarctions. BMI and mild parkinsonian signs, while related to AD pathology, are more likely to be a consequence of pathology and an early sign of clinical disease. Education and conscientiousness were not directly related to AD pathology but modified the relation of pathology to cognition. Depressive symptoms and distress proneness were related to clinical disease through as yet unknown mechanisms. Finally, we did not find a strong relation of statins to clinical or neuropathologic phenotypes. The overall goal of the proposed continuation is to identify novel genetic variants associated with risk of AD. The central idea of the proposal is that the effect of particular alleles on the accumulation of AD neuropathology is more specific and stronger, and therefore more easily detectable, compared to clinically diagnosed AD, which we have demonstrated to be a complex function of AD pathology and many other factors. In Aim 1, we will conduct a genome-wide association scan to identify loci associated with AD neuropathology in deceased participants from the Exploratory Cohort (Religious Orders Study). Aim 2 will conduct a second genome-wide scan in deceased participants from the Confirmatory Cohort (Memory and Aging Project), and in pooled analysis of data from both cohorts, to confirm the loci identified in Aim 1 and identify loci that were missed in Aim 1. Aim 3 will investigate the clinical relevance of the loci identified in Aims 1 and 2 by examining their relation to incident AD, incident MCI, and change in cognitive function over up to 20 years. Aims 4 and 5 will conduct fine mapping and examine gene-gene and gene-environmental interactions on phenotypes relevant to both neuropathologic and clinical phenotypes. Support for the proposal comes from the compelling preliminary data demonstrating the dramatically increased power and much reduced sample size required to identify associations with quantitative neuropathologic phenotypes compared to clinical phenotypes. We are not aware of any other studies of older men and women of comparable size, and follow-up and autopsy rates, in which these analyses can be performed. Thus, the proposed study represents a timely, novel and potentially powerful approach to the identification of genetic variants associated with risk of AD that strongly complements other ongoing large, case-control, family, and population-based epidemiologic studies seeking to identify such variants. Public Health Relevance: The prevention of Alzheimer's disease (AD) is the best long-term strategy to reduce the human and economic toll of disease. Thus, the identification of genetic and environmental factors associated with risk of disease is an urgent public health priority. Further, understanding the biologic pathways linking risk factors to clinical disease is essential for developing therapeutic interventions to treat and ultimately prevent AD. [unreadable] [unreadable] [unreadable]

It has long been recognized that some type of reserve can protect the nervous system from expressing injury or pathology as functional impairment or clinically diagnosed disease. The overall goal of the proposed study is to identify the structural bases of neural reserve and examine the neurobiologic mechanisms through which environmental and genetic risk factors lead to the functional consequences of aging and Alzheimer's disease. We hypothesize that redundancy of several cellular and subcellular components of thel neural systems responsible for cognitive and motor function are crucial for efficient performance of these systems,and thereby comprise the structural basis of neural reserve. Furthermore, we hypothesize that some risk factors lead to the clinical expression of disease by promoting the accumulation of disease pathology within selectively vulnerable neural systems, whereas other risk factors reduce the likelihood that disease pathology is expressed clinically by increasing or maintaining reserve capacity (i.e., the ability of the nervous system to tolerate pathology thereby delaying the clinical expression of Alzheimer's disease and other common diseases). To test these hypotheses, we propose a longitudinal, epidemiologic clinical-pathologic study of 1,200 older persons with a wide range of educational and lifetime experiences who agree to annual detailed clinical evaluation and brain donation after death. Identifying factors that increase or maintain neural reserve offers a new and potentially powerful method whereby the clinical signs of Alzheimer's disease and other neurodegenerative conditions can be delayed. Even relatively small reductions of risk from common disabling conditions will have a major public health impact for future generations.

medical outreach /case finding; patient /disease registry; tissue /organ preservation; tissue resource /registry

[unreadable] DESCRIPTION (provided by applicant): The overall goal of this proposed renewal of the Rush Alzheimer's Disease Core Center (Rush ADCC) is to continue to provide an infrastructure to support cutting edge research on MCI, AD, and other dementias by providing researchers with clinical data and biologic specimens from persons with and without cognitive impairment for independently funded projects. The Rush ADCC has been in continuous operation since 1991. It has six Cores carefully designed to support a variety of timely and important areas of research including: 1) Studies of the neurobiology of MCI, AD, and other dementias; 2) Studies linking risk factors to ante-mortem and post-mortem indices of MCI, AD, and other dementias; 3) Studies with substantial participation by racial and ethnic minorities; and 4) Studies that facilitate the overall goals and mission of the Rush ADCC, the Alzheimer's Disease Centers program, and the AD research community. [unreadable] [unreadable] The six Rush ADCC cores are designed to achieve these overall goals. The Administrative Core provides scientific leadership to the ADCC as a whole. The Clinical Core collects data using the uniform data set procedures as designed and implemented by the AD Centers Clinical Task Force, and emphasizes careful follow-up and autopsy of racial and ethnic minorities, and persons with atypical dementias. The Religious Orders Study Core, begun in 1993, follows a group of more than 1000 older men and women members of Catholic religious communities who have agreed to annual detailed clinical evaluations and to brain donation at death. The Neuropathology Core stores obtains, processes, stores and evaluates ante-mortem and postmortem biologic specimens tissue in accordance with the Neuropathology Data Set defined by NACC from persons evaluated by the Clinical and Religious Orders Study Cores. The Education and Information Transfer Core provides a wide range of educational programs to support outreach and recruitment of racial and ethnic minorities into the Clinical and Religious Orders Study Core. The Data Management and Biostatistics Core, begun in 1995, supplies computer systems for data acquisition and unified data management for all ADCC cores, biostatistical consultation both to the Cores and to investigators using Core data, and transfer of data to NACC and approved investigators outside the Rush ADCC utilizing the data and resource sharing policies in the Administrative Core. [unreadable] [unreadable] [unreadable]

PROJECT SUMMARY (See instructions): The overall goal of the proposed renewal of the Rush Alzheimer's Disease Core Center (Rush ADCC) is to continue to support the performance of cutting edge and innovative research on the etiology, pathogenesis, diagnosis, treatment, and prevention of MCI, AD, and other common dementias, by providing researchers with a stimulating multi-disciplinary environment, and unique and highly valued clinical and post-mortem data, and ante- and post-mortem biologic specimens. The Rush ADCC has been in continuous operation since 1991. It has six Cores carefully designed to support a variety of timely and important areas of research including studies: 1) of the transition from normal aging to MCI and to the earliest stages of dementia with substantial participation by racial and ethnic minorities, 2) of the neurobiology of normal aging, MCI, AD, and mixed dementias, 3) linking risk factors to normal aging, incident MCI and incident AD, and to post-mortem indices of AD and other common coexisting pathologies, 4) that incorporate contemporary biochemical and molecular techniques into clinical-pathologic cohort studies, including genomics, epigenomics, proteomics, metabolomic, and next generation sequencing, and 5) that facilitate the overall goals and missions of other Federal, State, and Local agency supported aging and AD research programs. The Administrative Core will provide scientific leadership to the ADCC as a whole. The Clinical Core will recruit and collect UDS and additional data on African Americans without dementia and work to obtain brain autopsy. The Religious Orders Study Core, begun in 1993, will recruit and follow older members of Catholic religious communities who have agreed to annual evaluation and brain donation at death. The Neuropathology Core will process, store, evaluate and distribute ante- and post-mortem biospecimens from subjects evaluated by the Clinical and Religious Orders Study Cores. The Education and Information Transfer Core will provide a wide range of educational programs to support outreach and recruitment of racial and ethnic minorities into the Clinical and Religious Orders Study Cores, and other NIA funded initiatives such as ADCS, ADNI, and the NIA LOAD Family Study. The Data Management and Biostatistics Core, begun in 1995, will continue to support all other Cores with PC- and web-based services and processes, and provide statistical support to users of Rush ADCC resources.

[unreadable] DESCRIPTION (provided by applicant): The burgeoning field of neuroeconomics, representing the interface between economics, psychology, and neuroscience, offers the opportunity to understand the neural mechanisms underlying a wide variety of human social behaviors. The proposed study, submitted in response to RFA-AG-06-011 Neuroeconomics of Aging (R21), will incorporate economic behaviors, including temporal discounting, risk tolerance, trust, and financial literacy into an ongoing longitudinal epidemiologic clinical-pathologic study of aging, the Rush Memory and Aging Project. We will test the hypothesis that Alzheimer's disease pathology accounts for individual differences in economic behaviors in older persons without dementia. Preliminary data is provided demonstrating that the majority of older persons without dementia accumulate Alzheimer's disease pathology (neurofibrillary tangles and amyloid) in neural systems that sub serve economic behaviors. These include regions that support analytic decision making including the dorsolateral prefrontal cortex, posterior parietal cortex, and anterior cingulate cortex, and regions that support affective decision making including nucleus accumbens, orbital frontal cortex, amygdala, anterior caudate nucleus, and anterior insular cortex. We introduce the term degraded rationality to refer to the consequences of pathological changes in the brain on both economic behaviors. The results have important implications for economic modeling of the economic decisions of older persons. [unreadable] [unreadable] The proposed study offers the possibility of identifying the pathologic basis individual differences in economic behaviors in older persons without clinical dementia. As the U.S. population ages, a greater understanding of economic decision making in old age as it applies to savings behavior, inter-generational transfers, retirement planning, advanced directives, and insurance decisions are needed. The results of the proposed study could lay the foundation for a series of studies that address these and other aspects of economic decision making in older persons without dementia. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): The prevention of cognitive decline and dementia is a major public health priority. The Memory and Aging Project (MAP) has made considerable progress elucidating the complex relationships between risk factors, common neuropathologies and resilience markers that increase or decrease the rate of cognitive decline, and risk of dementia. In nearly 200 peer-reviewed manuscripts, we reported genetic, medical, experiential, and psychological factors associated with increased or decreased rates of cognitive decline and dementia risk. We reported that Alzheimer's, vascular, and Lewy body pathologies (AD, CVD, LBD) explain about 40% of the variation of cognitive decline, and that resilience markers (e.g., cortical presynaptic proteins and locus coeruleus neurons) were associated with a slower rate of decline accounting for 8% of the variation, and that many risk factors with little direct relation o pathologies or resilience markers accounted for >10% of the variation of decline, controlling for pathologies. Additional factors related to cognitive decline await discovery. The overall goal of the planned continuation of MAP is to discover additional proteins associated with the slope of cognitive decline, after accounting for the effects of common pathologies. We use the term residual cognitive decline to describe this innovative primary study outcome. Methods to interrogate the genome, and therefore, the proteome, have improved markedly over the past decade, making the discovery of proteins that underlie cognitive decline both timely and feasible. We plan to continue collecting clinical and post-mortem data on MAP participants. Aim 1, Discovery and Verification Phase, will combine omics-wide association studies with innovative integrative pathway analyses on genomic, epigenomic, and transcriptomic data from human brain from 500 MAP participants to discover proteins associated with residual cognitive decline; it will select 200 proteins for quantitation in human brain to verify that protein level i associated with residual cognitive decline. Aim 2, Validation Phase, will quantify the 200 proteins selected and verified in Aim 1 with a new sample of 350 brains from MAP participants that will accrue by the end the funding period, followed by a joint statistical analysis to increas power (n=850). Aim 3 will link the validated proteins to the wealth of available risk factor data t discover novel biologic pathways linking risk factors to cognitive decline and dementia. Our plan is supported by extensive and compelling new preliminary data that demonstrate its high likelihood of success and demonstrate that the study is innovative, high yield and low risk. The continuation of MAP will discover additional proteins associated with cognitive decline and novel biologic pathways linking risk factors to cognitive decline. These proteins will represent either unknown pathologies that increase rates of cognitive decline or resilience markers that decrease rates of cognitive decline. Both sets of proteins will offer new therapeutic targets for the prevention and treatment of cognitive decline and dementia. Thus, the study has the potential to have a high and sustained impact on aging and dementia research.

DESCRIPTION (provided by applicant): As a result of declining fertility and increasing life expectancy, the 21st century will continue to witness the remarkable increase in the number and proportion of older persons that began in the last century. By 2030, more than 70 million Americans, about one in five, will be over age 65. The aging of the population has wide ranging health-related consequences as older persons are at risk for a number of chronic conditions, especially cognitive decline and dementia, that impair their ability to function optimally in the community, reduce wellbeing for both the individuals and their families, and are associated with significant health care costs that must be borne by individuals, their families, and society at large. The overall goal of the proposed project is to explore the role of the epigenome in modulating the effect of life experiences on cognition and dementia in older persons. The proposed study is motivated, in large part, from our work with two large, longitudinal studies of aging and dementia over the past 15 years. We have found that while cognitive decline in old age often results from one or more of three common brain diseases (i.e., Alzheimer's disease, cerebrovascular disease, and Lewy body disease), these conditions only account for about 20% of the variance of cognition in older persons. Thus, factors other than neuropathology must make important contributions to cognitive function in old age. Over the past decade, our group has identified a wide range of life experiences that affect an individual's adult cognitive function but are not involved in the development of known age-related neuropathologic processes, including indices of socioeconomic status, psychological distress, and life activities. A burgeoning literature suggests that the brain may use epigenetic marks as a means of linking these kinds of experiential factors to stable behavioral changes including long term memory storage. Building on our prior work, we propose to conduct epigenome-wide DNA methylation scans on brain tissue from participants in an Exploratory Cohort consisting of the Rush Memory and Aging Project (R01AG17917) and a Confirmatory Cohort consisting of the Religious Orders Study (P30AG10161; R01AG15819). The results of these epigenome-wide scans will be used in a programmatic series of analyses to explore the relation of epigenetic marks to age-related cognitive decline and dementia. The convergence of findings from these two sets of analyses on both cohorts will point to potential DNA methylation sites linking life experiences to cognitive decline and dementia. In additional analyses, we will take advantage of available genome-wide genotyping data on these subjects to examine the interaction between genetic variation and epigenetic marks on cognition and life experiences. In a substudy, we will examine the epigenome wide DNA methylation and histone acetylation from multiple brain regions and on peripheral blood lymphocytes over time. Finally, in secondary analyses, we will examine the relation of epigenetic marks to quantitative measures of the pathologic burden of the three most common causes of cognitive decline and dementia in old age. Together, this integrative proposal represents a timely, novel and powerful approach that will transform our understanding of epigenetic contributions to age-related loss of cognition and dementia in humans. We are not aware of any other studies of older men and women of comparable size, relevant life experiences, clinical data, and follow-up and autopsy rates, in which these analyses can be performed. Thus, the project is well positioned to create a new paradigm for studying age- related cognitive decline and dementia that will lay the groundwork for a wide range of potential interventions that are truly distinct from approaches currently under investigation.

DESCRIPTION (provided by applicant): The overall goal of the proposed project is to explore the role of the brain histone epigenome in modulating the effect of life experiences on cognitive decline and dementia. In prior work, we found that while cognitive decline in old age often results from one or more of three common brain diseases, AD, cerebrovascular disease, and Lewy body disease, these conditions only account for about 20% of the variance of cognition in older persons. Thus, factors other than neuropathology must make important contributions to cognitive function in old age. Over the past decade, our group has identified a range of life experiences that affect an individual's adult cognition but are not involved in the development of known age-related neuropathologic processes. A burgeoning literature suggests that the brain uses epigenetic marks as a means of linking experiential factors to stable behavioral changes including long term memory storage. We propose to conduct 900 epigenome- wide histone acetylation and phosphorylation scans on brain tissue from participants in an Exploratory Cohort (Rush Memory and Aging Project;R01AG17917) and a Confirmatory Cohort (Religious Orders Study (P30AG10161). The results of these epigenome-wide scans will be used in a programmatic series of analyses to explore the relation of the histone epigenome to detailed cognitive function tests and dementia status performed annually for up to 18 years, and to a wide range of life experiences (e.g., socioeconomic status, cognitive activities, psychological distress). The convergence of findings from these analyses will point to potential histone modifications linking life experiences to cognitive decline and dementia. We also will take advantage of available genome-wide genotyping and DNA methylation data on these subjects to examine the interaction between genetic variation and epigenetic marks on cognition and life experiences. In addition, the proposal will examine the relation of epigenetic marks to quantitative measures of the pathologic burden of the three most common causes of cognitive decline and dementia in old age, and a substudy will examine histone methylation in addition to acetylation and phosphorylation in multiple brain regions. Finally, the data will be made available to the research community to enable the investigation of fundamental genomic-epigenomic relationships in different brain regions, and to be explored for associations with a wide range of other clinical and biologic phenotypes available in these cohorts. Together, this integrative proposal represents a timely, novel and powerful approach that will transform our understanding of epigenetic contributions to age-related loss of cognition and dementia in humans. We are not aware of any other studies of older men and women of comparable size, relevant life experiences, clinical data, and follow-up and autopsy rates, in which these analyses can be performed. Thus, the project is well positioned to greatly accelerate the pace of research on age-related cognitive decline and dementia that will lay the groundwork for a wide range of potential interventions that are truly distinct from approaches currently under investigation. PUBLIC HEALTH RELEVANCE: Cognitive decline and dementia represent a large and growing public health problem. The prevention of dementia provides the best long-term strategy to reduce the human and economic toll of disease. The identification of epigenetic marks that link experiential factors with cognitive decline and dementia could provide important clues for the treatment and prevention of a common and devastating problem of aging and thereby improve the health and well being of older person.

The major goal of the Neuropathology Core of the Rush ADCC is to facilitate research on normal aging, mild cognitive impairment, Alzheimer's disease and other dementias by collecting and then providing a diverse range of investigators a resource of optimally preserved, processed and stored biospecimens, and state-of the-art neuropathoiogic data and diagnoses, from clinically well-characterized older subjects. Over the past years, the Core has supported a diverse range of different studies including clinical-pathologic studies, studies of normal aging and mild cognitive impairment and studies linking risk factors to the neuropathology and neurobiology underlying normal aging, MCI, clinical AD and other dementias. In addition the core has distributed biospecimens to externally-funded investigators at Rush, at other NIA funded Alzheimer's disease centers, and other researchers across the country, and has facilitated the publication of numerous manuscripts in peer-reviewed journals. The Core will continue to facilitate these studies and publications by continuing to practice optimal autopsy and collection procedures to obtain optimal ante-mortem and postmortem specimens and continue to use the uniform, standard and flexible techniques for preservation, processing and storage that allow for diverse research studies. The core will implement and maintain a DNA bank for all living and deceased participants. The Core will continue to use state-of-the-art diagnostic assessments on brain tissue to diagnose Alzheimer's disease, cerebral infarcts, and Lewy body disease, and will expand assessments for novel markers of pathology including TDP-43 and FUS. Using modern data management systems the Neuropathology Core will index and store data and diagnoses making these readily available for external research. The Neuropathology Core will continue to distribute high quality specimens and neuropathoiogic data and diagnoses for externally funded investigators to facilitate and expand the scope of research on normal aging, MCI, Alzheimer's disease and other dementias.

PROJECT SUMMARY (See instructions): The overall goal of the Education and Information Transfer Core (EITC) is to enhance minority research participation in studies of Mild Cognitive Impairment (MCI), Alzheimer's Disease (AD), and other common dementias by providing multi-culturally sensitive educational services tailored to meet the needs of communities with large numbers of racial and ethnic minorities. The ethnic diversity of metropolitan Chicago including, but not limited to, the presence of large African American communities has shaped the approach to this general goal for the Rush Alzheimer's Disease Center Core (Rush ADCC). The EITC has the responsibility for providing liasion services between the communities served by the Rush ADCC and ADCC researchers. EITC activities will continue to include: 1) networking with community leaders to nurture mutually beneficial long-term relationships; 2) giving first to meet the needs of minorities and the communities that serve them; 3) advocating for minority research participation; 4) giving back through education and outreach by sharing research findings with participants, communities and the professionals serving those communities, and 5) evaluating these activities in order to ensure they address all stakeholder needs and to ensure minority participation in ADCC research projects and National Institute on Aging (NIA) special research initiatives.

The overall goal of the Religious Orders Study Core is to continue to support high quality, cutting edge, externally-funded clinical, epidemiologic and neurobiologic studies of aging, MCI, AD and related disorders by providing a rich and diverse source of unique and highly valued clinical and neuropsychological data, ante-mortem biologic specimens, and neuropathological data and post-mortem specimens from well characterized persons representing the full spectrum of cognition from normality to MCI to the earliest stages of dementia. The Core will build on its continued success during the past funding period and continue recruiting and performing annual evaluations on older members of Catholic Religious Communities without dementia with an emphasis. More than 1150 participants have enrolled. The overall follow-up rate exceeds 95% with up to 17 waves of data, and the autopsy rate exceeds 90% with more than 500 autopsies. The Core supports numerous externally funded projects. Core resources have resulted in more than 150 peer-reviewed publications including more than 90 in the past project period. The manuscripts have been published by a wide variety of authors from Rush, several other NIA-funded AD Centers, and other centers in the United States, Canada, and Europe. 23 publications have more than 100 citations and the top ten have 2843 citations (Google Scholar, accessed October 6). Core resources are currently supporting a wide range of genomic, epigenomic, proteomic, and RNA microarray studies by investigators across the country. The continuation of this Core for five more years will result in up to 23 waves of data on about 1400 persons and brain tissue from about 700 persons. Such a rich and diverse resource will allow the Core to continue to support numerous investigators. It will also offer the AD research community new opportunities to use clinical pathologic studies in novel ways to understand the complex relation between post-mortem indices and the progressive cognitive decline from normality, to MCI, to dementia, and to link genetic and environmental risk factors obtained prior to dementia onset to post-mortem indices and the full spectrum of cognition documented proximate to death.

PROJECT SUMMARY (See instructions): The Data Management and Statistics Core will support the other cores in the Center by (1) maintaining a center-wide system of random subject ID numbers, (2) maintaining PC- and web-based electronic data collection systems for each core to collect data, (3) processing and maintaining item-level data in a secure relational database management system, (4) storing computed summary variables in a secure relational database management system, (5) providing flexible, comprehensive, automatic and timely status reports for study coordination, and (6) designing, maintaining and tracking usage of the Center's internal and external websites. The Data Management and Statistics Core will also maintain tracking systems for (1) scheduling and prioritizing study participants and biospecimens for the Clinical, Neuropathology, and Religious Order Study Cores, (2) tracking biospecimen inventory and requests for distributions for Neuropathology and Administrative Cores, (3) tracking data requests and distributions for the Administrative Core, (4) tracking activities and outcomes for the Education and information Transfer Core, (5) tracking publications using Rush ADCC resources, and (6) scheduling and prioritization of data management and statistics activities. The Core will provide expert statistical assistance with design and analysis to Rush ADCC investigators and pilot project applicants and awardees, and more limited guidance to independently funded studies that utilize Rush ADCC data and/or specimens, especially for new investigators and investigators in training. The Core will implement a system for building data sets in the Neuropathology (NP) and Uniform Data Set (UDS) formats for transmission to NACC that will integrate with automated data auditing, inter and intra form error checks, and reports for the operational reconciliation of errors and omissions, to ensure that data are accurately shared at regular intervals and in a timely manner. The Core will support systems for providing data to support externally funded projects and secondary analyses, with an emphasis on projects funded by the National Institutes of Health, the Alzheimer's Association, and other reputable foundations. The Data Management and Statistics Core will maintain an online system for investigators inside or outside the Rush ADCC to submit requests for Rush ADCC data and biospecimens. The Core will maintain tools that extract approved datasets for distribution, and generate accompanying clear and accurate data element dictionaries.

The overall goal of the Clinical Core is to generate data and biospecimens required to support high quality, cutting edge, externally-funded clinical and clinical-pathologic studies that focus on the full spectrum of cognition from normal aging to mild cognitive impairment (MCI) to the earliest stages of dementia among older African Americans. Historically, progress in Alzheimer's disease (AD) research has been most striking among members of the U.S. non-Hispanic white population. However, because of the expected increase in the growth of the older African American population, because African Americans may be at greater risk of AD than whites, and the burden of AD and mixed dementias is projected to increase dramatically for this population, the Rush Clinical Core will focus on enrolling and following African Americans longitudinally to accomplish the following Specific Aims: 1) Continue to recruit and enroll African Americans without dementia who agree to annual, detailed clinical evaluations and collection of ante-mortem biologic specimens; 2) Continue to conduct uniform structured baseline and annual follow-up evaluations, including neurological examination and neuropsychological performance testing, of community-dwelling Clincal Core participants, apply uniform diagnostic criteria for incident AD, MCI, and mixed dementias as specified in the UDS, and supplement UDS data collection with an extended battery of tests to increase compatibility with the Religious Orders Studies Core; 3) Integrate innovative and culturally tailored educational programs into the clinical evaluation to increase awareness of the importance of brain autopsy in African Americans and to facilitate a high autopsy rate with a short post-mortem interval; and continue to harvest and preserve the brain tissue in a fashion that retains maximum flexibility to support a diverse array of studies; and 4) Increase capacity to conduct externally funded clinical, neuropsychological, and clinical-pathological research studies, including studies that incorporate contemporary biochemical and molecular techniques, by contributing data to NACC and providing an environment and resources to facilitate entry of subjects, clinical data, and post-mortem tissue into research projects at Rush and within the AD research community at large.

DESCRIPTION (provided by applicant): The overall goal of the proposed study is the discovery and preclinical validation of novel targets associated with molecular processes that lead to cognitive decline, the primary outcome of most AD trials. The recent NIA Alzheimer's Disease Research Summit 2012: Path to Treatment and Prevention that led to the RFA to which we are responding, made a number of recommendations which motivated the strategy adopted in the proposed study. Our proposal brings together an exceptionally strong and unique multi-disciplinary team with the relevant skills needed to achieve our overall goal. In Aim 1, we take a systems biology approach to mine a truly unique set of deep clinical, paraclinical, pathologic, genomic, epigenomic, and transcriptomic data assembled from frozen dorsolateral prefrontal cortex brain tissue of 1000 subjects from two cohort studies of aging and dementia, the Religious Order Study and the Memory and Aging Project, in conjunction with other publicly available functional datasets. These unique data provide an excellent substrate for the identification and nomination of molecular targets for drug discovery. Target discovery is coupled with a flexible translational strategy that first validates targets by a targeted proteomic study of brain tissue from the same region and subjects in Aim 2. In Aim 3, an RNA interference (RNAi) and overexpression functional validation study in cultured human neurons and astrocytes is executed in parallel in Aim 3. Finally, these data come together in Aim 4 which performs high throughput small molecule screens on neurons and astrocytes derived from induced pluripotent stem cells (iPSC) on the most promising targets. Our proposal is ambitious but realistic: it reflects the deployment of cutting-edge approaches with a practical mindset in which redundancies have been carefully considered to mitigate risk and ensure the delivery of data, network models and lead compounds. The proposed study will discover and validate novel targets associated with molecular processes that lead to cognitive decline, and it will demonstrate the druggability of one or more targets, setting the stage for clinical trials with new and novel approaches to the prevention and treatment of AD.

DESCRIPTION (provided by applicant): This proposal uses proteomics to better understand Alzheimer's disease pathogenesis with a large-scale, unbiased, and direct approach to discover and validate novel disease processes in postmortem AD brain, and to prioritize new targets for early stage therapeutic intervention. The AD proteome mediates the effects of aging, genetics and other risk factors and contains unidentified protein targets for therapies. The approach leverages the strengths of a national team of collaborating AD Centers and associated studies of aging, an innovative proteomics platform, advanced systems biology, and model systems to produce new treatment targets. The first aim will identify novel proteomic targets selectively altered in asymptomatic AD brain. Brains will be analyzed by mass spectrometry (MS), yielding discovery proteomes to compare 1) controls free of AD and other pathologies; 2) asymptomatic controls with AD pathology; 3) non-demented mildly impaired cases with AD pathology, 4) definite AD, and 5) other neurodegenerative diseases. Protein changes in synapses, insoluble aggregates, glial and neuron-specific nuclei, and select posttranslational modifications will be determined. Bioinformatics will be used with available large-scale data to identify potentially druggable targets in key networks and cellular processes. The second aim will validate candidate proteomic targets in postmortem brains from independent community and clinic-based cohorts and determine relationships with clinicopathological features, including cognition. Absolute levels of candidate proteins will be quantified using selected reaction monitoring MS. The third aim will establish links between the validated proteome and AD pathogenesis and druggability. The most promising candidates will be studied for effects on neuronal viability and interactions with Ass and tau using cell culture and drosophila models. These results and other data will drive selection of the most promising candidates to advance to mouse models to assess therapeutic potential.

Project Summary Alzheimer's disease (AD) is a devastating neurodegenerative disorder for which there is no cure or effective treatment. A thorough understanding of its molecular mechanisms is a prerequisite for discovering novel diagnostic and therapeutic strategies against AD. DNA methylation at the fifth position of cytosine (5mC) is a well-studied epigenetic mark that is implicated in AD. The newly discovered 5-hydroxymethylcytosine (5hmC) is an oxidative product of 5mC that is essential for DNA demethylation. 5hmC is particularly enriched in the brain, accumulates with aging process, and is dynamically regulated by life experiences. 5hmC exhibits distinctive genomic distribution as compared to 5mC, and altered 5hmC influences gene expression. These findings suggest that 5hmC represents a new dimension of epigenetic regulation for brain function and neurodegeneration. However, there is little research examining the genome-wide pattern of 5hmC in human brain and its role in AD in human populations. Building on our prior work in human brain and animal models, we hypothesize that aberrant 5hmC modification is causally associated with AD pathology. Our goal is to identify causative 5hmC alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose four specific aims: (1) Identify differentially hydroxymethylated regions associated with AD pathology by genome-wide profiling of 5hmC in 740 postmortem brains collected by two large, community-based population studies of aging and dementia: the Religious Order Study (discovery sample) and the Rush Memory and Aging Project (replication sample). As traditional methods cannot discriminate between 5mC and 5hmC, we will perform 5hmC-capture sequencing, followed by TET-assisted bisulfite sequencing using novel techniques developed by our group and collaborators. (2) Conduct targeted methylation sequencing to identify additional AD-associated 5mC alterations that may have been missed by our previous EWAS as a result of the limited resolution and genome coverage of the Illumina platform. (3) Functionally validate the putative genes identified in Aims 1 and 2 using existing RNA-seq data from the same brain cortex and a fly model for AD. (4) Perform integrative `omics' analyses to test the joint and interactive effects of multi-layer `omics' markers on AD pathology. This innovative project leverages the wealth of deep clinical and neuropathological phenotypes and multi-level `omics' datasets generated in the same brain tissue, and provides unprecedented opportunities to uncover novel molecular mechanisms underlying AD pathology. Our proposal brings together an exceptionally strong and unique multi- disciplinary team with complementary expertise needed to achieve our goal. The work proposed represents the frontier in the interface between AD and `omics' research. Findings of this study will provide important mechanistic insights into disease etiology, and are highly likely to lead to the discovery of novel strategies for early detection, prevention and therapeutic intervention of AD.

ABSTRACT The proposed study, African Ancestry and the Genomic Architecture of AD and Other Common Neurodegenerative Disease Neuropathologies, is in response to PAR-15-356. To be called the Study of Ancestry and Neurodegenerative Diseases (SAND), the proposal is highly responsive to the RFA whose funding purpose is to support projects in cognitive epidemiology and genetics/genomics relevant to AD, especially projects enhancing the power of multiethnic cohort studies, exploring trends in the risk of AD and their explanation via putative risk and protective factors, and by collecting and sequencing DNA samples from well characterized cases and controls. The overall goal of SAND is to identify genomic variants of African and European Ancestry associated with AD and other common neurodegenerative disease pathologies, including: cerebrovascular disease, Lewy body disease, TDP-43, and hippocampal sclerosis. We will leverage a unique resource to procure post-mortem data on brain pathologies, and genomic data, from 10,000 admixed Brazilian brains. In an innovative series of admixture analyses applying cutting edge genomic approaches, we will characterize the entire genome for African, European, and Native Brazilian Ancestry. Aim 1 will use 6000 brains in a discovery GWAS, followed by replication in Aim 2 with 4000 additional brains, and a joint analyses of all 10,000. Additional analyses will determine the relevance of the variants that emerge to clinical dementia among the same 10,000 persons. Translational Aims 3 and 4 will extend the findings to North Americans by examining the relation of the genomic variants to AD in African Americans and non-Latino Whites from the USA. Additional analyses will leverage available neuropathologic and neuroimaging data from the USA for further extension of the findings. The proposed study brings together a unique team of neurologists, epidemiologists, neuropathologists, geneticists, statisticians, and geriatricians from the USA and Faculty of Medicine at the University of São Paulo to conduct a study that is simply not possible in the USA. The study will deliver novel genomic variants associated with the pathologies of the five most common causes of dementia. By leveraging neuropathologic traits, the approach can target the full spectrum of each disease from asymptomatic to clinically demented. Finding additional genomic variants related to neuropathologic traits of African and European ancestry will greatly facilitate our understanding of the complex processes that lead to dementia and have a strong and sustained effect on the field.

? DESCRIPTION (provided by applicant): Alzheimer's disease (AD) is a devastating neurodegenerative disorder for which there is no cure or effective treatment. A thorough understanding of its molecular mechanisms is a prerequisite for discovering novel diagnostic and therapeutic strategies against AD. DNA methylation at the fifth position of cytosine (5mC) is a well-studied epigenetic mark that is implicated in AD. The newly discovered 5-hydroxymethylcytosine (5hmC) is an oxidative product of 5mC that is essential for DNA demethylation. 5hmC is particularly enriched in the brain, accumulates with aging process, and is dynamically regulated by life experiences. 5hmC exhibits distinctive genomic distribution as compared to 5mC, and altered 5hmC influences gene expression. These findings suggest that 5hmC represents a new dimension of epigenetic regulation for brain function and neurodegeneration. However, there is little research examining the genome-wide pattern of 5hmC in human brain and its role in AD in human populations. Building on our prior work in human brain and animal models, we hypothesize that aberrant 5hmC modification is causally associated with AD pathology. Our goal is to identify causative 5hmC alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose four specific aims: (1) Identify differentially hydroxymethylated regions associated with AD pathology by genome-wide profiling of 5hmC in 740 postmortem brains collected by two large, community-based population studies of aging and dementia: the Religious Order Study (discovery sample) and the Rush Memory and Aging Project (replication sample). As traditional methods cannot discriminate between 5mC and 5hmC, we will perform 5hmC-capture sequencing, followed by TET-assisted bisulfite sequencing using novel techniques developed by our group and collaborators. (2) Conduct targeted methylation sequencing to identify additional AD-associated 5mC alterations that may have been missed by our previous EWAS as a result of the limited resolution and genome coverage of the Illumina platform. (3) Functionally validate the putative genes identified in Aims 1 and 2 using existing RNA-seq data from the same brain cortex and a fly model for AD. (4) Perform integrative `omics' analyses to test the joint and interactive effects of multi-layer `omic' markers on AD pathology. This innovative project leverages the wealth of deep clinical and neuropathological phenotypes and multi-level `omics' datasets generated in the same brain tissue, and provides unprecedented opportunities to uncover novel molecular mechanisms underlying AD pathology. Our proposal brings together an exceptionally strong and unique multi- disciplinary team with complementary expertise needed to achieve our goal. The work proposed represents the frontier in the interface between AD and `omics' research. Findings of this study will provide important mechanistic insights into disease etiology, and are highly likely to lead to the discovery of novel strategies for early detection, prevention and therapeutic intervention of AD.

ABSTRACT ? ADMINISTRATIVE CORE The Rush Alzheimer's Disease Core Center (Rush ADCC) Administrative Core is the mechanism for providing scientific leadership for the ADCC. It coordinates the activities of the Cores and pilot projects, facilitates communication among the investigators, provides for efficient allocation of resources, and oversees data and resource sharing activities. The responsibility for overall scientific leadership will rest with Dr. Bennett as ADCC Director and is shared with and exercised through the Executive Committee composed of the Core Leaders, Administrator, Data Manager, a non-ADCC Core Leader, and non-ADCC ad hoc members that have staggered rotations. Four other committees carry out specific functions. The External Advisory Committee, composed of distinguished investigators active in AD research at institutions outside the Chicago area, assesses Rush ADCC progress and provides advice concerning the directions ADCC efforts should take. The Resource Distribution Committee evaluates all requests for data, requests for access to participants for recruitment into externally-funded studies, and for ante-mortem and post-mortem specimens from persons evaluated by the Clinical and Religious Orders Study Cores, and advises the Director and Executive Committee concerning priorities in distributing these resources. The Administrative Core places strong emphasis on facilitating wide access to ADCC data and tissue resources, while assuring that only scientifically sound investigations will receive this access, resolving issues related to competing uses for limited specimens, and avoiding wasteful overlap in effort. The Pilot Project Committee conducts the competitive review of all pilot project proposals submitted to the ADCC. A major criterion for success of each pilot project is whether it will likely lead to a fully developed, scientifically excellent study that secures independent funding. A new Research Education Committee will evaluate applications for mini-internships and structured mentoring by Rush ADCC and other personnel.

ABSTRACT ? RELIGIOUS ORDERS STUDY CORE The overall goal of the Religious Orders Study Core is to continue to facilitate externally funded high quality research on MCI, AD, and related disorders. The Core supports a variety of studies by investigators at Rush and across the county, including studies of the transition from normality to MCI to AD; studies linking post- mortem findings to the spectrum of cognition from normality, to MCI, to AD; and studies that link genetic and environmental risk factors to post-mortem indices and clinical data obtained proximate to death; studies that support drug discovery pipelines with contemporary high throughput biochemical and molecular techniques; and studies of the causes, consequences, and neurobiology of impaired motor function. The Core will continue recruiting and performing annual evaluations on older members of Catholic Religious Communities without dementia. More than 1,300 participants have enrolled. The overall follow-up rate exceeds 95% with up to 22 waves of data, and the autopsy rate exceeds 90% with more than 650 autopsies. More than 350 peer-reviewed manuscripts have been published including 201 in the past project period. The manuscripts have been published by a wide variety of authors from Rush, and many other NIA-funded AD Centers, and other centers in the United States, Canada, and Europe, and have had a strong and sustained impact on the field The continuation of this Core for five more years will result in up to 27 waves of data on more than 1450 persons and brain tissue from about 800 persons. Such a rich and diverse resource will allow the Core to continue to support numerous investigators. It will also offer the AD research community unprecedented opportunities to mine multi-level omics data to find novel therapeutic targets for all common neurodegenerative diseases of aging.

There is an unmet need to develop novel biomarkers for Alzheimer?s disease (AD) that are minimally invasive and that more broadly serve as accurate indicators of the underlying pathogenic mechanisms in brain, including impaired neuronal and synaptic function, neuroinflammation, and neurodegeneration. Previous attempts to profile blood proteomes have been hindered by the relatively small number of proteins measured, difficulties linking their expression to AD brain and various disease processes, and poor replicability. The goal of this proposal is to develop a novel plasma protein biomarker platform for AD by deeply profiling the proteomes of matched brain and plasma samples from the same cases, linking the protein networks to the extensive clinical, pathological, and molecular data available in the Accelerating Medicine Partnership for AD (AMP-AD) to nominate candidate plasma protein biomarkers and validate their performance in several independent cohorts. The research will extend and leverage our contributions to the AMP-AD consortium using discovery proteomics and systems biology to generate protein co-expression networks for human post- mortem AD brain. Our initial studies have revealed biologically meaningful groups of co-expressed proteins (i.e., modules) in cortex of AD cases that strongly correlate with key traits such as diagnosis, cognition and neuropathology. The modules identify proteins and pathways involved in AD pathophysiological processes (e.g., synaptic and cytoskeletal dysfunction, inflammation, apoptosis, and others), with stronger trait- associations than in RNA expression networks, high reproducibility across all AMP-AD cohorts, and progressive change from preclinical stages to advanced AD. In the proposed research, our collaborative teams of experts from Emory, Rush, and Oxford will first extend the discovery proteomic analyses in AMP-AD using next generation mass spectrometry and aptamer arrays, increasing the depth of protein coverage several-fold, measuring ~6000 proteins in brain (Aim 1) and plasma (Aim 2) from the same control, AD, and non-AD dementia cases in the Religious Orders Study and Memory Aging Project. An integrative analysis and machine learning will be used to nominate ~100 plasma protein candidate biomarkers most strongly associated with diagnosis, and key clinical, molecular and pathological endophenotypes. The performance of the candidate biomarkers will then be assessed using >2000 samples in three independent cohorts from the M²OVE-AD consortium, the European Medical Information Framework, and Dementia Platform United Kingdom (Aim 3), The results will amplify the impact of the AMP-AD and M²OVE-AD consortia with rapid and full data sharing, and establish an innovative pipeline for discovery and validation of plasma proteomics biomarkers that serve as robust and reproducible indicators of AD, including the dysregulated processes that occur in brain.

DESCRIPTION (provided by applicant): This proposal uses proteomics to better understand Alzheimer's disease pathogenesis with a large-scale, unbiased, and direct approach to discover and validate novel disease processes in postmortem AD brain, and to prioritize new targets for early stage therapeutic intervention. The AD proteome mediates the effects of aging, genetics and other risk factors and contains unidentified protein targets for therapies. The approach leverages the strengths of a national team of collaborating AD Centers and associated studies of aging, an innovative proteomics platform, advanced systems biology, and model systems to produce new treatment targets. The first aim will identify novel proteomic targets selectively altered in asymptomatic AD brain. Brains will be analyzed by mass spectrometry (MS), yielding discovery proteomes to compare 1) controls free of AD and other pathologies; 2) asymptomatic controls with AD pathology; 3) non-demented mildly impaired cases with AD pathology, 4) definite AD, and 5) other neurodegenerative diseases. Protein changes in synapses, insoluble aggregates, glial and neuron-specific nuclei, and select posttranslational modifications will be determined. Bioinformatics will be used with available large-scale data to identify potentially druggable targets in key networks and cellular processes. The second aim will validate candidate proteomic targets in postmortem brains from independent community and clinic-based cohorts and determine relationships with clinicopathological features, including cognition. Absolute levels of candidate proteins will be quantified using selected reaction monitoring MS. The third aim will establish links between the validated proteome and AD pathogenesis and druggability. The most promising candidates will be studied for effects on neuronal viability and interactions with Ass and tau using cell culture and drosophila models. These results and other data will drive selection of the most promising candidates to advance to mouse models to assess therapeutic potential.

DESCRIPTION (provided by applicant): The overall goal of the proposed study is the discovery and preclinical validation of novel targets associated with molecular processes that lead to cognitive decline, the primary outcome of most AD trials. The recent NIA Alzheimer's Disease Research Summit 2012: Path to Treatment and Prevention that led to the RFA to which we are responding, made a number of recommendations which motivated the strategy adopted in the proposed study. Our proposal brings together an exceptionally strong and unique multi-disciplinary team with the relevant skills needed to achieve our overall goal. In Aim 1, we take a systems biology approach to mine a truly unique set of deep clinical, paraclinical, pathologic, genomic, epigenomic, and transcriptomic data assembled from frozen dorsolateral prefrontal cortex brain tissue of 1000 subjects from two cohort studies of aging and dementia, the Religious Order Study and the Memory and Aging Project, in conjunction with other publicly available functional datasets. These unique data provide an excellent substrate for the identification and nomination of molecular targets for drug discovery. Target discovery is coupled with a flexible translational strategy that first validates targets by a targeted proteomic study of brain tissue from the same region and subjects in Aim 2. In Aim 3, an RNA interference (RNAi) and overexpression functional validation study in cultured human neurons and astrocytes is executed in parallel in Aim 3. Finally, these data come together in Aim 4 which performs high throughput small molecule screens on neurons and astrocytes derived from induced pluripotent stem cells (iPSC) on the most promising targets. Our proposal is ambitious but realistic: it reflects the deployment of cutting-edge approaches with a practical mindset in which redundancies have been carefully considered to mitigate risk and ensure the delivery of data, network models and lead compounds. The proposed study will discover and validate novel targets associated with molecular processes that lead to cognitive decline, and it will demonstrate the druggability of one or more targets, setting the stage for clinical trials with new and novel approaches to the prevention and treatment of AD.

Project Summary/Abstract A diagnosis of Alzheimer's disease dementia (AD) represents the confluence of multiple different molecular processes affecting different cell types in different regions of the aging brain to cause neuronal loss, diminished communication among brain regions, and cognitive decline that ultimately leads to a syndromic diagnosis of AD. In our earlier work, we generated RNA sequence data from the dorsolateral prefrontal cortex (DLPFC), a hub of cognitive and mood circuits, in two prospective cohorts of aging, the Religious Order Study and Memory and Aging project designed to be analyzed jointly (ROSMAP). In our funded AMP-AD project, we explore the relation of these data to AD and cognitive decline, using a molecular network modeling approach that identified sets of critical co-expressed genes that we validated to be involved in AD in independent samples. Further, we used these directional network maps to identify novel regulator genes for AD that we confirmed at the protein level in the target brain tissue and in human iPSC model systems. However, these results explain only a small fraction of the disease biology. In this proposal, we address this limitation in two important ways: (1) we generate single nucleus data to uncover the detailed neuronal and non-neuronal cell population architecture of the aging brain and (2) we bring in additional pathologic and new imaging outcome measures that capture the effect of neurovascular disease. Getting a transcriptome-wide profile on each of the 2000 nuclei profiled in each of 500 brains, we propose to generate an unparalleled dataset of over 1 million individual transcriptomes from the human brain, which will offer a qualitatively different, more refined exploration of the human cortex in AD. Coupled with neuroimaging outcome measures, this dataset will create an ideal platform to integrate the AMP-AD and M2OVE-AD projects since these 500 subjects have all relevant outcome measures for both sets of studies. Finally, we extend the single nucleus profiling to two key validation systems: iPSC-derived neurons, astrocytes, and microglia as well as the new mouse models created by the MODEL-AD project. These reference data create an integrated framework of high-resolution transcriptomic data that will facilitate the selection of an optimal model system for validation and drug discovery to follow up results in AMP-AD and M2OVE-AD.

In the first period of the Accelerating Medicines Partnership for Alzheimer?s Disease (AMP-AD), we completed an arc of novel target validation that began with molecular network construction and confirmation, progressed to identifying driver genes within the network, and ended with target gene validation, through both in vitro perturbation and proteomic measurement in the target organ. Here, we characterize those validated genes in greater detail and deploy a third-generation network map that incorporates data from single cells extracted from 500 brains to produce a cell-type specific version of our networks. Further, in the discovery phase, we will use an assessment of protein post-translational modifications to identify targets that are typically masked in the tissue-level brain RNA and generic protein levels that have been available to date. The new network will also integrate the latest AMP-AD data, spanning genomic, transcriptomic, epigenomic, proteomic, and metabolomic data sets from the various member groups. The resulting new targets, along with those validated in the first funding cycle, will undergo further dissection to understand which protein isoform or modification is most relevant to disease. We go on to perform perturbation experiments for each of the prioritized genes in an enriched in vitro multicellular culture context and to identify critical protein domains within selected candidates. Finally, we expand our Research Resource Sharing Hub that facilitates the distribution of samples and data from our project.

Project Summary Alzheimer?s disease (AD) is the most common form of dementia among older people with no cure or effective treatment. A thorough understanding of its molecular mechanisms is required for discovering novel diagnostic and therapeutic strategies against AD. Chemical modifications of DNA such as methylation play critical roles in regulating gene expression and many other key biological processes, and altered DNA methylation pattern has been implicated in brain aging and AD. While much attention has focused on DNA methylation at the fifth position on cytosine (5mC), recent research identified a new form of DNA modification at the sixth position on adenine (6mA) in mammalian brains. However, little is known about its presence, genomic distribution, and possible functions in human brain and relevance to AD. Our preliminary data in mouse and human brain indicated that 6mA is dynamically responsive to environmental stress and accumulates in human AD brain. Our central hypothesis is that altered signature of 6mA modification is causally associated with AD neuropathology. The objectives of this project are to generate the first detailed map of brain 6mA methylome and identify causative genes harboring aberrant 6mA alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose three specific aims: (1) Genome-wide mapping of brain DNA 6mA methylome to identify differentially methylated genes/regions harboring altered 6mA sites (D6AMRs) associated with AD pathology in 1,200 postmortem brain tissue samples collected by two large, community-based population cohorts of aging and dementia. (2) Integrated multiomics analysis to elucidate the potential mechanistic role of 6mA alteration in AD pathology; and (3) Functionally validation of top-ranked candidate genes in 3D brain organoids derived from human iPSCs. This innovative project leverages the wealth of deep clinical and neuropathological phenotypes along with rich omics data including genetic (GWAS, WGS), epigenetic (5mC, 5hmC, 6mA, H3K9Ac), and transcriptome (RNA-seq) profiled on the same prefrontal cortex, and will provide unprecedented opportunities to uncover novel molecular mechanisms implicated in AD pathology. Our proposal brings together an exceptionally strong and unique multidisciplinary team with complementary expertise in genetic epidemiology, statistical genetics, bioinformatics, molecular and neuroepigenetics, and Alzheimer?s research. The work proposed represents the frontier in the interface between AD and omics research. Findings of this study will provide novel mechanistic insight into AD pathogenesis, and are likely to discover new molecular targets with important clinical and translational implications.

ABSTRACT ? RELIGIOUS ORDERS STUDY CORE The overall goal of the Religious Orders Study (ROS) Core is to support high quality, cutting edge, research projects on the etiology, pathogenesis, diagnosis, treatment, and prevention of Alzheimer?s disease and related dementias (AD/ADRD). The ROS Core will support a wide range of research studies that address several NAPA milesstones, including, 1) Population Studies; 2) Precision Medicine & Health Disparities; and 3) Disease Mechanisms, and Biomarkers & Diagnosis. The ROS Core, will 1) recruit, enroll, older Catholic religious men and women, who agree to annual clinical evaluations, blood draw and brain donation; 2) support studies: a) of the transition from no cognitive impairment (NCI) to MCI to the earliest stages of dementia; b) linking risk factors to normality, incident MCI, and incident AD/ADRD; c) of the progression and consequences of impaired motor function; and 3) facilitate externally funded research that aligns with the recommendations of the 2017 NIA strategic plan, including studies that: a) recognize the heterogeneity and multifactorial nature of dementias; b) support extensive molecular profiling to fill the gaps in large-scale human data needed to build predictive models of disease and wellness; c) employ new research paradigms such as systems biology and innovative human cell modeling; d) enable rapid and extensive sharing of data, disease models, specimens, and support open science; e) build multidisciplinary translational teams in virtual and real spaces for these teams to operate; and f) develop new precompetitive public-private partnerships. The ROS Core has been in operation since 1994. It supports studies a) of the heteogenety of cognitive aging and mixed brain pathologies, b) of exensive molecular profiling, c) that employ systems biology and human cell modeling, d) whose data are rapidly disseminated via the RADC Hub, AMP-AD, and NIAGADS, e) that employ multi- and inter-disciplinary teams across the country and across the globe, and f) that work in public-private partnerships in the precompetitive space with AMD-AD and its sister studies. Excluding consortium papers, it has resulted in more than 650 peer-reviewed manuscripts that have been highly impactful on the field with 4 papers having 1000-1499 citations, 3 with 700-999, and 7 with 500-699. The top 10 papers were cited an average of 922 times. Further, ROS Core data and biospecimens have been shared with investigators at nearly all other NIA-funded AD Centers, across the county and north America, south America, Europe, the middle east, Asia and Australia as further evidence of the value of the resource (see Overall Tables 1-6 and Resource Sharing Plan). The ROS Core set the standard for harmonization with the Clinical and Latino Cores, affiliated studies Rush Memory and Aging Project and the Minority Aging Research Study, and with the Chicago Health and Aging Proect.

ABSTRACT ? OVERALL The overall goal of the proposed Rush ADRC is to create an inter-disciplinary environment that supports innovative research on the causes, treatments, and prevention of AD/ADRD. While the proposed Rush ADRC is for a new grant, it builds on three decades of work by the current Rush ADCC. The Rush ADRC has eight cores and one component, which align with the recommendations of the 2017 NIA strategic plan, including studies that: 1) recognize the heterogeneity and multifactorial nature of dementias; 2) support extensive molecular profiling to fill the gaps in large-scale human data needed to build predictive models of disease and wellness; 3) employ new research paradigms, e.g., systems biology, human cell modeling; 4) enable rapid and extensive sharing of data, disease models, specimens, and support open and team science; 5) develop computational tools and infrastructure for storage, integration, and analysis of large-scale biological and patient-relevant data; 6) build multidisciplinary translational teams in virtual and real spaces; 7) develop new pre-competitive public-private partnerships; 8) change academic, publishing, and funding incentives to promote collaborative, transparent, and reproducible research; and 9) engage patients, caregivers, and citizens as direct partners in research. The Administrative Core will provide scientific leadership to the Rush ADRC as a whole. The Religious Orders Study (ROS) Core will recruit and conduct annual evaluations of Catholic clergy without dementia who agree to organ donation. The Clinical and Latino Cores will collect data harmonized with on Blacks and Latinos without dementia and work to obtain brain autopsy. The Neuropathology Core will process, store, evaluate and distribute biospecimens obtained by the Clinical, ROS, and Latino Cores. The Outreach, Recruitment, and Engagement Core will provide a wide range of educational programs to support outreach and recruitment of racial and ethnic minorities into the Clinical, ROS and Latino Cores, and other NIA funded initiatives. The Biomarker/Neuroimaging Core will process neuroimaging generated with other funds from all three Cores and affiliated studies, and document neuroimaging and biofluid biomarker data. The new Research and Education Component will provide structured mentoring of students and faculty at all levels. The Data Management and Statistical Core will provide the infrastructure that allows all other Cores and the REC to be maximally successful and impactful and will provide statistical support to users of ADRC resources especially junior investigators and trainees.