M I. Kamboh - US grants

Core G: Neurogenetics Abstract The Neurogenetics Core builds on the strengths of genetics of dementia at the University of Pittsburgh. Genetics studies as part of the University of Pittsburgh Alzheimer's Disease Research Center (PITT-ADRC) were started by Dr. Kamboh (Core Leader) in 1995 when we initiated blood collection and APOE genotyping on all participants of the PITT-ADRC. In addition to collecting blood samples from PITT- ADRC participants, we collect blood samples from ADRC and non-ADRC ancillary studies that provide additional well-characterized older controls essential for genetic association studies and endophenotype data that would help to identify novel genes for dementia. The resources built by the PITT-ADRC Neurogenetics Core have contributed to the identification of several new genes for AD and also have served as an educational and training hub for graduate students and junior faculty at the University of Pittsburgh. The goal of the PITT-ADRC Neurogenetics Core is to continue collecting and archiving DNA and blood samples from new and existing AD patients and controls in order to enlarge our case-control and family sample and to augment the amount of existing DNA that would be critical to future efforts in identifying new genes/variants for AD. DNA and genotype (APOE and new risk markers) data will be provided to investigators upon request.

? DESCRIPTION (provided by applicant): This competitive renewal application seeks to continue a project on the genetics of Alzheimer's disease (AD). As part of the funded project we performed genome-wide association study (GWAS) on our case-control sample that has contributed to the identification of multiple novel loci for AD as part of national and internationl collaborations. In addition to GWASs, we also performed several association studies on candidate genes that resulted in >50 publications during the current grant period. Confirmed loci identified for AD risk using the case-control association design account for only ~30% of the phenotypic variance. An alternative approach focusing on AD quantitative phenotypes/endophenotypes may help to identify additional genes for AD, as this approach can be more powerful than using the binary case-control design. As part of our preliminary data for this renewal, we have completed GWASs on four AD-related phenotypes: deposition of Aß in the brain measured by amyloid imaging, short-term disease progression measured by change in Mini-Mental State Examination (MMSE) score over 12 months, disease progression measured by time to reach MMSE 9 score (indicator of moderate to severe AD), and survival time in AD. We have identified novel loci for each AD- related phenotype. Using pathway analysis we have also identified multiple potentially novel candidate genes in the networks of GWAS-implicated genes. Since GWAS arrays use an indirect approach that relies on linkage disequilibrium to detect association signals, rarely are the identified significant variants the causal variants. Thu, it is important to resequence the candidate gene regions implicated by GWASs and those that participate in their networks in order to characterize the full spectrum of common, low-frequency and rare causal variants associated with AD-related phenotypes. The objective of this renewal application is to perform targeted resequencing of selected top gene regions implicated by GWASs and additional candidate genes in the networks of GWAS-implicated genes in order to identify causal variants associated with four AD-related phenotypes. Replication of significant variants obtained in the discovery stage will be sought in independent sets of replication samples. Finally, we will examine the functional nature of the identified significant variants usin bioinformatics tools and brain gene expression data. The successful completion of the proposed comprehensive studies will likely lead to the identification of new AD-related genes/variants.

Project Summary/Abstract In order to enhance and focus research on Alzheimer's disease (AD)-specific proteinopathies, the 2018 research framework proposed by the National Institute on Aging and Alzheimer's Association (NIA-AA) recommends that AD be defined by its specific biological signatures that can be documented at autopsy or in living people by biomarkers rather than by its non-specific neurodegenerative and clinical syndromic features. Of the three proposed biomarkers by the NIA-AA research framework in living people (amyloid A-beta (A?), pathologic tau and neurodegeneration), only the two AD-specific proteinopathies (A? and pathologic tau) are considered obligatory for the biological definition of AD, while neurodegeneration, although contribute to cognitive impairment and is part of the fully manifested disease, can also occur in other brain disorders and thus is not specific to AD. The purpose of this harmonized biological definition of AD in living people that includes the preclinical phase is to distinguish AD from other types of brain disorders and dementia, to accelerate and focus research on AD-specific proteinopathies that manifest decades before the clinical manifestation of first symptoms of AD, to enhance better understanding in the underlying mechanisms of AD clinical expression, and to use (and discover) targeted disease modifying interventions that can prevent or delay the onset of AD symptoms. Our ongoing and long-term research interest coincides well with the NIA-AA research framework in living people where we have already performed genome-wide association studies (GWAS) on CSF A?42/tau levels and A? deposition in the brain measured by amyloid-PET and identified known and novel associations in the APOE and non-APOE regions. However, the identified signals do not explain all of the phenotypic variation in the two AD-specific proteinopathies or endophenotypes. Here we propose a collaborative study between leading experts in the field to extend our ongoing efforts to delineate the complete genetic basis of the two AD- specific proteinopathies (A? and pathologic tau) by whole genome sequencing (WGS) using well-characterized and large amyloid-PET and CSF A?42/tau datasets with clinical outcomes of dementia followed by testing the effects of identified significant variants on downstream neurodegeneration markers, and performing extensive bioinformatics and functional studies. The primary objective of this application is to perform and analyze WGS in adequately powered large discovery samples with well-characterized A? and tau data along with clinical outcomes of dementia to identify putative functional variants associated with A? and tau pathologies followed by replications in independent and large samples with A? and tau data (Aims 1-2). We will integrate genetic information to create polygenic risk scores in order to predict A? and tau pathologies and will also examine the role of AD pathology-associated variants with downstream neurodegeneration, neuropathologies that coexist with AD and the risk and age-at-onset of AD (Aim3). Finally, we will functionally characterize genetic association using bioinformatics and in vitro experiments to understand their roles in affecting gene expression as being expression quantitative traits loci, and affecting intracellular and extracellular APP/A? and tau levels. The successful completion of this study will help to identify novel AD-related genes and pathways, and to uncover underlying possible mechanisms for AD.

Core G: Biomarker and Neurogenetics Core (BNGC): Summary/Abstract: The Biomarker and Neurogenetics (BNG) Core builds on the existing strengths of genetics of dementia and Alzheimer?s disease (AD) biomarkers at the University of Pittsburgh. Over nearly 25 years, we have amassed DNA and plasma samples along with endophenotype data from approximately 12,000 University of Pittsburgh ADRC (PITT-ADRC) and non-ADRC participants. This rich resource has enabled our research team to play a significant role in understanding the complex genetic architecture of late-onset AD and AD-related endophenotypes. The goal of the BNG Core is to continue collecting and archiving DNA and blood samples from new and existing AD patients and controls in order to enlarge case-control and endophenotype samples and to augment the amount of existing DNA and plasma that would be critical to current and future efforts in identifying new genetic markers and plasma biomarkers for AD in Pittsburgh and at external sites. Specifically, we will collect and bank DNA and plasma from blood samples and obtain endophenotype data from ADRC and non-ADRC ancillary studies (aim1); generate APOE and other new genetic risk markers associated with AD and provide the genetic data to qualified investigators (aim 2); and generate plasma A? and neurofilament light (NFL) biomarkers data and provide this to studies assessing the utility of blood-based biomarkers to predict individual A? and tau deposition, as well as neurodegeneration, as determined by PET and MRI imaging.

Project Summary/Abstract In order to enhance and focus research on Alzheimer's disease (AD)-specific proteinopathies, the 2018 research framework proposed by the National Institute on Aging and Alzheimer's Association (NIA-AA) recommends that AD be defined by its specific biological signatures that can be documented at autopsy or in living people by biomarkers rather than by its non-specific neurodegenerative and clinical syndromic features. Of the three proposed biomarkers by the NIA-AA research framework in living people (amyloid-beta (A?), pathologic tau and neurodegeneration), only the two AD-specific proteinopathies (A? and pathologic tau) are considered obligatory for the biological definition of AD, while neurodegeneration, although contribute to cognitive impairment and is part of the fully manifested disease, can also occur in other brain disorders and thus is not specific to AD. The purpose of this harmonized biological definition of AD in living people that includes the preclinical phase is to distinguish AD from other types of brain disorders and dementia, to accelerate and focus research on AD-specific proteinopathies that manifest decades before the clinical manifestation of first symptoms of AD, to enhance better understanding in the underlying mechanisms of AD clinical expression, and to use (and discover) targeted disease modifying interventions that can prevent or delay the onset of AD symptoms. Our ongoing and long-term research interest coincides well with the NIA-AA research framework in living people where we have already performed genome-wide association studies (GWAS) on CSF A?42/tau levels and A? deposition in the brain measured by amyloid-PET and identified known and novel associations in the APOE and non-APOE regions. However, the identified signals do not explain all of the phenotypic variation in the two AD-specific proteinopathies or endophenotypes. Here we propose a collaborative study between leading experts in the field to extend our ongoing efforts to delineate the complete genetic basis of the two AD- specific proteinopathies (A? and pathologic tau) by whole genome sequencing (WGS) using well-characterized and large amyloid-PET and CSF A?42/tau datasets with clinical outcomes of dementia followed by testing the effects of identified significant variants on downstream neurodegeneration markers, and performing extensive bioinformatics and functional studies. The primary objective of this application is to perform and analyze WGS in adequately powered large discovery samples with well-characterized A? and tau data along with clinical outcomes of dementia to identify putative functional variants associated with A? and tau pathologies followed by replications in independent and large samples with A? and tau data (Aims 1-2). We will integrate genetic information to create polygenic risk scores in order to predict A? and tau pathologies and will also examine the role of AD pathology-associated variants with downstream neurodegeneration, neuropathologies that coexist with AD and the risk and age-at-onset of AD (Aim3). Finally, we will functionally characterize genetic association using bioinformatics, causality tests and in vitro experiments to understand their roles in affecting gene expression as being expression quantitative traits loci, affecting intracellular and extracellular APP/A? and tau levels, and in myeloid cell function. The successful completion of this study will help to identify novel AD-related genes and pathways, and to uncover underlying possible mechanisms for AD.