NG00135 – UAB ADRC Genetic Data

• Objectives: In this project, we seek to holistically investigate the genetic and molecular drivers of sex dimorphism in Alzheimer’s disease across ancestries. • Study design: This study integrates large-scale population genetics with multi-omics and endophenotype analyses. We are integrating all data available from ADGC and ADSP, together with other data from AMP-AD and biobanks such as UKB, FinnGen, and MVP to conduct large-scale multi-ancestry GWAS, rare-variant gene aggregation analyses, QTL studies, PWAS, TWAS, etc. We also particularly focus on X chromosome association studies. The study design also interrogates interactions with ancestry, hormone exposures, and with APOE*4, as well as comparisons to non-stratified GWAS/XWAS of Alzheimer’s disease. Further, we will also employ genetic correlation analyses, mendelian randomization, colocalization, and pleiotropy analyses, to interrogate overlap with other complex traits to better understand the mechanisms underlying sex dimorphism in Alzheimer’s disease. • Analysis plan, including the phenotypic characteristics that will be evaluated in association with genetic variants: Our phenotypes will include Alzheimer’s disease risk, conversion risk, various endophenotypes (including amyloid/tau biomarkers, brain imaging metrics, etc.) as well as molecular traits. As noted above, we will conduct large-scale multi-ancestry GWAS, XWAS, rare-variant gene aggregation analyses, QTL studies, PWAS, TWAS, etc. Specific aims include interrogating these question and analyses on (1) the autosomes, (2) the X chromosome, and (3) leveraging sex stratified QTL studies to drive discovery of risk genes.

Alzheimer’s disease (AD) manifests itself differently across men and women, but the genetic and molecular factors that drive this remain elusive. AD is the most common cause of dementia and till today remains largely untreatable. It is thus crucial to study the genetics of AD in a sex-specific manner, as this will help the field gain important insights into disease pathophysiology, identify novel sex-specific risk factors relevant to personalized genetic medicine, and uncover potential new AD drug targets that may benefit both sexes. This project uses large-scale genomics and multi-omics to elucidate novel sex agnostic and sex-specific AD risk genes. We will interrogate sex dimorphism for AD risk on the autosomes and the sex chromosomes. We similarly interrogate sex dimorphism in the genetic regulation of gene expression and protein levels, which we will integrate with genetic risk for Alzheimer’s disease to further discovery risk genes. Throughout, we will also interrogate how sex-specific risk for AD interactions with hormone exposures, ancestry, and the APOE*4 risk allele.

The goal of this study is to identify new genes and mutations that cause or increase risk for Alzheimer disease (AD), as well as protective factors. Individuals and families were selected from the Knight-ADRC (Washington University) and the NIA-LOAD study. Only families with at least three first-degree affected individuals were included. Families with pathogenic variants in the known AD or FTD genes, or in which APOE4 segregated with disease were excluded. At least two cases and one control were selected per family. Cases had an age at onset (AAO) after 65 yo and controls had a larger age at last assessment than the latest AAO within the family. Whole exome (WES) and whole genome sequencing (WGS) was generated for 1,235 individuals (285 families) that together with data from our collaborators and the ADSP family-based cohort (3,449 individuals and 757 families) will provide enough statistical power to identify new genes for AD. Dr. Tanzi (Harvard Medical School) will provide WGS from 400 families from the NIMH Alzheimer disease genetics initiative study. We will perform single variant and gene-based analyses to identify genes and variants that increase risk for disease in AD families. Single variant analysis will consist of a combination of association and segregation analyses. We will run family-based gene-based methods to identify genes that show and overall enrichment of variants in AD cases. We will also look for protective and modifier variants. To do this we will identify families loaded with AD cases, that also include individuals with a high burden of known risk variants but that do not develop the disease (escapees). We will use the sequence data and the family structure to identify variants that segregate with the escapee phenotype. The most promising variants and genes will be replicated in independent datasets (ADSP case-control, ADNI, Knight-ADRC, NIA-LOAD ). We will perform single variant and gene-based analyses to replicate the initial findings, and survival analysis to replicate the protective variants. We will select the most promising variants/genes for functional studies

Family-based approaches led to the identification of disease-causing Alzheimer’s Disease (AD) variants in the genes encoding APP, PSEN1 and PSEN2. The identification of these genes led to the A?-cascade hypothesis and to the development of drugs that target this pathway. Recently, we have identified rare coding variants in TREM2, ABCA7, PLD3 and SORL1 with large effect sizes for risk for AD, confirming that rare coding variants play a role in the etiology of AD. In this proposal, we will identify rare risk and protective alleles using sequence data from families densely affected by AD. We hypothesize that these families are enriched for genetic risk factors. We already have sequence data from 695 families (2,462 individuals), that combined with the ADSP and the NIMH dataset will lead to a dataset of more than 1,042 families (4,684 individuals). Our preliminary results support the flexibility of this approach and strongly suggest that protective and risk variants with large effect size will be found, which will lead to a better understanding of the biology of the disease.

We are studying the effects of rare (minor allele frequency < 5%) genetic variants on the risk of developing late-onset Alzheimer’s Disease (AD). We are interested in variants that have a protective effect in subjects who are at an increased genetic risk, or variants that lead to multiple dementias. Our aim is to identify any genetic variants that are present in the “case” group but not the “AD control” groups for both types of variants. The raw data we receive will be annotated to identify SNP locations and frequencies using existing databases such as 1,000 Genomes. We will filter the data based on genetic models such as compounded heterozygosity, recessive and dominant models to identify different types of variants.

Current genetic understanding of Alzheimer’s Disease (AD) does not fully explain its heritability. The APOE4 allele is a well-established risk factor for the development of Alzheimer’s Disease (AD). However, some individuals who carry APOE4 remain cognitively healthy until advanced ages. Additionally, the cause of mixed dementia pathology development in individuals remains largely unexplained. We aim to identify genetic factors associated with these “protected” and mixed pathology phenotypes.

Explore somatic transposable elements and their Alzheimer's disease-related patterns using genomic and phenotypic data from large cohorts:In order to explore the impact of the transposable element in Alzheimer's disease, we propose to conduct a systematic survey in the available large cohorts. The ADSP dataset in NIAGAlzheimer's diseaseS (Accession No. NG00067) includes 16,906 whole-genome sequences and 20,504 whole-exome sequences for case-control and family-based studies of Alzheimer's disease from diverse populations, which is a perfect resource to leverage in this project. Under the support of the Michigan Alzheimer's Disease Center, we will request to access NIAGADS. To detect somatic transposable elements in the ADSP dataset, we will employ established computational pipelines to resolve the transposable elements in the sequencing data, MELT and xTEA for WGS and SCRAMble for WES, respectively. Parameters in these tools, for instance, the calling threshold of supporting reads, will be adjusted accordingly to cooperate with the detection of somatic transposable elements in cells at low frequency. To exclude potential germline transposable elements, we will leverage a master set of polymorphic transposable elements from diverse populations, which are based on our previous projects at the Human Genome Structural Variation Consortium, and the case-control information provided by ADSP. We aim to summarize a spectrum of somatic transposable elements that would be Alzheimer's disease-relevant along with various clinical and phenotypic information. To build Alzheimer's disease-related genetic patterns we will implement Mutect2 (GATK) and Strelka2 to discover SNVs from WGS and WES data and link them with transposable elements in the same haplotype. After obtaining this set of patterns, we will collect phenotypic information from the ADSP dataset to conduct family-based associated analysis and gene-burden analysis. RegulomeDB will be used to annotate the effects of non-coding functional impact and regulatory changes for these Alzheimer's disease-related patterns.

It seeks to explore the connection between the somatic transposable elements in the human genome and Alzheimer’s disease and related dementias. It will leverage large-scale datasets to extensively explore the genome-wide transposable elements and then stratify Alzheimer’s disease-relevant ones by using the rich clinical information from the cohorts. Further analysis pipelines will be built based on the results of the proposed project to investigate the functional impact of these transposable elements on Alzheimer’s disease and would improve the understanding of genetic causes of Alzheimer’s disease and related dementias.

Can blood-based protein biomarkers of aging predict functional decline in organ health and in systemic health? We have developed organ-specific aging models derived from plasma proteins, and previously found that the blood proteome can be used to monitor organ health and aging in smaller cohorts (Oh, et., al., Nature 624, 164–172 (2023)). We aim to test this hypothesis at scale with diversified datasets. Aim 1. Validate our approach to modeling aging and brain health with NIAGADS cohorts. Approach: we will use protein biomarker data from cohorts to train machine learning models of organ aging. We will employ machine learning best practice for data curation, data augmentation, data normalization, and training/testing, to evaluate whether we can reproducibly estimate brain aging in diversified healthy cohorts and disease cohorts. Aim 2. Test the effects of brain aging on future disease risk and functional decline. We will focus particularly on the aging brain to investigate the relationship between organ aging and cognitive decline. Approach: we will evaluate the relationships between our model aging predictions and aging, diseases, and clinical phenotypes, such as mortality and lab and physical assessments. This is primarily done by first calculating the difference between a sample’s chronological age and its predicted organ age. This organ age residual is then tested for association with phenotypes of interest, such as Alzheimer’s Disease status or future risk of cognitive decline.

As we age, our risk of getting sick increases, but did you know that everyone ages differently? Some people's bodies deteriorate faster than others, and we don't fully understand why. By studying how our bodies change with age, we aim to identify which organs are aging the most and find ways to improve quality of life tailored to each individual's needs. We want to understand how people age differently, both as individuals and as a population on organ specific levels. By analyzing molecules in blood, we aim to: - Identify how aging affects people uniquely - Link aging patterns to diseases and lifespan - Use advanced computer models to connect blood changes to organ function Our research can lead to: - Personalized patient care - New discoveries for medicines - Improved understanding of aging and age-related diseases We'll use a large, diverse dataset to validate our approach and gain valuable insights into the aging process. By unlocking these secrets, we can work towards a healthier future for everyone.