STATISTICAL ANALYSES TO IDENTIFY GENETIC VARIANTS ASSOCIATED WITH NEUROPATHOLOGICAL AND MRI-BASED ENDOPHENOTYPES OF ALZHEIMER’S DISEASE

Aged individuals often accumulate multiple brain pathologies that contribute individually and synergistically to cognitive decline and dementia. Alzheimer’s disease (AD) is the most commonly diagnosed form of dementia, constituting over 50% of dementia diagnoses, and poses an enormous burden on human health and well-being. In the United States alone, over six million individuals are living with AD, and the disease imposes financial costs of treatment and care of over $300 billion annually. The most common form of AD, late-onset AD (LOAD), presents in individuals aged 65 years and older and is highly heritable, with twin and family studies estimating its heritability at ~60%. Genome-wide association studies (GWAS), in which millions of genetic variants are individually assessed for association with a trait through generalized linear regression models, have been an enormously successful approach for studying the genetic risk of LOAD. Recent GWAS of AD have included upwards of 700,000-1,200,000 participants and have identified more than 70 individual genetic risk loci for LOAD. However, the simple clinical or proxy definitions of LOAD used in these studies do not reflect the complexity of the underlying disease. In addition to the pathognomonic LOAD neuropathologies of amyloid-beta plaques and tau neurofibrillary tangles, the majority of dementia patients also have TDP-43, alpha-synuclein, cerebrovascular pathology, or some combination thereof. Individual neuropathologies likely have both independent and shared genetic risk factors, and studying precisely defined neuropathologic phenotypes through GWAS can act as a complementary approach to large case-control based studies; however, neuropathologic endophenotypes have been relatively neglected in GWAS relative to clinical phenotypes. Brain volumes are another class of endophenotypes associated with a variety of important life and health outcomes, including LOAD. GWAS have identified genetic loci associated with brain MRI volumes measured via magnetic resonance imaging (MRI), although these studies have either exclusively studied genetic variants with minor allele frequencies (MAF) ≥1% or have primarily focused on participants of European ancestry. Investigating the relationship between rare genetic variants (MAF In the first study, we performed a genome-wide association study of brain arteriolosclerosis. We then performed a gene-based analysis to prioritize genes and Bayesian colocalization analyses to identify functional effects of risk loci. In the second study, we expanded our investigation, performing GWAS and functional analyses on 11 neuropathologic endophenotypes. We then performed targeted analyses to confirm association between DNA methylation and RNA expression with neuropathologic endophenotypes. In the third study, we investigated the genetic factors of four brain volume endophenotypes (intracranial volume, total brain volume, hippocampal volume, and lateral ventricular volume) using whole-genome sequence data in a cohort of participants with diverse ancestry

Multiple Gene Variants Linked to Alzheimer\u27s-Type Clinical Dementia via GWAS are Also Associated with Non-Alzheimer\u27s Neuropathologic Entities

The classic pathologic hallmarks of Alzheimer’s disease (AD) are amyloid plaques and neurofibrillary tangles (AD neuropathologic changes, or ADNC). However, brains from individuals clinically diagnosed with “AD-type” (amnestic) dementia usually harbor heterogeneous neuropathologies in addition to, or other than, ADNC. We hypothesized that some AD-type dementia associated genetic single nucleotide variants (SNVs) identified from large genomewide association studies (GWAS) were associated with non-ADNC neuropathologies. To test this hypothesis, we analyzed data from multiple studies with available genotype and neuropathologic phenotype information. Clinical AD/dementia risk alleles of interest were derived from the very large GWAS by Bellenguez et al. (2022) who reported 83 clinical AD/dementia-linked SNVs in addition to the APOE risk alleles. To query the pathologic phenotypes associated with variation of those SNVs, National Alzheimer’s disease Coordinating Center (NACC) neuropathologic data were linked to AD Sequencing Project (ADSP) and AD Genomics Consortium (ADGC) data. Separate data were obtained from the harmonized Religious Orders Study and the Rush Memory and Aging Project (ROSMAP). A total of 4811 European participants had at least ADNC neuropathology data and also genotype data available; data were meta-analyzed across cohorts. As expected, a subset of dementia-associated SNVs were associated with ADNC risk in Europeans—e.g., BIN1, PICALM, CR1, MME, and COX7C. Other gene variants linked to (clinical) AD dementia were associated with non-ADNC pathologies. For example, the associations of GRN and TMEM106B SNVs with limbic-predominant age-related TDP-43 neuropathologic changes (LATE-NC) were replicated. In addition, SNVs in TNIP1 and WNT3 previously reported as ADrelated were instead associated with hippocampal sclerosis pathology. Some genotype/neuropathology association trends were not statistically significant at P \u3c 0.05 after correcting for multiple testing, but were intriguing. For example, variants in SORL1 and TPCN1 showed trends for association with LATE-NC whereas Lewy body pathology trended toward association with USP6NL and BIN1 gene variants. A smaller cohort of non-European subjects (n = 273, approximately one-half of whom were African-Americans) provided the basis for additional exploratory analyses. Overall, these findings were consistent with the hypothesis that some genetic variants linked to AD dementia risk exert their affect by influencing non-ADNC neuropathologies

Analysis of Genes (\u3ci\u3eTMEM106B\u3c/i\u3e, \u3ci\u3eGRN\u3c/i\u3e, \u3ci\u3eABCC9\u3c/i\u3e, \u3ci\u3eKCNMB2\u3c/i\u3e, and \u3ci\u3eAPOE\u3c/i\u3e) Implicated in Risk for LATE-NC and Hippocampal Sclerosis Provides Pathogenetic Insights: A Retrospective Genetic Association Study

Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is the most prevalent subtype of TDP-43 proteinopathy, affecting up to 1/3rd of aged persons. LATE-NC often co-occurs with hippocampal sclerosis (HS) pathology. It is currently unknown why some individuals with LATE-NC develop HS while others do not, but genetics may play a role. Previous studies found associations between LATE-NC phenotypes and specific genes: TMEM106B, GRN, ABCC9, KCNMB2, and APOE. Data from research participants with genomic and autopsy measures from the National Alzheimer’s Coordinating Center (NACC; n = 631 subjects included) and the Religious Orders Study and Memory and the Rush Aging Project (ROSMAP; n = 780 included) were analyzed in the current study. Our goals were to reevaluate disease-associated genetic variants using newly collected data and to query whether the specific genotype/phenotype associations could provide new insights into disease-driving pathways. Research subjects included in prior LATE/HS genome-wide association studies (GWAS) were excluded. Single nucleotide variants (SNVs) within 10 kb of TMEM106B, GRN, ABCC9, KCNMB2, and APOE were tested for association with HS and LATE-NC, and separately for Alzheimer’s pathologies, i.e. amyloid plaques and neurofibrillary tangles. Significantly associated SNVs were identified. When results were meta-analyzed, TMEM106B, GRN, and APOE had significant gene-based associations with both LATE and HS, whereas ABCC9 had significant associations with HS only. In a sensitivity analysis limited to LATE-NC + cases, ABCC9 variants were again associated with HS. By contrast, the associations of TMEM106B, GRN, and APOE with HS were attenuated when adjusting for TDP-43 proteinopathy, indicating that these genes may be associated primarily with TDP-43 proteinopathy. None of these genes except APOE appeared to be associated with Alzheimer’s-type pathology. In summary, using data not included in prior studies of LATE or HS genomics, we replicated several previously reported gene-based associations and found novel evidence that specific risk alleles can differentially affect LATE-NC and HS

Brain arteriolosclerosis

Brain arteriolosclerosis (B-ASC), characterized by pathologic arteriolar wall thickening, is a common finding at autopsy in aged persons and is associated with cognitive impairment. Hypertension and diabetes are widely recognized as risk factors for B-ASC. Recent research indicates other and more complex risk factors and pathogenetic mechanisms. Here we describe aspects of the unique architecture of brain arterioles, histomorphologic features of B-ASC, relevant neuroimaging findings, epidemiology and association with aging, established genetic risk factors, and the co-occurrence of B-ASC with other neuropathologic conditions such as Alzheimer’s disease and limbic-predominant age-related TDP-43 encephalopathy (LATE). There may also be complex physiologic interactions between metabolic syndrome (e.g. hypertension and inflammation) and brain arteriolar pathology. Although there is no universally applied diagnostic methodology, several classification schemes and neuroimaging techniques are used to diagnose and categorize cerebral small vessel disease pathologies that include B-ASC, microinfarcts, microbleeds, lacunar infarcts, and cerebral amyloid angiopathy (CAA). In clinical-pathologic studies that include consideration of comorbid diseases, B-ASC is independently associated with impairments in global cognition, episodic memory, working memory, and perceptual speed, and has been linked to autonomic dysfunction and motor symptoms including parkinsonism. We conclude by discussing critical knowledge gaps related to B-ASC and suggest that there are probably subcategories of B-ASC that differ in pathogenesis. Observed in over 80% of autopsied individuals beyond 80 years of age, B-ASC is a complex and under-studied contributor to neurologic disability

Whole genome sequence association analysis of Brain MRI measures

BackgroundGenome-wide association studies (GWAS) of brain volumes have identified common genetic variants with modest effect sizes that lie mainly in non-coding regions. We sought to identify low frequency and rare variants influencing brain volumes by performing association analyses using whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) Program.MethodWe analyzed up to 7,607 participants (57% women; 62% European ancestry, 21% African-Americans, 15% Hispanic/Latino, 2% Chinese-American), mean age of 60.5 (16.2), from eight TOPMed population- or family-based studies (FHS, GENESTAR, CHS, GENOA, ARIC, CARDIA, MESA, and SAFS). We excluded participants with dementia, stroke, presence of large brain infarcts, tumor or low-quality scans. We tested the association of hippocampal (HV), total brain (TBV), lateral ventricular (LVV) and intracranial (ICV) volumes to individual genetic variants with minor allele counts ≥ 15 using mixed-effect linear regression models adjusted for age, age2, sex, study and the first 10 principal components. Models for HV, TBV and log(LVV) were adjusted for ICV. We accounted for relatedness using an empirical kinship matrix and trait variance variability by using a random effect for study.ResultWe detected one novel region with low frequency variants associated with HV (13q14, P = 5.8×10−9). The top 13q14 variant for HV (rs115674829) minor allele frequency (MAF) was 2% in our pooled sample but was more common in the pan-African 1000 Genomes population (MAF = 14%). This variant lies in LINC00598 at 237kb from FOXO1, a member of the forkhead family of transcription factors that has been linked to Alzheimer’s Disease. Additionally, we detected new suggestive associations (P≤10−7) for TBV (16p11) and LVV (1q25, 2q22, 3q13, 5q14, and 10q23), including common variants. Finally, we confirmed the association of common variants in GWAS loci for all traits.ConclusionOur whole genome sequence analyses revealed intriguing new loci of low-frequency and common variants, and replicated loci previously associated with brain volumes. Future work will include ancestry-specific and conditional analyses, as well as gene-based and scan tests.Supported by: AG058589, AG052409, AG054076, NO1-HC-25195, HHSN268201500001I and 75N92019D00031, R01HL131136, P30 AG066546, and K99AG066849.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/175473/1/alz064947.pd

LATE-NC risk alleles (in TMEM106B, GRN, and ABCC9 genes) among persons with African ancestry.

Limbic-predominant age-related TDP-43 encephalopathy (LATE) affects approximately one-third of older individuals and is associated with cognitive impairment. However, there is a highly incomplete understanding of the genetic determinants of LATE neuropathologic changes (LATE-NC) in diverse populations. The defining neuropathologic feature of LATE-NC is TDP-43 proteinopathy, often with comorbid hippocampal sclerosis (HS). In terms of genetic risk factors, LATE-NC and/or HS are associated with single nucleotide variants (SNVs) in 3 genes-TMEM106B (rs1990622), GRN (rs5848), and ABCC9 (rs1914361 and rs701478). We evaluated these 3 genes in convenience samples of individuals of African ancestry. The allele frequencies of the LATE-associated alleles were significantly different between persons of primarily African (versus European) ancestry: In persons of African ancestry, the risk-associated alleles for TMEM106B and ABCC9 were less frequent, whereas the risk allele in GRN was more frequent. We performed an exploratory analysis of data from African-American subjects processed by the Alzheimer's Disease Genomics Consortium, with a subset of African-American participants (n = 166) having corroborating neuropathologic data through the National Alzheimer's Coordinating Center (NACC). In this limited-size sample, the ABCC9/rs1914361 SNV was associated with HS pathology. More work is required concerning the genetic factors influencing non-Alzheimer disease pathology such as LATE-NC in diverse cohorts

Genetic associations with dementia‐related proteinopathy: Application of item response theory

IntroductionAlthough dementia-related proteinopathy has a strong negative impact on public health, and is highly heritable, understanding of the related genetic architecture is incomplete.MethodsWe applied multidimensional generalized partial credit modeling (GPCM) to test genetic associations with dementia-related proteinopathies. Data were analyzed to identify candidate single nucleotide variants for the following proteinopathies: Aβ, tau, α-synuclein, and TDP-43.ResultsFinal included data comprised 966 participants with neuropathologic and WGS data. Three continuous latent outcomes were constructed, corresponding to TDP-43-, Aβ/Tau-, and α-synuclein-related neuropathology endophenotype scores. This approach helped validate known genotype/phenotype associations: for example, TMEM106B and GRN were risk alleles for TDP-43 pathology; and GBA for α-synuclein/Lewy bodies. Novel suggestive proteinopathy-linked alleles were also discovered, including several (SDHAF1, TMEM68, and ARHGEF28) with colocalization analyses and/or high degrees of biologic credibility.DiscussionA novel methodology using GPCM enabled insights into gene candidates for driving misfolded proteinopathies.HighlightsLatent factor scores for proteinopathies were estimated using a generalized partial credit model. The three latent continuous scores corresponded well with proteinopathy severity. Novel genes associated with proteinopathies were identified. Several genes had high degrees of biologic credibility for dementia risk factors