Genetic Risk For Alzheimer's Disease Research Articles

Genetic characterization of the ALFA study: Uncovering genetic profiles in the Alzheimer's continuum.

In 2013, the ALzheimer's and FAmilies (ALFA) project was established to investigate pathophysiological changes in preclinical Alzheimer's disease (AD), and to foster research on early detection and preventive interventions. We conducted a comprehensive genetic characterization of ALFA participants with respect to neurodegenerative/cerebrovascular diseases, AD biomarkers, brain endophenotypes, risk factors and aging biomarkers. We placed particular emphasis on amyloid/tau status and assessed gender differences. Multiple polygenic risk scores were computed to capture different aspects of genetic predisposition. We additionally compared AD risk in ALFA to that across the full disease spectrum from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Results show that the ALFA project has been successful at establishing a cohort of cognitively unimpaired individuals at high genetic predisposition of AD. It is, therefore, well-suited to study early pathophysiological changes in the preclinical ADcontinuum. Highlights Prevalence of ε4 carriers in ALzheimer and FAmilies (ALFA) is higher than in the general European population The ALFA study is highly enriched in Alzheimer's disease (AD) genetic risk factors beyond APOE AD genetic profiles in ALFA are similar to clinical groups along the continuum ALFA has succeeded in establishing a cohort of cognitively unimpaired individuals at high genetic AD risk ALFA is well suited to study pathogenic events/early pathophysiological changes in AD.

Proof-of-concept recall-by-genotype study of extremely low and high Alzheimer’s polygenic risk reveals autobiographical deficits and cingulate cortex correlates

BackgroundGenome-wide association studies demonstrate that Alzheimer’s disease (AD) has a highly polygenic architecture, where thousands of independent genetic variants explain risk with high classification accuracy. This AD polygenic risk score (AD-PRS) has been previously linked to preclinical cognitive and neuroimaging features observed in asymptomatic individuals. However, shared variance between AD-PRS and neurocognitive features are small, suggesting limited preclinical utility.MethodsHere, we recruited sixteen clinically asymptomatic individuals (mean age 67; range 58–76) with either extremely low / high AD-PRS (defined as at least 2 standard deviations from the wider sample mean (N = 4504; NEFFECTIVE = 90)) with comparable age sex and education level. We assessed group differences in autobiographical memory and T1-weighted structural neuroimaging features.ResultsWe observed marked reductions in autobiographical recollection (Cohen’s d = − 1.66; PFDR = 0.014) and midline structure (cingulate) thickness (Cohen’s d = − 1.55, PFDR = 0.05), with no difference in hippocampal volume (P > 0.3). We further confirm the negative association between AD-PRS and cingulate thickness in a larger study with a comparable age (N = 31,966, β = − 0.002, P = 0.011), supporting the validity of our approach.ConclusionsThese observations conform with multiple streams of prior evidence suggesting alterations in cingulate structures may occur in individuals with higher AD genetic risk. We were able to use a genetically informed research design strategy that significantly improved the efficiency and power of the study. Thus, we further demonstrate that the recall-by-genotype of AD-PRS from wider samples is a promising approach for the detection, assessment, and intervention in specific individuals with increased AD genetic risk.

Developing Topics.

Alzheimer's disease (AD) is associated with the accumulation of neuropathological beta-amyloid (Ab) plaques, which is thought to be caused by an imbalance between Ab overproduction and dysfunctional Ab clearance. Both animal and human studies have shown that increased cerebrospinal fluid (CSF) levels of Ab peptides, especially Ab-40 and Ab-38 due to their high solubility, may be indicative of overall Ab dysregulation in preclinical AD, years before pathological Ab plaques begin to aggregate. The apolipoprotein E (APOE) e4 allele, which is the strongest genetic risk factor for AD, has been linked to impaired Ab clearance and disruption of the amyloid precursor protein (APP) pathway that is responsible for Ab production. However, the association between early Ab dysregulation and other genetic risk variants remains understudied. Thus, we aimed to explore whether genetic risk for AD is related to early markers of Ab overproduction by examining associations between polygenic risk scores (PRS) and CSF Ab-40 and Ab-38 in an AD-vulnerable population. We selected 88 non-demented Veterans (Age: M = 68.22, SD = 3.75 years) from the Alzheimer's Disease Neuroimaging Initiative-Department of Defense (ADNI-DOD) database with available genetic markers and CSF measures for Ab-40 and Ab-38. Genetic propensity for AD was assessed using genome-wide PRS, both with and without the APOE region, employing a p-value threshold < 0.01. CSF Ab concentrations were measured using a 2D-UPLC-tandem mass spectrometry method outlined by ADNI-DOD. Partial spearman's correlations related PRS to CSF Ab-38 and Ab-40 levels adjusting for age. CSF Ab-40 levels were positively associated with PRS for AD (rhopartial = 0.22, p = 0.037). When variants in the APOE region were excluded from the score, the relationship between CSF Ab-40 and PRS remained significant (rhopartial = 0.23, p = 0.035). The relationship between PRS for AD and CSF Ab-38 levels was not significant, regardless of whether APOE regions were included in the score (all p's > 0.1). Genetic risk for AD may lead to early Ab overproduction, as evidenced by elevated CSF Ab levels, particularly Ab-40. Other genetic variants, in addition to APOE, may play an integral role in disrupting the APP pathway and dysregulating Ab production.

Poorer online cognitive performance is associated with genetic risk for Alzheimer’s disease and brain phenotypes in healthy mid‐life and older adults.

AbstractBackgroundSelf‐administered online cognitive testing offers a cost‐effective and flexible alternative to in‐person neuropsychological assessments. We used the Creyos platform (previously named Cambridge Brain Sciences) to assess cognitive function in a large sample (N = 1673) of middle aged and older adults participating in the PISA (Prospective Imaging Study of Aging) study. PISA aims to characterise the early symptoms and progression of Alzheimer’s disease at its prodromal phase.MethodWe have utilised our Australia‐wide population based sample recruitment pool of research participants with genome wide genotyping. Participants completed a comprehensive online survey and online cognitive assessments, including Creyos, consisting of 12 self‐administered tasks covering memory, executive function, language, and visuo‐spatial domains. Using genetic profile scores in a sample size of 1,673 (70% female, aged 42‐75 years, mean 60.8). We tested the association between cognitive test results and genetic risk for Alzheimer’s disease and related phenotypes including structural neuroimaging measures.ResultsOur findings indicate a significant association of Alzheimer’s polygenic risk scores (PRS) with cognitive test results in healthy individuals within memory and executive function domains. The results of analyses with additional genetic profile scores including psychiatric traits and structural neuroimaging measures will also be presented.ConclusionThose who are at high genetic risk for Alzheimer’s disease have reduced cognitive function prior to dementia diagnosis from middle age. Our results highlight the utility of online cognitive testing as a cost‐effective alternative to in person testing for large scale studies and the potential for it’s used as a pre‐screening approach to identify those at high risk of Alzheimer’s disease.

Investigating epigenetic regulation of microglia in a human‐mouse chimera model of Alzheimer’s disease

AbstractBackgroundMicroglia, the resident macrophages of the brain, are implicated in Alzheimer’s disease (AD). The genetic risk for AD is significantly enriched near microglial genes and enhancers. In the human brain, APOE is the strongest genetic risk factor for late onset AD and is primarily expressed in microglia and astrocytes. The “disease associated microglia” (DAM) state, in which inflammatory pathways are upregulated in amyloid plaque‐associated microglia, is a characteristic pathological response in AD.MethodHere, we studied how amyloid pathology interacts with genetic risk for AD to regulate the DAM state.We profiled gene regulation in human iPS‐derived microglia. We xenotransplanted the microglia into the APPNL‐G‐F mouse model of AD using isogenic APOE2/3/4 and APOE knockout (KO) microglia (n = 5 animals per microglial APOE genotype). We characterized dissociated iPS‐derived microglia from each animal by RNA‐seq, CUT&amp;Tag for H3K27ac, and ATAC‐seq. We performed quantitative analyses of the epigenetic landscapes of microglial populations across heterogeneous activation states. This allowed us to infer the regulatory pathways that are responsible for the differential microglia response to amyloid aggregation, depending on APOE.ResultWe observed widespread differences in gene regulation across microglia related to APOE genotype. While we observed upregulation of chemokine and interferon response signalling in AD‐risk variant e4, we observed corresponding downregulation in the AD‐protective variant e2. Additional analyses identified increased chromatin accessibility at vitamin D receptor binding motifs in e2 through motif analysis. Finally, we identified gene expression networks and modules underlying differential microglial activation states.ConclusionOur findings are important for understanding microglia and their activation in AD and neurodegenerative diseases. Here, we profiled comprehensive epigenetic landscapes in a human‐mouse chimera in the context of APOE genotype. This enabled us to leverage the realistic biological environment for the microglia offered by this model, and dissect genetic effects underlying microglial responses for the first time.

Alzheimer’s disease plasma markers and depressive symptoms: an IPD meta‐analysis

AbstractBackgroundDepression has been associated with an increased risk of Alzheimer’s disease (AD), but the biological mechanisms are still not fully understood. Plasma biomarkers, such as amyloid‐beta, tau, glial fibrillary acidic protein (GFAP), and neurofilament light (NfL), have been associated with AD pathophysiology. However, the relationship with depression is unclear. Assessing these biomarkers in the blood allows for the opportunity to assess if AD pathology is related to depressive symptoms on a large‐scale. We hypothesized if depression is part of the AD process, then these markers will be associated with depressive symptoms.MethodA two‐stage IPD meta‐analysis was performed based on eight cohorts of individuals without dementia as part of the Netherlands Consortium of Dementia Cohorts (NCDC). We examined the cross‐sectional association between each plasma marker for AD (amyloid‐beta42/40 ratio, p‐tau181, NfL, and GFAP) with depressive symptoms (the GDS‐15, PHQ‐9, CES‐D, and SF‐36). Plasma markers were assessed using Single Molecular Array (Simoa; Quanterix) assays. Both plasma markers and depressive symptoms were standardized. We estimated the effect per plasma marker with depressive symptoms using linear regressions, correcting for age, sex, education, and APOE e4 allele presence, in each cohort. The effect estimates were entered into a random‐effects meta‐analysis. We also performed subgroup analyses assessing sex differences and between those with and without an APOE e4 allele.ResultThis study involved 7210 participants with an age range of 38 to 102 years. Based on clinical cut‐offs per questionnaire, high depressive symptomology ranged from one to 22% per cohort. None of the plasma markers were associated with depressive symptoms in the meta‐analysis. However, subgroup analyses found an association with NfL and depressive symptoms in women (beta 0.07; 95% CI: 0.03‐0.10, p &lt; 0.001) and in those with an APOE e4 allele (beta 0.11; 95% CI: 0.05‐0.17, p = 0.001).ConclusionAD pathology did not show an overall relationship with depressive symptoms. However, in women and in those with a genetic risk for AD, NfL showed an association. As NfL is a marker of overall neurodegeneration, this pathology in plasma may be specific to depressive symptoms in certain subgroups.

Cerebrovascular features of Alzheimer’s disease in adults with Down syndrome

AbstractBackgroundCerebrovascular disease contributes to clinical onset and course of Alzheimer’s disease (AD) but it is unclear if it is related directly to AD pathogenesis. In late onset AD, MRI markers of small vessel cerebrovascular disease relate to AD diagnosis, genetic risk for AD, and severity of AD symptoms, but it is not possible to determine whether these associations reflect comorbidity due to risk factor exposure or whether they represent a core feature of AD. We have been studying cerebrovascular features of Alzheimer’s disease in adults with Down syndrome, who are at genetic risk for developing AD but have very low prevalence of classical vascular risk factors.MethodIn the context of the Alzheimer’s Biomarker Consortium – Down Syndrome (ABC‐DS), a US‐based multisite observational study of the clinical, biomarker, and pathological features of AD in adults with Down syndrome, our laboratory has analyzed high‐resolution, harmonized MRI scans for markers of cerebrovascular disease, including white matter hyperintensities (WMH), enlarged perivascular spaces, microbleeds, and infarcts, in adults with Down syndrome across the adult lifespan. We tested the association of these markers with age, AD‐related clinical diagnoses, proteomic profiles of vascular function and inflammation, and AD‐related biofluidic biomarker concentrations.ResultOur studies show that MRI‐derived markers of cerebrovascular disease are prevalent in adults with Down syndrome and increase in severity across AD‐associated clinical diagnoses. Age analyses suggest that there is an inflection of these markers at around age 40, when other pathological features also begin to emerge. Proteomic correlates of these cerebrovascular disease markers suggest an association with inflammatory processes in presymptomatic and neurodegenerative processes in symptomatic adults with Down syndrome. Finally, markers of cerebrovascular disease are particularly associated with plasma phosphorylated tau concentrations in adults with Down syndrome.ConclusionOur work shows that MRI‐derived markers of cerebrovascular disease are prevalent, related to AD symptoms, temporally track with AD pathology, relate to inflammation and neurodegeneration markers, and associate with markers of tau pathology. Without the confound of exposure to peripheral vascular risk factors, these observations suggest that cerebrovascular disease represents a “core feature” of AD that contributes both to symptoms and to disease pathogenesis.

India ENIGMA Initiative for Global Aging &amp; Mental Health–A globally coordinated study of brain aging and Alzheimer’s Disease

AbstractBackgroundThere is a “diversity” crisis in brain research, as most brain research is conducted in Caucasian populations. This lack of ethnic diversity means that we do not know if predictors of health (and disease) generalize to other ethnic groups.We have recently launched the India ENIGMA Initiative for Global Aging &amp; Mental Health ‐ a globally coordinated study of brain aging and Alzheimer’s disease (AD), funded by the NIA/NIH, USA. Our overall goal is to identify predictive markers in the blood, genome, and epigenome that influence brain aging in India, to better understand prognosis, and to support personalized risk evaluations on each continent. To do this, we will leverage our global consortium, ENIGMA (http://enigma.ini.usc.edu), creating new links between international biobanks, and building research capacity.MethodAim 1. Create Lifespan Charts of brain aging Trajectories in India using MRI, DWI and Resting State Functional MRI. Aim 2. Identify Blood and Epigenetic Markers that Predict Brain Aging and AD in India. Aim 3. Using a combination of multimodal imaging, blood markers, and clinical data to predict clinical decline in India. We test structural equation models that hypothesize how brain aging depends on lifestyle and psychosocial factors (diet, family support, drug abuse, literacy, sleep, and depression), as well as sex, education, and AD genetic risk.ResultWe test structural equation models that hypothesize how brain aging depends on lifestyle and psychosocial factors (diet, family support, drug abuse, literacy, sleep, and depression), as well as sex, education, and AD genetic risk. With novel machine learning methods, we will analyze blood markers and plasma proteomic analytes, to define processes that are harmful to brain aging.ConclusionThe data emerging from this study is expected to help in personalized risk evaluations as well as identify etiological pathways to resilience across genetically and psychosocially diverse populations. This collaborative India‐US initiative will also enable future science initiatives, and equip the team from India with the necessary tools to train new scientists and independently conduct high impact research in the field of disorders of brain aging.

APOE‐dependent and ‐independent polygenic pathways determining early Alzheimer’s Disease pathological changes in CSF and MRI

AbstractBackgroundLittle is known about the genetic factors and downstream molecular pathways determining individual variability in fluid and imaging biomarkers associated with Alzheimer’s disease(AD). We studied polygenic risk scores (PRS) and pathway‐specific PRS in relationship with AD fluid and imaging biomarkers, in non‐demented individuals from the European Prevention of Alzheimer’s Dementia (EPAD) cohort.MethodEPAD inclusion criteria were age&gt;50 and Clinical Dementia Rating = 0.5 (n = 1886, Table 1). AD‐PRS was based on 85 previously identified loci, including and excluding APOE (PRSAPOE, PRSnoAPOE)[1]. Using gene‐variant and variant‐pathway mapping[2], six pathway‐specific PRSnoAPOE were identified:1) immune‐activation, 2) signal‐transduction, 3) inflammatory‐response, 4) migration, 5) amyloid‐production, and 6) clearance. Linear models were used to assess the relationship of all PRS with fluid AD biomarkers, including Aß1‐42, p‐Tau181, and t‐tau; and several imaging biomarkers, including hippocampal volume, global and lobar white matter hyperintensities (WMH) volumes, fractional anisotropy (FA) in 14 regions of interest from diffusion tensor imaging, and 10 resting‐state network connectivity from functional MRI. Models were adjusted for age, sex, site, and multiple comparisons.ResultModels’ coefficients are reported in Table 2. PRSAPOE was significantly associated with decreased Aß1‐42, and increased p‐Tau181 and t‐Tau. PRSnoAPOE showed a weaker, but still significant, negative association with Aß1‐42 levels, and a significant positive association with p‐Tau181 and t‐Tau. Aß1‐42 was only significantly associated with the migration, amyloid, and clearance pathways, while all pathways were significantly positively associated with p‐Tau181 and t‐Tau. Hippocampal volume was only significantly associated with PRSAPOE. Regarding WMH load, PRSAPOE showed a positive association with global, frontal periventricular, and parietal deep lobes. Furthermore, the clearance pathway was related to WMH load in all regions, most strongly in periventricular areas. Only the migration pathway was related to increases in FA in the splenium, body, and genu of the corpus callosum. Only the PRSAPOE was related to reduced functional connectivity (FC) in the default mode, control, and visual networks.ConclusionWe show that genetic risk beyond APOE facilitates the manifestation of AD related pathologies. Moreover, clearance and migration pathways were associated with neuroimaging measures of white matter integrity, while FC and hippocampal volume were associated with overall AD genetic risk.

APOE‐dependent and ‐independent polygenic pathways determining early Alzheimer’s Disease pathological changes in CSF and MRI

AbstractBackgroundLittle is known about the genetic factors and downstream molecular pathways determining individual variability in fluid and imaging biomarkers associated with Alzheimer’s disease(AD). We studied polygenic risk scores (PRS) and pathway‐specific PRS in relationship with AD fluid and imaging biomarkers, in non‐demented individuals from the European Prevention of Alzheimer’s Dementia (EPAD) cohort.MethodEPAD inclusion criteria were age&gt;50 and Clinical Dementia Rating≤0.5 (n = 1886, Table 1). AD‐PRS was based on 85 previously identified loci, including and excluding APOE (PRSAPOE, PRSnoAPOE)[1]. Using gene‐variant and variant‐pathway mapping[2], six pathway‐specific PRSnoAPOE were identified:1) immune‐activation, 2) signal‐transduction, 3) inflammatory‐response, 4) migration, 5) amyloid‐production, and 6) clearance. Linear models were used to assess the relationship of all PRS with fluid AD biomarkers, including Aβ1‐42, p‐Tau181, and t‐tau; and several imaging biomarkers, including hippocampal volume, global and lobar white matter hyperintensities (WMH) volumes, fractional anisotropy (FA) in 14 regions of interest from diffusion tensor imaging, and 10 resting‐state network connectivity from functional MRI. Models were adjusted for age, sex, site, and multiple comparisons.ResultModels’ coefficients are reported in Table 2. PRSAPOE was significantly associated with decreased Aβ1‐42, and increased p‐Tau181 and t‐Tau. PRSnoAPOE showed a weaker, but still significant, negative association with Aβ1‐42 levels, and a significant positive association with p‐Tau181 and t‐Tau. Aβ1‐42 was only significantly associated with the migration, amyloid, and clearance pathways, while all pathways were significantly positively associated with p‐Tau181 and t‐Tau.Hippocampal volume was only significantly associated with PRSAPOE. Regarding WMH load, PRSAPOE showed a positive association with global, frontal periventricular, and parietal deep lobes. Furthermore, the clearance pathway was related to WMH load in all regions, most strongly in periventricular areas.Only the migration pathway was related to increases in FA in the splenium, body, and genu of the corpus callosum. Only the PRSAPOE was related to reduced functional connectivity (FC) in the default mode, control, and visual networks.ConclusionWe show that genetic risk beyond APOE facilitates the manifestation of AD related pathologies. Moreover, clearance and migration pathways were associated with neuroimaging measures of white matter integrity, while FC and hippocampal volume were associated with overall AD genetic risk.

A new risk locus on chromosome 1 is suggested by genome‐wide association study in Peruvians for Alzheimer disease

AbstractBackgroundIncreasing ethnic/ancestral diversity in genetic studies is critical for defining the genetic architecture of Alzheimer disease (AD). Amerindian (AI) populations are substantially underrepresented in AD genetic studies. The Peruvian (PE) population, with up to ∼80% of AI ancestry, provides a unique opportunity to assess the role of AI ancestry in AD. We performed the first genome‐wide association study (GWAS) in the PE population to identify novel AD susceptibility loci and characterize known AD genetic risk loci.MethodThe PE dataset includes array‐genotype and phenotype data from 542 individuals (189 cases; 353 controls), imputed to the NHLBI TOPMedv5 haplotype reference panel. We used a generalized linear mixed‐model (SAIGE software) for the GWAS analysis. We analyzed two separate models; the first model accounted for sex, age, and population substructure, while the second model also included the dosage of APOEe4. In both models, we included a genetic relationship matrix as a random effect to account for any potential relatedness. To determine if the associations are specific to specific ancestries, we employed ancestry‐aware approaches using the RFMix software.ResultAPOE was significantly associated with AD with an effect size comparable to that found in non‐Hispanic white (NHW) populations (OR = 3.3(2.2‐4.8),pv = 8.0×10−10). Two additional known AD loci, TREML2 (pv = 0.008) and CLU (pv = 0.012), showed nominal significance Variants at three additional loci reached suggestive significance (pv&lt;1×10−6): NFASC (pv = 9.4×10−8;chromosome 1), STK32A (pv = 9.3×10−7; chromosome 5), and LOC100132830 (pv = 6.7×10−7;chromosome 6). The NFASC locus neared genome‐wide significance in the APOE adjusted model (pv = 6.7×10−8). The haplotypes associated with AD at the NFASC locus were found to be of European origin. Additionally, the STK32A locus was found to have a protective effect specifically among individuals of AI background. We did not observe significant heterogeneity of effect at the APOE and LOC100132830 loci across different ancestral backgrounds.ConclusionPE GWAS identified a novel, promising AD susceptibility locus in the NFASC gene of European origin. We also detected a potential protective effect in the STK32A locus on AI background, emphasizing the importance of incorporating ancestry‐aware approaches in gene discovery in admixed populations.

Effects of Alzheimer’s disease genetic risk on brain morphometric development in three multiple‐ancestry pediatric datasets

AbstractBackgroundFew prior studies have investigated whether genetic risk for Alzheimer’s disease (AD) can manifest through altered neurodevelopment of AD‐vulnerable brain regions. This pre‐registered study tests the effects of AD polygenic risk on morphometric neurodevelopment across 3 large datasets totaling 8,364 youths aged 3‐22 (Table 1)MethodPolygenic risk score (PRS) was calculated using PRS‐CS software, with summary scores from Kunkle et al. (2021) for African ancestry individuals (AA) and Jansen et al. (2019) for European ancestry individuals (EA). For EA only, PRS were calculated with (PRS‐APOE+) and without (PRS‐APOE‐) the APOE locus included. All individuals had T1‐weighted MRI processed with FreeSurfer that passed quality assessment checks. ComBAT was used to harmonize sites within‐cohort. Primary analyses investigated effects of PRS, age and their interaction on bilateral hippocampal volume and AD MetaROI cortical thickness using generalized additive models. Age interactions were not evaluated in ABCD due to limited age range. Exploratory analysis examined effects of age and PRS on cortical thickness, volume, surface area and subcortical volume across Desikan‐Killiany regions, adjusting for multiple comparisons (FDR). For exploratory analyses only, ABCD was split into training and test sets. All analyses were conducted for EA and AA separately; sex, total intracranial volume, image quality (Euler number) and ten genetic principal components were included as model covariates.ResultTable 1 summarizes primary results. Hippocampal volume increased with age in 3/6 datasets, while MetaROI thickness decreased with age in all datasets. Surprisingly, increased PRS was associated with larger hippocampi in three datasets. In one dataset only, greater PRS was associated with increased metaROI thickness (Fig 1). 2/3 AA datasets showed age*PRS interactions on hippocampal volume, but in opposite directions. An age*PRS interaction on metaROI thickness was found in one dataset (Fig. 2A‐C). For exploratory analyses, no regions survived multiple comparisons for any contrast in 5/6 datasets; APOE only PRS was associated with larger supramarginal surface area in one dataset (Fig 2E). Effects were not correlated across studies (Fig 2D)ConclusionThis large, pre‐registered study provides little evidence that AD genetic risk manifests during pediatric brain morphometric development.

Discovery of disease‐associated, tau, and inflammatory microglial subpopulations and molecular drivers in Alzheimer’s disease using network‐based deep learning integration of human brain single‐cell RNA‐sequencing data

AbstractBackgroundMicroglia have been implicated in the pathophysiology of Alzheimer’s disease (AD) for over 100 years, and substantial progress has been made in characterizing microglial heterogeneities and biology, including disease‐associated microglia (or DAM, amyloid‐pathology related, neuro‐protective), tau microglia (tau‐pathology related), and inflammatory microglia (neuro‐toxic). However, the crucial next step knowing how to apply these findings to develop new treatments for AD, through uncovering the functional roles and molecular drivers of each microglial subtype, has not yet been accomplished.MethodIn this study, we conducted single‐cell RNA‐sequencing data integration analyses of ∼0.8 million cells/nuclei by leveraging frozen brain samples from AD subjects across different brain regions from The Alzheimer’s Cell Atlas (https://taca.lerner.ccf.org/) using a deep learning analytic approach. We annotated three microglial subtypes (including DAM, tau, and inflammatory microglia) using well‐established marker genes and then used a human protein‐protein interactome network‐based approach to identify potential molecular drivers of different microglial subtypes across the spectrum of AD. We also applied transition gene network analysis to characterize microglial subtype transition from non‐disease associated to disease‐associated stages at transcriptomic levels.ResultVia trajectory analysis we pinpointed the existence of three microglial subtypes across AD progression. We also identified that tau microglia were significantly associated with synaptic processes. Compared to DAM, upregulated genes within inflammatory microglia were more significantly enriched within key immune pathways (e.g., NF‐kappa B and toll‐like receptor signaling pathways). In addition, transition gene networks of inflammatory microglia and DAM were found to contain potential AD pathobiology regulators (e.g., SYK, LYN, IRF8, and CSF1R) and genetic risk genes (including INPP5D, PICALM, and MEF2A). We further conducted network‐based drug repurposing prediction by simultaneously activating DAM while inhibiting inflammatory microglia, which indicated that several predicted repurposable drugs (i.e., fluticasone and mometasone) are significantly associated with reduced risk of AD in large patient databases.ConclusionThis study identifies potential underlying mechanisms of microglial subtypes involved in human AD brains, leading to potential drug targets for future development of microglia‐targeted therapies for AD.

Lower blood levels of miR‐29b‐3p in healthy middle‐aged AD risk gene carriers

AbstractBackgroundA number of late‐onset Alzheimer’s disease (AD) risk genes have been discovered, among which the most studied but not fully explored is the apolipoprotein E gene (APOE). PICALM (coding Phosphatidylinositol Binding Clathrin Assembly Protein) is another well‐recognized risk‐gene, shown to interact with the APOE gene in conferring AD risk. MicroRNAs (miRNAs) are post‐transcriptional regulators of mRNAs, some of which are known to be involved in AD pathology. The purpose of this study was to investigate in middle‐aged, healthy participants the association between AD risk‐genes (APOE and PICALM) and circulating miRNAs that were previously identified as altered in AD patients.MethodBlood samples were collected from 76 healthy individuals (36 F, 36 M; age: 56.38±3.16), assigned to three groups: A+P+ (APOE/PICALM risk), A+P‐ (APOE risk, PICALM neutral alleles) and N group (APOE/PICALM neutral alleles). RT‐qPCR was used to compare the levels of 11 microRNA identified by us in previous studies as candidate early AD biomarkers in blood plasma (hsa‐miR‐29b‐3p, hsa‐miR‐34a‐5p, hsa‐miR‐125b, hsa‐miR‐146a, hsa‐miR‐135a, hsa‐miR‐30b‐5p, hsa‐miR‐142‐3p, hsa‐miR‐200a‐3p, hsa‐miR‐483‐5p, hsa‐miR‐486‐5p, hsa‐miR‐502‐3p) [1, 2]. We followed standard procedures of blood assays.ResultSingle gene risk (APOE) carriers had lower levels of miR‐29b‐3p than non‐carriers and double risk carriers (F(2,73) = 12.75, p &lt; 0.001 with Welch homogeneity correction; post‐hoc with Tukey correction: p &lt; 0.01 for A+P‐ versus N, p &lt; 0.001 for A+P‐ versus A+P+). No other changes in miRNA panels were discovered.ConclusionDownregulation of miR‐29b‐3p in blood was detected repeatedly before in patients with AD, in 4 independent studies [1]. Here we show the same effect in a subpopulation of middle‐age, healthy individuals with APOE related genetic risk for AD. Further research is needed to understand the interaction reversing this effect in PICALM risk carriers. Longitudinal follow‐up may validate this blood‐based miRNA not only as an easy‐to‐access diagnostic biomarker, but also as a risk‐assessment biomarker for AD prevention.Funding: This work was funded by the Polish National Science Centre (NCN) grant no. 2018/31/N/HS6/03551, 2016/20/W/NZ4/00354 and 2018/29/B/NZ7/02757.[1], [2] https://doi.org/10.1016/j.arr.2018.10.008; 10.18632/oncotarget.15109.

Depression and Hippocampal Subfield Volume in Older Adults

AbstractBackgroundMajor Depressive Disorder (MDD) is associated with higher risk for developing Alzheimer’s Disease (AD), (Bennett &amp; Thomas, 2014). Both conditions are associated with smaller hippocampal subfield volumes, and both preferentially affect females (Shi et al., 2021). We examined the relationship between depression diagnosis and hippocampal subfield volume, by carrier status for AD genetic risk variant APOE4 and sex. We hypothesized that the association between depression and subfield volume would be stronger in females due to the higher rate of depression.MethodWe examined 1726 cognitively intact older adults from the Health and Aging Brain Study ‐ Health Disparities (HABS‐HD) cohort (Table1) who had available hippocampal high resolution MRI scans (Siemens Skyra or Vida‐3T). Scans were segmented into CA1, CA23DG, and subiculum using Automatic Segmentation of Hippocampal Subfields (ASHS) software and subfield volume was averaged bilaterally. We used separate multiple linear regressions to assess the association between depression and each hippocampal subfield volume, covarying for age, sex, years of education, number of MRI slices segmented, intracranial volume, and scanner. We corrected for multiple comparisons across regions using FDR correction. We also evaluated CA1 and CA23DG volume to depression diagnosis, stratifying by APOE4 positivity and sex and testing for formal interactions.ResultSee Table 2 for results. Depression was associated with smaller CA1 and CA23DG volume across all participants. Depression was associated with smaller CA1 and CA23DG in the APOE4 negative group, but not the APOE4 positive group. The depression by APOE4 interaction was significant for CA23DG volume (𝛽 = 0.25, p = 0.049). Depression was associated with smaller CA1 and CA23DG volumes in males, but not in females, with trend level interaction effects in the CA1 (𝛽 = 0.13, p = 0.095) and CA23DG (𝛽 = 0.17, p = 0.067).ConclusionDepression was associated with smaller CA1 and CA23DG volumes in older adults consistent with past literature. In contrast to our hypotheses, depression was associated with lower hippocampal subregional volumes more in those with lower risk for Alzheimer’s disease (male and APOE4‐ adults).Variability induced by other AD risk factors may mask the relationship between depression and hippocampal subregion volume when AD risk is higher.

Interest in genetic susceptibility testing and disclosure of AD dementia risk in cognitively normal adults: A survey study

AbstractBackgroundApolipoprotein‐E (APOE) genetic susceptiblity testing for Alzheimer’s disease (AD) dementia is becoming more important as clinical trials are increasingly targeting individuals carrying APOE4‐genotypes. As little is known about about the interest in knowing genetic risk for AD dementia in the general population. Our objective was to examine this in a sample of cognitively normal adults within a population‐based online research registry with the goal to implement APOEε4 status for trial recruitment.MethodAn online survey was completed by 442 cognitively normal participants between the age of 49 and 75 years (56% female) from the Dutch Brain Research Registry. The survey assessed interest in participation in research into, and disclosure of, genetic risk for dementia, and the knowing their genetic risk in different hypothetical risk scenarios (10%, 30%, and 50% genetic risk for dementia at age 85, corresponding to APOEε2/ε2 or ε2/ε3, APOEε3/ε4 or ε2ε4, and APOEε4/ε4 genotypes). All hypothetical scenarios were randomly presented to all participants. Cochran’s Q‐tests was used to analyse differences in frequencies across scenarios.ResultThe vast majority of participants was interested in participating in research and disclosure of their genetic risk (81%; Figure 1). The most reported reason was to contribute to scientific research (94%). Interest was higher in males, while lower‐educated participants more often reported to be unsure. When provided with different risk scenario’s, interest in knowing their risk was somewhat higher in the scenario’s with higher risk (50% scenario (79%) and 30% scenario (77%)) than in the 10% scenario (73%; χ2(2) = 19.91;p&lt;.001). Most individuals expected they would share their genetic risk with close relatives (77‐89%), would participate in medication trials (79‐88%), and would make long‐term arrangements, e.g. retirement, health care, will (69‐82%), with larger proportions for scenarios with higher hypothetical genetic risk.ConclusionOur findings indicate that the vast majority of cognitively normal adults participating in a research registry is interested in AD genetic risk research participation and disclosure. Interest in genetic risk disclosure is higher in scenarios corresponding to the APOEε4 genotypes. This suggests APOEε4 screening within an online research registry is potentially a well‐received method to accelerate inclusion for preclinical trials ultimately disclosing genetic risk.

Single cell multi‐omics implicates immune and vascular cells in Alzheimer’s etiology

AbstractBackgroundUnderstanding the genetic etiology of Alzheimer’s disease (AD) is critical to inform effective therapies but remains a challenge. Genetic heritability of late‐onset AD is ∼60‐80%, and genome‐wide association studies (GWAS) have uncovered dozens of noncoding single nucleotide polymorphisms (SNPs) that influence AD risk. Two challenges for the functional interpretation of AD genetic risk are (1) determining the cell types in which SNPs operate and (2) identifying the genes they dysregulate to drive AD pathogenesis. Single‐nucleus sequencing studies of human neurons, microglia, and other brain cell types have begun addressing these challenges. Yet, many AD risk SNPs remain unmapped. One possibility is that they are expressed in immunovascular brain cell types largely missed by current methods.MethodHere, we optimized Vessel Isolation and Nuclei Extraction for Sequencing (VINE‐seq) to capture multimodal gene expression and chromatin accessibility assays across all major brain cell types from 30 cognitively normal, MCI, and AD human prefrontal cortex samples.ResultWe discover early gene dysregulation in immune and vascular cell types along AD progression. We highlight the gene regulatory networks mediating this dysregulation and implicate processes associated with AD pathology and cognitive decline. Finally, we map noncoding AD risk variants to diverse immune and vascular cell types, thereby expanding our understanding of AD etiology.ConclusionDysfunction of diverse human brain immune and vascular cell types mediate the genetic risk for Alzheimer’s disease.

Mood disturbance and tau pathology in older women at risk for Alzheimer’s disease

AbstractBackgroundNeuropsychiatric symptoms, particularly depression, have been associated with Alzheimer’s disease (AD) biomarkers in individuals on the AD continuum. Although mood changes are a clinical manifestation of AD, research examining how the spectrum of common mood symptoms relates to AD biomarkers is limited. We examined the association between mood disturbance and tau pathology measured with positron emission tomography (PET) in older women at risk for AD and particular mood domains driving any associations.MethodParticipants included 18 women (Mage = 71.5, SDage = 3.3 years) with higher AD genetic risk (polygenetic hazard score ≥50th percentile) and mild impairment on the Montreal Cognitive Assessment who had completed the Profile of Mood States (POMS) questionnaire and a PET Scan as part of a larger research study. Those with formal psychiatric or neurodegenerative diagnoses were excluded. The POMS assessed six mood subcategories. The Total Mood Disturbance (TMD) was calculated as the sum of Tension, Depression, Anger, Fatigue, and Confusion subscores, minus the Vigor subscore. Tau standardized uptake value ratio (SUVR) were calculated for each Braak region of interest (ROI) (i.e., Braak 1‐2: transentorhinal stage, Braak 3‐4: limbic stage, and Braak 5‐6: isocortical stage). Linear regression models were conducted with TMD as the predictor and each Braak‐derived ROI as the outcome while controlling for age. Significant relationships were further probed by repeating analyses with each POMS subcategory as the predictor.ResultHigher POMS TMD scores significantly predicted higher tau‐PET SUVRs in Braak 1‐2 (β = 0.73, p&lt;0.01), Braak 3‐4 (β = 0.88, p&lt;0.001), and Braak 5‐6 (β = 0.72, p&lt;0.01) (Figure 1). Further analysis showed that the Tension subscore significantly predicted tau‐PET in all three regions (Figure 2) and Confusion significantly predicted tau‐PET in Braak 1‐2 and Braak 5‐6 (Figure 3).ConclusionMood disturbance was consistently associated with higher tau across all Braak regions in older women with higher AD risk. These relationships were strongest when reflecting the combination of mood symptoms, but tension may have a stronger influence than other subcategories. Longitudinal research should be done to assess the directionality of this relationship and to explore whether treatments for mood symptoms may have protective effects on Alzheimer’s pathogenesis before diagnosis.

Screening Alzheimer’s genetic risk factors against amyloid‐βeta synaptotoxicity

AbstractBackgroundSynapse degeneration is one of the earliest events in Alzheimer’s disease (AD) and toxic oligomers of amyloid‐beta (Aβ) peptide, cleavage product of APP, plays a major role in this process. Genome‐wide association studies recently reported 75 genomic risk loci for developing AD, but how the potential risk genes contribute to AD remains unknown. This project aims to identify AD genetic risk factors that mediate Aβ‐induced synaptotoxicity.MethodWe conducted a high‐content shRNA screening to assess the impact of ca. 200 AD risk genes on synaptic density and connectivity. Twenty‐four genes expressed in neurons with highest impact on synapses when silenced were shortlisted for a medium‐throughput screening to assess their capacity to block Aβ‐induced synaptotoxicity. Synaptotoxicity was modelled in microfluidic devices that allow primary postnatal rat neurons to be co‐cultured with Chinese hamster ovary cells, that overexpress wild‐type APP or APP with V717I (or London) mutation with increased secretion of Aβ1‐42 oligomers. Microfluidic devices allow the fluidic isolation of neurites from neuronal cell bodies and therefore provide exclusive access to pre‐ and post‐synaptic neurons. Target genes expression will be modulated either in pre‐ or post‐synaptic neurons and its impact on synaptic connectivity will be assessed.ResultBased on the shRNA screening, we shortlisted 17 detrimental genes, for which we obtained overexpression vectors packed in lentiviruses, and 6 protective genes. We have developed a medium‐throughput co‐culture device that permits screening twelve genes per imaging session using the INCell 6000 automated microscope, as well as an automated image analysis workflow for detecting and assigning presynaptic to postsynaptic puncta based on their relative proximity. Gene expression modulation is validated and the screen is on‐going.ConclusionWe have developed a microfluidic co‐culture model to rapidly and systematically interrogate genetic risk factors for their impact on synaptic connectivity. This study will help us identify AD genetic risk factors with a potential to block Aβ‐induced synaptotoxicity in vitro. Hit genes will be functionally validated via microelectrode array recordings.

Skipping of FCER1G Exon 2 Is Common in Human Brain But Not Associated with the Alzheimer's Disease Genetic Risk Factor rs2070902.

Understanding the mechanisms whereby genetic variants influence the risk of Alzheimer's disease (AD) may provide insights into treatments that could reduce AD risk. Here, we sought to test the hypothesis that a single nucleotide polymorphism (SNP) associated with AD risk, rs2070902, influences splicing of FCER1G exon 2. AD and non-AD brain samples were analyzed for FCER1G expression by genotyping, immunohistochemistry, immunofluorescence, and qPCR. The protein encoded by FCER1G, FcRγ, is robustly expressed in microglia in both AD and non-AD brain. The FCER1G isoform lacking exon 2 (D2-FCER1G) was readily detectable. Moreover, the proportion of FCER1G expressed as this isoform was increased in brains with high AD neuropathology. However, the proportion of FCER1G expressed as the D2-FCER1G isoform was not associated with rs2070902 genotype. In summary, the proportion of FCER1G expressed as the D2-FCER1G isoform is increased with AD neuropathology but is not associated with rs2070902.