Alzheimer's Disease Risk Genes Research Articles

Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer's disease progression.

Late onset Alzheimer's disease (AD) is a progressive neurodegenerative disease, with brain changes beginning years before symptoms surface. AD is characterized by neuronal loss, the classic feature of the disease that underlies brain atrophy. However, GWAS reports and recent single-nucleus RNA sequencing (snRNA-seq) efforts have highlighted that glial cells, particularly microglia, claim a central role in AD pathophysiology. Here, we tailor pattern-learning algorithms to explore distinct gene programs by integrating the entire transcriptome, yielding distributed AD-predictive modules within the brain's major cell-types. We show that these learned modules are biologically meaningful through the identification of new and relevant enriched signaling cascades. The predictive nature of our modules, especially in microglia, allows us to infer each subject's progression along a disease pseudo-trajectory, confirmed by post-mortem pathological brain tissue markers. Additionally, we quantify the interplay between pairs of cell-type modules in the AD brain, and localized known AD risk genes to enriched module gene programs. Our collective findings advocate for a transition from cell-type-specificity to gene modules specificity to unlock the potential of unique gene programs, recasting the roles of recently reported genome-wide AD risk loci.

Identification of senescent, TREM2-expressing microglia in aging and Alzheimer's disease model mouse brain.

Alzheimer's disease (AD) and dementia in general are age-related diseases with multiple contributing factors, including brain inflammation. Microglia, and specifically those expressing the AD risk gene TREM2, are considered important players in AD, but their exact contribution to pathology remains unclear. In this study, using high-throughput mass cytometry in the 5×FAD mouse model of amyloidosis, we identified senescent microglia that express high levels of TREM2 but also exhibit a distinct signature from TREM2-dependent disease-associated microglia (DAM). This senescent microglial protein signature was found in various mouse models that show cognitive decline, including aging, amyloidosis and tauopathy. TREM2-null mice had fewer microglia with a senescent signature. Treating 5×FAD mice with the senolytic BCL2 family inhibitor ABT-737 reduced senescent microglia, but not the DAM population, and this was accompanied by improved cognition and reduced brain inflammation. Our results suggest a dual and opposite involvement of TREM2 in microglial states, which must be considered when contemplating TREM2 as a therapeutic target in AD.

An X Chromosome Transcriptome Wide Association Study Implicates ARMCX6 in Alzheimer's Disease.

The X chromosome is often omitted in disease association studies despite containing thousands of genes that may provide insight into well-known sex differences in the risk of Alzheimer's disease (AD). To model the expression of X chromosome genes and evaluate their impact on AD risk in a sex-stratified manner. Using elastic net, we evaluated multiple modeling strategies in a set of 175 whole blood samples and 126 brain cortex samples, with whole genome sequencing and RNA-seq data. SNPs (MAF > 0.05) within the cis-regulatory window were used to train tissue-specific models of each gene. We apply the best models in both tissues to sex-stratified summary statistics from a meta-analysis of Alzheimer's Disease Genetics Consortium (ADGC) studies to identify AD-related genes on the X chromosome. Across different model parameters, sample sex, and tissue types, we modeled the expression of 217 genes (95 genes in blood and 135 genes in brain cortex). The average model R2 was 0.12 (range from 0.03 to 0.34). We also compared sex-stratified and sex-combined models on the X chromosome. We further investigated genes that escaped X chromosome inactivation (XCI) to determine if their genetic regulation patterns were distinct. We found ten genes associated with AD at p < 0.05, with only ARMCX6 in female brain cortex (p=0.008) nearing the significance threshold after adjusting for multiple testing (α=0.002). We optimized the expression prediction of X chromosome genes, applied these models to sex-stratified AD GWAS summary statistics, and identified one putative AD risk gene, ARMCX6.

A systems biology-based identification and invivo functional screening of Alzheimer's disease risk genes reveal modulators of memory function.

Genome-wide association studies (GWASs) have uncovered over 75 genomic loci associated with risk for late-onset Alzheimer's disease (LOAD), but identification of the underlying causal genes remains challenging. Studies of induced pluripotent stem cell (iPSC)-derived neurons from LOAD patients have demonstrated the existence of neuronal cell-intrinsic functional defects. Here, we searched for genetic contributions to neuronal dysfunction in LOAD using an integrative systems approach that incorporated multi-evidence-based gene mapping and network-analysis-based prioritization. A systematic perturbation screening of candidate risk genes in Caenorhabditis elegans (C.elegans) revealed that neuronal knockdown of the LOAD risk gene orthologs vha-10 (ATP6V1G2), cmd-1 (CALM3), amph-1 (BIN1), ephx-1 (NGEF), and pho-5 (ACP2) alters short-/intermediate-term memory function, the cognitive domain affected earliest during LOAD progression. These results highlight the impact of LOAD risk genes on evolutionarily conserved memory function, as mediated through neuronal endosomal dysfunction, and identify new targets for further mechanistic interrogation.

The ABC's of Alzheimer risk gene ABCA7.

Alzheimer's disease (AD) is a growing problem worldwide. Since ABCA7's identification as a risk gene, it has been extensively researched for its role in the disease. We review its recently characterized structure and what the mechanistic insights teach us about its function. We furthermore provide an overview of identified ABCA7 mutations, their presence in different ancestries and protein domains and how they might cause AD. For ABCA7 PTC variants and a VNTR expansion, haploinsufficiency is proposed as the most likely mode-of-action, although splice events could further influence disease risk. Overall, the need to better understand expression of canonical ABCA7 and its isoforms in disease is indicated. Finally, ABCA7's potential functions in lipid metabolism, phagocytosis, amyloid deposition, and the interplay between these three, is described. To conclude, in this review, we provide a comprehensive overview and discussion about the current knowledge on ABCA7 in AD, and what research questions remain. HIGHLIGHTS: Alzheimer's risk-increasing variants in ABCA7 can be found in up to 7% of AD patients. We review the recently characterized protein structure of ABCA7. We present latest insights in genetics, expression patterns, and functions of ABCA7.

The Alzheimer's disease risk gene BIN1 regulates activity-dependent gene expression in human-induced glutamatergic neurons.

Bridging Integrator 1 (BIN1) is the second most important Alzheimer's disease (AD) risk gene, but its physiological roles in neurons and its contribution to brain pathology remain largely elusive. In this work, we show that BIN1 plays a critical role in the regulation of calcium homeostasis, electrical activity, and gene expression of glutamatergic neurons. Using single-cell RNA-sequencing on cerebral organoids generated from isogenic BIN1 wild type (WT), heterozygous (HET) and homozygous knockout (KO) human-induced pluripotent stem cells (hiPSCs), we show that BIN1 is mainly expressed by oligodendrocytes and glutamatergic neurons, like in the human brain. Both BIN1 HET and KO cerebral organoids show specific transcriptional alterations, mainly associated with ion transport and synapses in glutamatergic neurons. We then demonstrate that BIN1 cell-autonomously regulates gene expression in glutamatergic neurons by using a novel protocol to generate pure culture of hiPSC-derived induced neurons (hiNs). Using this system, we also show that BIN1 plays a key role in the regulation of neuronal calcium transients and electrical activity via its interaction with the L-type voltage-gated calcium channel Cav1.2. BIN1 KO hiNs show reduced activity-dependent internalization and higher Cav1.2 expression compared to WT hiNs. Pharmacological blocking of this channel with clinically relevant doses of nifedipine, a calcium channel blocker, partly rescues electrical and gene expression alterations in BIN1 KO glutamatergic neurons. Further, we show that transcriptional alterations in BIN1 KO hiNs that affect biological processes related to calcium homeostasis are also present in glutamatergic neurons of the human brain at late stages of AD pathology. Together, these findings suggest that BIN1-dependent alterations in neuronal properties could contribute to AD pathophysiology and that treatment with low doses of clinically approved calcium blockers should be considered as an option to slow disease-onset and progression.

Early amyloid-induced changes in microglia gene expression in male APP/PS1 mice.

Alzheimer's disease (AD) is a progressive neurodegenerative disease and the most common cause of dementia, characterized by deposition of extracellular amyloid-beta (Aβ) aggregates and intraneuronal hyperphosphorylated Tau. Many AD risk genes, identified in genome-wide association studies (GWAS), are expressed in microglia, the innate immune cells of the central nervous system. Specific subtypes of microglia emerged in relation to AD pathology, such as disease-associated microglia (DAMs), which increased in number with age in amyloid mouse models and in human AD cases. However, the initial transcriptional changes in these microglia in response to amyloid are still unknown. Here, to determine early changes in microglia gene expression, hippocampal microglia from male APPswe/PS1dE9 (APP/PS1) mice and wild-type littermates were isolated and analyzed by RNA sequencing (RNA-seq). By bulk RNA-seq, transcriptomic changes were detected in hippocampal microglia from 6-months-old APP/PS1 mice. By performing single-cell RNA-seq of CD11c-positive and negative microglia from 6-months-old APP/PS1 mice and analysis of the transcriptional trajectory from homeostatic to CD11c-positive microglia, we identified a set of genes that potentially reflect the initial response of microglia to Aβ.

Differential effects of SORL1 deficiency on the endo-lysosomal network in human neurons and microglia.

The endosomal gene SORL1 is a strong Alzheimer's disease (AD) risk gene that harbours loss-of-function variants causative for developing AD. The SORL1 protein SORL1/SORLA is an endosomal receptor that interacts with the multi-protein sorting complex retromer to traffic various cargo through the endo-lysosomal network (ELN). Impairments in endo-lysosomal trafficking are an early cellular symptom in AD and a novel therapeutic target. However, the cell types of the central nervous system are diverse and use the ELN differently. If this pathway is to be effectively therapeutically targeted, understanding how key molecules in the ELN function in various cell types and how manipulating them affects cell-type specific responses relative to AD is essential. Here, we discuss an example where deficiency of SORL1 expression in a human model leads to stress on early endosomes and recycling endosomes in neurons, but preferentially leads to stress on lysosomes in microglia. The differences observed in these organelles could relate to the unique roles of these cells in the brain as neurons are professional secretory cells and microglia are professional phagocytic cells. Experiments to untangle these differences are fundamental to advancing the understanding of cell biology in AD and elucidating important pathways for therapeutic development. Human-induced pluripotent stem cell models are a valuable platform for such experiments. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.

Cell type-specific functions of Alzheimer's disease endocytic risk genes.

Endocytosis is a key cellular pathway required for the internalization of cellular nutrients, lipids and receptor-bound cargoes. It is also critical for the recycling of cellular components, cellular trafficking and membrane dynamics. The endocytic pathway has been consistently implicated in Alzheimer's disease (AD) through repeated genome-wide association studies and the existence of rare coding mutations in endocytic genes. BIN1 and PICALM are two of the most significant late-onset AD risk genes after APOE and are both key to clathrin-mediated endocytic biology. Pathological studies also demonstrate that endocytic dysfunction is an early characteristic of late-onset AD, being seen in the prodromal phase of the disease. Different cell types of the brain have specific requirements of the endocytic pathway. Neurons require efficient recycling of synaptic vesicles and microglia use the specialized form of endocytosis-phagocytosis-for their normal function. Therefore, disease-associated changes in endocytic genes will have varied impacts across different cell types, which remains to be fully explored. Given the genetic and pathological evidence for endocytic dysfunction in AD, understanding how such changes and the related cell type-specific vulnerabilities impact normal cellular function and contribute to disease is vital and could present novel therapeutic opportunities. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.

Integrative Analysis of the Age-Related Dysregulated Genes Reveals an Inflammation and Immunity-Associated Regulatory Network in Alzheimer's Disease.

Alzheimer's disease (AD) is a neurodegenerative disease with a long incubation period. While extensive research has led to the construction of long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) regulatory networks, which primarily derived from differential analyses between clinical AD patients and control individuals or mice, there remains a critical knowledge gap pertaining to the dynamic alterations in transcript expression profiles that occur with age, spanning from the pre-symptomatic stage to the onset of AD. In the present study, we examined the transcriptomic changes in AD model mice at three distinct stages: the unaffected (un-) stage, the pre-onset stage, and the late-onset stage, and identified 14, 57, and 99 differentially expressed mRNAs (DEmRs) in AD model mice at 3, 6, and 12months, respectively. Among these, we pinpointed 16 mRNAs closely associated with inflammation and immunity and excavated their lncRNA-mRNA regulatory network based on a comprehensive analysis. Notably, our preliminary analysis suggested that four lncRNAs (NONMMUT102943, ENSMUST00000160309, NONMMUT083044, and NONMMUT126468), eight miRNAs (miR-34a-5p, miR-22-5p, miR-302a/b-3p, miR-340-5p, miR-376a/b-5p, and miR-487b-5p), and four mRNAs (C1qa, Cd68, Ctss, and Slc11a1) may play pivotal roles in orchestrating immune and inflammatory responses during the early stages of AD. Our study has unveiled age-related AD risk genes, and provided an analytical framework for constructing lncRNA-mRNA networks using time series data and correlation analysis. Most notably, we have successfully constructed a comprehensive regulatory ceRNA network comprising genes intricately linked to inflammatory and immune functions in AD.

Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer’s disease

Triggering receptor expressed on myeloid cells 2 (TREM2) plays a critical role in microglial activation, survival, and apoptosis, as well as in Alzheimer’s disease (AD) pathogenesis. We previously reported the MS4A locus as a key modulator for soluble TREM2 (sTREM2) in cerebrospinal fluid (CSF). To identify additional novel genetic modifiers of sTREM2, we performed the largest genome-wide association study (GWAS) and identified four loci for CSF sTREM2 in 3,350 individuals of European ancestry. Through multi-ethnic fine mapping, we identified two independent missense variants (p.M178V in MS4A4A and p.A112T in MS4A6A) that drive the association in MS4A locus and showed an epistatic effect for sTREM2 levels and AD risk. The novel TREM2 locus on chr 6 contains two rare missense variants (rs75932628 p.R47H, P=7.16×10-19; rs142232675 p.D87N, P=2.71×10-10) associated with sTREM2 and AD risk. The third novel locus in the TGFBR2 and RBMS3 gene region (rs73823326, P=3.86×10-9) included a regulatory variant with a microglia-specific chromatin loop for the promoter of TGFBR2. Using cell-based assays we demonstrate that overexpression and knock-down of TGFBR2, but not RBMS3, leads to significant changes of sTREM2. The last novel locus is located on the APOE region (rs11666329, P=2.52×10-8), but we demonstrated that this signal was independent of APOE genotype. This signal colocalized with cis-eQTL of NECTIN2 in the brain cortex and cis-pQTL of NECTIN2 in CSF. Overexpression of NECTIN2 led to an increase of sTREM2 supporting the genetic findings. To our knowledge, this is the largest study to date aimed at identifying genetic modifiers of CSF sTREM2. This study provided novel insights into the MS4A and TREM2 loci, two well-known AD risk genes, and identified TGFBR2 and NECTIN2 as additional modulators involved in TREM2 biology.

Negative Regulation of Cathepsins by β-Amyloid.

Genome wide association study (GWAS) uncovered Alzheimer's disease (AD) risk genes linked to the endo-lysosomal pathway. This pathway seems to be the gateway of protein aggregates, such as tau and α-synuclein, to the cytoplasm. Furthermore, we and others reported that the amyloid precursor protein (APP) C99 is predominantly processed by γ-secretase in the endo-lysosomal compartments, and β-amyloid (Aβ) peptides are enriched in the same subcellular loci. While the role(s) of APP/Aβ in the endo-lysosomal pathway has not been fully established, a recent study reported that Aβ, in particular Aβ42, inhibits cathepsin D (CTSD) activity. Here, we show using a cell-free in vitro assay that Aβ42 also blocks cathepsin B (CTSB) activity. Furthermore, we uncovered that the autocatalytic processing (i.e., conversion of single chain to heavy/light chains) of CTSB and CTSD is accelerated in APP-deficient cells compared with wild-type controls. Taken together, our findings further support the negative regulation of cathepsins by Aβ.

Identification of candidate DNA methylation biomarkers related to Alzheimer’s disease risk by integrating genome and blood methylome data

Alzheimer disease (AD) is a common neurodegenerative disease with a late onset. It is critical to identify novel blood-based DNA methylation biomarkers to better understand the extent of the molecular pathways affected in AD. Two sets of blood DNA methylation genetic prediction models developed using different reference panels and modelling strategies were leveraged to evaluate associations of genetically predicted DNA methylation levels with AD risk in 111,326 (46,828 proxy) cases and 677,663 controls. A total of 1,168 cytosine-phosphate-guanine (CpG) sites showed a significant association with AD risk at a false discovery rate (FDR) < 0.05. Methylation levels of 196 CpG sites were correlated with expression levels of 130 adjacent genes in blood. Overall, 52 CpG sites of 32 genes showed consistent association directions for the methylation-gene expression-AD risk, including nine genes (CNIH4, THUMPD3, SERPINB9, MTUS1, CISD1, FRAT2, CCDC88B, FES, and SSH2) firstly reported as AD risk genes. Nine of 32 genes were enriched in dementia and AD disease categories (P values ranged from 1.85 × 10-4 to 7.46 × 10-6), and 19 genes in a neurological disease network (score = 54) were also observed. Our findings improve the understanding of genetics and etiology for AD.

The association between 73 Alzheimer’s disease risk variants and white matter microstructural decline in aging

AbstractBackgroundAlthough several prior diffusion MRI studies have indicated a role of medial temporal lobe (MTL) white matter microstructural decline in Alzheimer’s disease (AD), it is unclear which AD risk genes are associated with this decline. The goal of this study is to leverage multi‐site harmonized diffusion MRI data to investigate the relationship between 73 AD risk variants and microstructural decline in MTL tracts.MethodThe dataset used in this study was collated from three longitudinal cohorts of aging [Alzheimer’s Neuroimaging Initiative (ADNI), Baltimore Longitudinal Study of Aging (BLSA), Vanderbilt Memory &amp; Aging Project (VMAP)]. In total, this dataset included 1,308 participants (70% cognitively unimpaired, 27% MCI, 3% AD) aged 50+ who had both diffusion MRI and genotype data and includes a total of 3,442 imaging sessions (mean number of visits: 2.68 ± 1.66, interval range: 1 ‐ 12 years). Genotype data was preprocessed using a standardized approach, and the dosage of the 73 AD risk variants was extracted. Diffusion MRI data was preprocessed using the PreQual pipeline and free‐water (FW) correction was conducted to obtain FW and FW‐corrected fractional anisotropy (FAFWcorr) maps. FW and FAFWcorr were quantified within 5 MTL tracts, including the cingulum, fornix, uncinate fasciculus, inferior longitudinal fasciculus, which were subsequently harmonized using the Longitudinal ComBat package. Linear regression was conducted to investigate the association between AD risk variants and MTL microstructure at baseline, while linear mixed effects regression was used for longitudinal analysis. All models were corrected for age at baseline and sex and corrected for multiple comparisons using the FDR approach.ResultAt baseline, APOE‐e4 dosage was strongly associated with MTL FW in all tracts, with additional associations for TMEM106B and CR1 dosages with fornix FW (Table 1). Longitudinally, APOE‐e4 dosage was a strong predictor of MTL FW decline in all tracts, and KAT8, CR1, and TMEM106B dosages exhibited significant associations with fornix microstructural decline (Table 2 and Figure 1).ConclusionThis study suggests that although APOE‐e4 is the strongest predictor of white matter microstructural decline, several other AD risk genes (i.e., CR1, SPI1, TMEM106B, KAT8) contribute to decline, particularly in the fornix.

RNA‐seq study on the effect of MAPT rs242557 deletion in HMC3 cells

AbstractBackgroundMicrotubule associated protein tau (MAPT) is associated with neurodegenerative diseases including Frontotemporal dementia (FTD), Progressive supranuclear palsy (PSP), Corticobasal degeneration (CBD), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Multiple GWAS on AD, PD, PSP and CBD have identified strong signal in MAPT intronic region (SNP, rs242557). Being part of FANTOM5 enhancer in eye and brain, we are interested in the effect of this region in HMC3 (human microglial clone 3) cell line.MethodUsing CRISPR‐Cas9 genome editing, a clone was isolated having homozygous 309 bp deletion encompassing rs242557 and its flanking sequences in HMC3. Sanger sequencing confirmed the deletion while whole genome sequencing corroborated the same and also confirmed no off‐target effects. To identify gene transcripts whose expression was altered due to the deletion, paired‐end RNA‐seq was performed using total RNA extracted from rs242557 KO and wild type (WT) clones.ResultThere were 272 up‐ and 861 down‐regulated transcripts (p&lt; = 0.01) between WT and KO cells. Down‐regulated transcripts include AD risk genes ICA1, EPDR1, PTK2B, SORL1, DOC2A, and TSPOAP1, and PD candidate gene, SNCA. Notable among up‐regulated transcripts was AD risk gene, CASS4. Enrichment analyses revealed biological processes and pathways that are related to structural constituents and organization of neurons and synapses. Currently, we are validating the transcript data.ConclusionOur preliminary data suggests that the genomic region encompassing rs242557 might affect multiple AD risk genes.

Deciphering the Genomic Regulatory Architecture of iPSC Derived Oligodendrocytes from Diverse Ancestries for Alzheimer’s Disease Studies

AbstractBackgroundThe effect of variants associated with Alzheimer’s disease (AD) can be influenced by ancestry, which determines the genomic regulatory architecture (GRA). A global understanding of GRA in the context of AD is imperative to interpret the variability associated with AD risk genes across populations. Most studies up to date have focused on studying GRA in European ancestry, in this study we aimed at determining the GRA in African, Amerindian, and European ancestries. Since GRA is cell specific, we developed a human induced pluripotent cells (hiPSC) based model for oligodendrocytes (OLs), a cell type which has limited studies focused on AD.MethodCells from AD patients or non‐cognitively impaired controls with &gt;90% of either Amerindian, African or European global ancestry were differentiated using a modified multi‐stage protocol that promotes the development and enrichment of oligodendrocytes in neural spheroids. After terminal differentiation, cells were collected and lysed to isolate nuclei for Multiomic profiling of chromatin accessibility and transcriptome using Single Cell ATAC and Single Cell RNA‐seq. Additionally, we examined chromatin interactions using Hi‐C analyses.ResultWe identified oligodendrocyte lineage cells at different stages of development ranging from dividing cells with transcriptional profiles consistent with those of oligodendrocyte precursor cells (OPC) to mature myelinating oligodendrocytes. We compared the oligodendrocytes clusters across ancestries, cases versus controls and APOE genotypes to characterize the genomic landmarks and signatures associated with AD related GWAS loci. Astrocytes and neurons were also derived within our 3D spheroids, allowing us to study ancestry‐related cell type specific changes in GRA.ConclusionOur results provide ancestry‐specific insights into oligodendrocyte chromatin structure and gene regulation in the context of AD. These results offer an integrated view of the GRA of a previously overlooked cell lineage that constitute a large population in the central nervous system and is compromised during AD in terms of abundance and function. This will expand the available functional resources for gene identification studies in African American and Hispanic/Latino studies.

Understanding the role of the mitochondrial AD risk gene LACTB in myeloid cells.

AbstractBackgroundAlthough powerful evidence points out the importance of myeloid cells in Alzheimer’s Disease (AD), the relevance of immunometabolism requires further exploration. Our analysis integrating AD genetics and myeloid cell genomics reported that lower LACTB expression is protective for AD, and proteomics studies have confirmed it (Wingo et al., 2021). LACTB is a mitochondrial serin protein that may influence mitochondrial morphology and bioenergetics. LACTB levels are associated with succinyl‐carnitine levels (Ghazalpour et al., 2014, Suhre et al., 2011), a metabolite that has been linked to AD risk (unpublished). LACTB has also been nominated as a tumor‐related and an obesity gene, but its function is not well defined.MethodsTHP1 cells were treated for 6 days with small‐interfering RNA to reduce LACTB expression. iPS cells were CRISPR‐edited to obtain LACTB knock‐out (KO) lines and differentiated into microglial cells (iMGLs). Functional experiments were performed. Collected samples were outsourced for RNAseq, metabolomic and lipidomic analysis.Resultswe characterized, for the first time, the role of LACTB in myeloid cells. We observed that LACTB expression is increased upon differentiation (in iMGLs compared to iPSC, and in THP1 macrophages compared to monocytes) and LPS stimulation. The downregulation of LACTB in THP1 led to an increase in succinyl‐carnitine (predicted to be protective for AD), and in histone succinylation, which may modify the cell epigenetics. Transcriptomics revealed an increase in the oxidative phosphorylation, which was validated by Seahorse experiments, and in the immune response to interferon and virus. In addition, LACTB knock‐down polarized THP1 macrophages towards a DAM‐like state. Lipidomics reported significant changes in specific lipid classes and a decrease in chain saturation. These experiments will be repeated in iMGLs.ConclusionLACTB may play a role in cell differentiation and response to stimulus in myeloid cells by modifying mitochondrial respiration and lipid metabolism. As future directions, iMGLs will be xenotransplanted in WT and 5xFAD mice to study LACTB role in vivo. Unlike other AD risk genes, LACTB encodes an enzyme, reduced expression is protective, and succinyl‐carnitine can be used as a biomarker, which highlights it as a promising AD therapeutic target.

Widespread transposable element dysregulation in human brains with Alzheimer’s disease

AbstractBackgroundTransposable elements (TEs), known as “jumping genes” or “viral elements”, constitute approximately 45% of the human genome. However, transposable element (TE) dysregulation of quantitative trait loci (QTL) has not been well‐characterized in human disease, such as Alzheimer’s disease (AD).MethodIn this study, we present the first catalog of transposable element quantitative trait loci (teQTLs) in human brains. By leveraging large‐scale RNA‐sequencing (RNA‐seq), whole‐genome sequencing (WGS), and various QTL data (xQTL) from three brain biobanks with Alzheimer’s disease (AD), we comprehensively characterize TE dysregulation across diverse AD pathobiology, including Tau, amyloid beta, APOE genotypes, and sex differences. We further integrate different types of QTLs with GWAS loci from 278,950 AD cases and 1,780,303 controls to identify AD likely causal genes regulated by brain teQTLs through colocalization analysis. Regulatory roles of brain teQTLs are dissected via long‐range cell type‐specific enhancer‐promoter chromatin interaction maps.ResultJoint‐analysis of WGS and RNA‐seq data identified 77,335 genome‐wide significant TE expression QTLs (teQTLs) in human AD brains. Colocalization analysis of teQTLs with GWAS loci from 278,950 AD cases and 1,780,303 controls identified key AD likely causal genes regulated by brain teQTLs. This identified new AD risk genes, including complement C1q tumor necrosis factor‐related protein 4 (C1QTNF4) and farnesyl‐diphosphate farnesyltransferase 1 (FDFT1). A TE from Plat_L3 subfamily (chr11: 47605296‐47605575) suppressed expression of C1QTNF4 (its nearest gene) via long‐range enhancer‐promoter chromatin interaction in neurons. We identified that a TE from AluSz6 subfamily (chr8: 11834847‐11835127) increased expression of FDFT1 (its nearest gene) via microglia‐specific long‐range chromatin looping. Expression perturbation of FDFT1 and C1QTNF4 were significantly correlated with Braak staging score of AD patients. We further identified that individuals with AD risk allele APOE4 displayed elevated expression of AluSz6 and FDFT1 in patient induced pluripotent stem cells (iPSC)‐derived microglia and superior frontal gyrus (SFG) microglia compared to APOE3 individuals.ConclusionThese findings demonstrate widespread TE dysregulation in human brains and teQTLs offer a useful QTL analytic approach to identify AD risk genes and other complex diseases if broadly applied.

TREM2‐related Polygenic Risk Score predicts defect Innate Immune Activation in Alzheimer’s Disease

AbstractBackgroundTREM2 plays a central role in immune response which, in turn, is strongly related to Alzheimer’s disease (AD) pathology. We previously found an AD‐subtype with and without innate immune activation based on CSF proteomics. Possibly, genes associated with TREM2 pathways could explain differences between these two subtypes since R47H and R62H mutations are associated with decreased microglial activation. We tested this hypothesis in a large single site cohort, and compared them on PRS including previously reported GWAS genes associated with TREM2 pathways.MethodWe included participants from the Amsterdam Dementia Cohort who had AD subtyping based on CSF proteomics available (n = 466). Based on literature, we labelled 19 of 83 known AD risk genes as belonging to TREM2 pathways and used these to construct a TREM2‐PRS. We studied associations between a standard AD‐PRS with 83 SNPs, TREM2‐PRS with 19 SNPs and non‐TREM2‐PRS with 64 SNPs between two AD‐subtypes being (1) without innate immune activation and (2) with innate immune activation, using logistic regression models (correcting for sex, age and 5 principal components).ResultThe cohort involved 146 controls (mean age 61 years, 34% female) and 195 AD cases: 97 without immune activation subtype (mean age 64 years, 52% female) and 98 with immune activation subtype (mean age 68 years, 54% female). Both subtypes showed comparable increased risk on the standard AD‐PRS compared to controls (OR 1.65, 95%CI 1.2‐2.3, p = 0.002 and OR 1.7, 95%CI 1.1‐2.5, p = 0.006) (Table 1). A higher TREM2‐PRS was associated with no immune activation subtype (OR 1.5, 95%CI 1.1‐2.1, p = 0.008). The PRS of the other 64 risk variants, which were not labelled as belonging to TREM2 pathways, was associated with immune activation subtype (OR 1.5, 95%CI 1.1‐2.1, p = 0.02).ConclusionAD individuals with a CSF proteomic‐based subtype without immune activation show more genetic variants in TREM2 pathways, whereas these SNPs are not related to the subtype with innate immune activation. These findings provide evidence for genetic differences underlying AD‐subtypes, and suggest that therapies targeting immune functioning may need to tailor therapies to AD‐subtype (i.e., additional activation vs. decreasing activation).

Alzheimer’s disease risk genes modulate interferon‐responsive microglia

AbstractBackgroundHuman genetic studies and quantitative trait loci (eQTL) analyses have implicated microglia, the innate immune cells of the brain, as critical players in Alzheimer’s disease (AD). In response, the field has focused on defining microglial transcriptional states across many models of neurodegeneration. Integrating these studies, we find several microglial activation states commonly enriched in AD. These include Disease Associated Microglia, Antigen‐Presenting Microglia, and Interferon‐Responsive Microglia. To truly make use of this data, we now must move towards understanding the functional consequence of these microglial activation states and uncovering the mechanisms that drive changes in cell states during disease.MethodTo determine regulators of the interferon‐responsive microglial activation state, we performed a functional genomic screen using CRISPR interference (CRISPRi). To avoid bottlenecking of CRISPR guide RNAs and accommodate the large numbers of cells needed for screening, we implemented a novel transcription‐factor driven approach to differentiate iPSC‐derived microglia. After differentiation, microglia harboring individual gene knockdowns were primed with type I interferon and screened on expression of IFIT1, a key marker of the interferon‐responsive microglial state.ResultThese experiments have uncovered both canonical regulators of interferon signaling as well as novel regulators of the interferon‐responsive microglial state. Furthermore, several known AD risk genes were shown to inhibit microglial entry into this state, suggesting a potential mechanism whereby these nodes may influence disease risk.ConclusionRecent transcriptomic studies have uncovered significant heterogeneity of microglial states including the discovery of several disease associated states. However, it remains unclear whether these states represent beneficial, disease‐fighting functions or detrimental, disease‐promoting functions. Gaining the ability to selectively control entry into specific microglial states will allow novel investigations into how these specific microglial states interact with and guide disease trajectories.