INTRODUCTION:Neuropsychiatric symptoms (NPSs) occur in up to 85% of Alzheimer's disease (AD) cases. Current treatments - repurposed from psychiatric disorders despite limited understanding of etiologic overlap - are often ineffective. METHODS:To characterize the genetic overlap between AD and major psychiatric disorders and identify shared molecular pathways, we conducted genetic correlation analyses between AD and depression, schizophrenia, bipolar disorder, and anxiety using MiXeR and Local Analysis of [co]Variant Annotation with genome wide association studies (GWAS) summary statistics (AD: n = 487,511; bipolar disorder: n = 413,466; depression: n = 1,154,267; schizophrenia: n = 130,644; anxiety: n = 1,096,458). RESULTS:Local genetic correlation analyses followed by fine mapping and functional analyses identified a missense variant in TMEM106B (rs3173615) shared between AD and depression and anxiety, a regulatory region variant in ACE (rs4292) shared between AD/schizophrenia, and two nonsense-mediated mRNA decay transcript variants in ERC2 (rs17288728; rs815460) shared between AD/anxiety. DISCUSSION:The specific molecular pathways associated with these variants provide critical information on shared etiologic components underlying these traits and inform development of improved therapeutic targets.

Multiple sclerosis (MS) is a complex immune-mediated disorder with polygenic and multicellular underpinnings, necessitating cell-type-specific molecular studies to delineate dysregulated pathways. Here, we profile 1,075 transcriptomes from 167 patients with MS and 42 healthy participants across six peripheral immune cell-type-states. MS-associated transcriptional differences are more pronounced in primary (unstimulated) immune cells than in in vitro-stimulated counterparts. We identify shared and cell-type-specific transcriptional alterations at the level of genes, pathways, and co-expressed gene modules, prioritizing regulators, such as ZBTB16, across T cells and monocytes, and replicating six MS-associated modules in independent datasets. The top T cell module is enriched for MS susceptibility genes and affects proliferation. The top monocyte module implicates dysregulated TNF-α/NF-κB signaling, for which an in silico drug screen and in vitro validation nominate alvespimycin as a candidate modulator. Together, these findings define stable peripheral immune dysregulation signatures in MS that may serve as diagnostic or prognostic biomarkers in at-risk individuals.

Alzheimer's disease (AD) is marked by the coordinated emergence of disease-associated cell states across multiple cell types. Here, we first performed a meta-analysis of single-nucleus transcriptomic (snRNAseq) data from 869 brains of diverse decedents, confirming the critical role of an SLC38A2 high SMTN high CACNA1D high astrocyte subset, Astrocyte 10 (Ast10), in AD and aging-related cognitive decline. We then investigated the signaling drivers of Ast10's emergence in the aging brain, focusing on interactions among microglial and astrocytic subsets. Analysis of the snRNAseq data prioritized a set of ligands and receptors that are robustly predictive of Ast10 proportions across participants, and we confirm our predictions in multiple studies. Independent validation with spatial transcriptomics reveals striking colocalization of these prioritized ligands with the Ast10 signature in AD brain tissue, but not with other astrocytic states. Genetic ablation of a top receptor PLXNB1 in murine and human iPSC-derived astrocytes decreased the Ast10 signature, confirming its regulatory role. Finally, we find that Ast10 may contribute to cognitive decline through synaptic loss and is associated with cognitive decline independent of AD. Thus, Ast10 and its regulators are potential points of convergence for multiple neurodegenerative mechanisms and may be promising targets for therapeutic development to preserve cognitive function.

Myeloid cells, including monocytes, macrophages, and microglia, play major roles in innate and adaptive immune responses. Alzheimer’s disease (AD) and inflammatory bowel disease (IBD) susceptibility loci are both enriched for genes expressed in myeloid cells, so we assessed whether these myeloid pathways may be shared. Leveraging genome-wide association study results, we investigated the causal effect of IBD (including ulcerative colitis and Crohn’s disease) variants on AD and its endophenotypes. Microglia and monocyte expression Quantitative Trait Locus (eQTLs) were used to examine the functional consequences of IBD and AD variants. Our results revealed that the sets of genes and pathways implicated in AD and IBD susceptibility are largely distinct. Specifically, AD loci were enriched for microglial eQTLs, while IBD loci were enriched for monocyte eQTLs. Nonetheless, genetically determined IBD was associated with a modest protective effect against AD (p < 0.03), whereas CD susceptibility was linked to a modest increase in amyloid accumulation (β = 7.14, p = 0.02) and AD risk. UC susceptibility, on the other hand, was associated with increased TDP-43 deposition (β = 7.58, p value = 6.11 × 10−4). Thus, the relationship between gastrointestinal inflammatory diseases and AD is complex, but there is evidence for a modest role of IBD susceptibility on AD risk that could yield valuable therapeutic insights.

Alzheimer’s disease (AD) is marked by the coordinated emergence of disease-associated cell states across multiple brain cell types. Among these, an astrocyte subset—Astrocyte 10 (Ast10), defined by high expression of SLC38A2 , SMTN , and CACNA1D —has been linked to cognitive decline in AD. However, the signaling mechanisms driving Ast10’s emergence remain unclear. Here, we aim to identify the intercellular signals that promote the differentiation of astrocytes into the Ast10 state. Targeting this cell-cell crosstalk may offer a strategy to prevent or delay AD-associated cognitive impairment. We used NicheNet to infer ligands that regulate the Ast.10 signature based on prior knowledge of the signaling pathways. We trained a partial least squares regression model using the prioritized ligand expression to predict Ast.10 frequency across donors. To validate these ligands, we performed spatial neighborhood analysis on Visium spatial transcriptomic profiles of human cortical tissues as well as an analysis of mouse and iPSC-derived astrocytes data. Our meta-analysis of 869 brains confirmed the strong association of Ast10 with AD and aging-related cognitive decline. Computational modeling identified ligand-receptor pairs predictive of Ast10 abundance across individuals. Spatial transcriptomics revealed selective colocalization of these ligands with the Ast10 signature in AD brain tissue. Genetic ablation of the receptor PLXNB1 , a top-ranked candidate, reduced the Ast10 transcriptional signature in astrocytes in in vivo and in vitro model systems, supporting its functional role in driving this state. Moreover, Ast10 was associated with synaptic loss and cognitive decline independently of AD pathology. Ast10 represents a transcriptionally distinct astrocyte state linked to cognitive decline in aging and AD. Its emergence appears to be driven by cell-cell interactions involving PLXNB1 . These findings suggest that Ast10 and its upstream regulators are potential therapeutic targets to mitigate cognitive decline across neurodegenerative contexts.

The genetic component of early-onset Alzheimer disease (EOAD), accounting for ~10% of all Alzheimer's disease (AD) cases, is largely unexplained. Recent studies suggest that EOAD may be enriched for variants acting in the lipid pathway. The current study examines the shared genetic heritability between EOAD and the lipid pathway using genome-wide multi-trait genetic covariance analyses. Summary statistics were obtained from the GWAS meta-analyses of EOAD by the Alzheimer's Disease Genetics Consortium (n=19,668) and five blood lipid traits by the Global Lipids Genetics Consortium (n=1,320,016). The significant results were compared between the EOAD and lipids GWAS and genetic covariance analyses were performed via SUPERGNOVA. Genes in linkage disequilibrium (LD) with top EOAD hits in identified regions of covariance with lipid traits were scored and ranked for causality by combining evidence from gene-based analysis, AD-risk scores incorporating transcriptomic and proteomic evidence, eQTL data, eQTL colocalization analyses, DNA methylation data, and single-cell RNA sequencing analyses. Direct comparison of GWAS results showed 5 loci overlapping between EOAD and at least one lipid trait harboring APOE, TREM2, MS4A4E, LILRA5, and LRRC25. Local genetic covariance analyses identified 3 regions of covariance between EOAD and at least one lipid trait. Gene prioritization nominated 3 likely causative genes at these loci: ANKDD1B, CUZD1, and MS4A64.The current study identified genetic covariance between EOAD and lipids, providing further evidence of shared genetic architecture and mechanistic pathways between the two traits.

Glial cells exhibit distinct transcriptional responses to β-amyloid pathology in Alzheimer’s disease (AD). While sophisticated single-cell based methods have revealed heterogeneous glial subpopulations in the human AD brain, the histological localization of these multicellular responses to AD pathology has not been fully characterized due to the loss of spatial information. Here, we combined spatial transcriptomics (ST) with immunohistochemistry to explore the molecular mechanisms in the neuritic plaque niche. 32 sections from the prefrontal cortices of 15 AD and 2 control cases were applied to ST arrays with spatially barcoded probes (spots) of 55µm diameter. Each of the 59,588 tissue-covering spots in our dataset detected a median of 2,202 genes and included a median of 4 nuclei. Amyloid plaques were stained with Thioflavin S (ThioS) and astrocytes were stained using GFAP in the same ST tissue section. The immunohistochemistry data were then projected onto the ST profiles. Clustering the spots reconstructed the cortical layer structure. We detected 263 ThioS + amyloid plaques, and spots within 150µm of plaques were compared to distant spots (≥500µm), adjusted for cortical layer and donor. This approach identified 182 plaque-associated genes and confirmed genes previously reported in mice, such as GFAP , CLU , MBP and MOBP . Interestingly, the AD-related gene SERPINA3 was found to be upregulated at neuritic plaques. SERPINA3 is a marker of an inflammatory astrocyte subpopulation, resembling previously discovered disease-associated astrocytes in mice. Indeed, computationally deconvoluting this astrocyte subpopulation from the ST data confirmed its enrichment at plaques. Further, we found a downregulation of metallothioneins, expressed by astrocytes, indicating a potential dysfunction of metal ion homeostasis. We validate these results using immunohistochemistry and in situ hybridization. Here, we demonstrate the heterogeneity in glial communities within the amyloid plaque microenvironment. We show evidence suggesting a spatial enrichment of SERPINA3 + astrocytes at neuritic plaques. Furthermore, the identification of the 182 plaque-proximal genes suggests involvement of processes related to inflammation, and ion transport and homeostasis. The role of these subtypes and molecular signatures in AD pathophysiology remains to be elucidated.

Spatial gene expression patterns underlie tissue organization, development, and disease, yet current methods for detecting spatially variable genes (SVGs) lack the flexibility to capture multi-scale structure, ensure robustness across platforms, and integrate with genetic data to assess disease relevance. We present Spacelink, a unified framework that models spatial variability of a gene at both whole-tissue and cell-type resolution using an adaptive mixture of data-driven spatial kernels and summarizes it using an Effective Spatial Variability (ESV) metric. Spacelink achieved up to 3.2x higher detection power over eight existing global SVG and cell-type SVG methods while showing consistently superior FDR control across 34 different simulation settings and also showed superior cross-platform concordance in matched tissue Visium and CosMx datasets. Applied to 3 healthy CosMx human tissues (brain cortex, lymph node, liver), Spacelink revealed that SVGs are highly informative for 113 complex traits and diseases (average N = 340,406). Spacelink showed up to 2.2x higher disease informativeness over competing methods in tissue-relevant complex diseases and traits, conditional on putative non-spatial expression-level confounders. Applied to a mouse organogenesis Stereo-seq atlas (8 developmental stages), Spacelink identified 145 genes with stage-associated ESV within brain independent of mean expression, that are enriched in pathways like Wnt signaling and Rap1 signaling characterizing early and late development, respectively. Integration with in vivo Perturb-seq targeting 35 de novo ASD risk genes revealed that perturbations in excitatory neurons and astrocytes preferentially altered spatially structured downstream gene programs (1.7-2.2x higher average ESV across stages than other cell types), many of which were enriched for polygenic autism GWAS loci. In neurodegeneration, analysis of 32 Visium dorsolateral prefrontal cortex samples spanning Alzheimer's disease (AD) pathology stages identified 334 genes with decreasing ESV along amyloid burden (enriched for glycolysis) and 216 genes with decreasing ESV along tau tangle accumulation (enriched for apoptotic pathways). Several AD risk genes (PKM, CLU, GPI) showed conserved reductions in spatial variability with AD pathology in both human and 5xFAD mouse, with PKM linking to a colocalized splicing QTL and amyloid burden QTL variant. These results highlight the utility of Spacelink in decoding spatially variable gene programs that connect tissue architecture to disease genetics.

Molecular omics studies of aging brains have identified genes and proteins related to cognitive decline. Identifying proteins that are linked to specific cognitive abilities has potential to catalyze the development of targeted therapies for specific cognitive deficits. Posttranslational modifications of proteins with glycans modify protein function. Here, we identified glycopeptiforms associated with decline in specific cognitive domains. We studied brains of 366 older decedents from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) with annual cognitive testing, postmortem indices of ten AD/ADRD pathologies and proteome-wide data, from dorsal lateral prefrontal cortex (DLPFC). We quantified 11,012 glycopeptiforms from DLPFC using liquid chromatography with tandem mass spectrometry, which is able to identify both glycated and glycosylated glycopeptiforms, two distinct molecular processes. We employed linear mixed-effects models controlling for age, sex and education to identify glycopeptiforms associated with decline in five cognitive domains (episodic memory, semantic memory, working memory, perceptual speed and visuospatial abilities) correcting for multiple comparisons (p<5×10-6). In further analyses, we adjusted for 10 neuropathologies and for the constituent proteins of the glycopeptiforms. We found eight glycated ( Table 1 ) and eight glycosylated glycopeptiforms ( Table 2 ) that were significantly associated with cognitive decline. Glycated glycopeptiformswere associated primarily with decline in working memory. In contrast, glycosylated glycopeptiforms were associated with all cognitive domains except for visuospatial abilities. Higher levels of glycated glycopeptiforms were always related to faster cognitive decline while higher levels of glycosylated glycopeptiforms were primarily associated with slower cognitive decline. Three glycopeptiforms identified weresituated on the protein neuronal pentraxin 2, linked to AD. The HexNAc(5)Hex(4)Fuc(2) glycan composition appeared in half of the significant glycosylated glycopeptiforms while only in <0.05% of the 11,000 glycopeptiforms, suggesting its specific involvement in cognition. Adjustment for 10 neuropathologies attenuated 3 of the 25 significant associations. Adjustment for the constituent proteins did not alter any of the results suggesting that the post-translational modification itself may have a role in cognitive decline. Glycopeptiforms in aging brains may contribute to decline in distinct cognitive abilities. Further drug discovery targeting these glycopeptiforms may lead to therapies that prevent specific cognitive deficits.

Human microglial heterogeneity is only beginning to be appreciated at the molecular level. Here, we present a large, single-cell atlas of expression signatures from 441,088 live microglia broadly sampled across a diverse set of brain regions and neurodegenerative and neuroinflammatory diseases obtained from 161 donors sampled at autopsy or during a neurosurgical procedure. Using single-cell hierarchical Poisson factorization (scHPF), we derived a 23-factor model for continuous gene expression signatures across microglia which capture specific biological processes (e.g., metabolism, phagocytosis, antigen presentation, inflammatory signaling, disease-associated states). Using external datasets, we evaluated the aspects of microglial phenotypes that are encapsulated in various in vitro and in vivo microglia models and identified and replicated the role of two factors in human postmortem tissue of Alzheimer’s disease (AD). Further, we derived a complex network of transcriptional regulators for all factors, including regulators of an AD-related factor enriched for the mouse disease-associated microglia 2 (DAM2) signature: ARID5B , CEBPA , MITF , and PPARG . We replicated the role of these four regulators in the AD-related factor and then designed a multiplexed MERFISH panel to assess our microglial factors using spatial transcriptomics. We find that, unlike cells with high expression of the interferon-response factor, cells with high expression of the AD DAM2-like factor are widely distributed in neocortical tissue. We thus propose a novel analytic framework that provides a taxonomic approach for microglia that is more biologically interpretable and use it to uncover new therapeutic targets for AD.

Single-nucleus transcriptomic studies have revealed glial cell states associated with Alzheimer's disease; however, these nuclei are dissociated from the complex architecture of the human neocortex. Here, we successfully performed an unbiased distance-based analytic strategy on spatially-registered transcriptomic data. Leveraging immunohistochemistry in the same tissue section, our analyses prioritized SERPINA3 and other genes, such as metallothioneins, as altered in the vicinity of neuritic amyloid plaques. Results were validated at the protein level by immunofluorescence, highlighting that a reactive SERPINA3 + astrocyte subtype, Ast.5, plays a role in the plaque microenvironment.

The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis ( cis -expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer’s disease pathology, after adjusting for APOEε4 , providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer’s disease, schizophrenia, educational attainment and Parkinson’s disease loci.

BACKGROUND AND OBJECTIVES:Molecular omics studies have identified proteins related to cognitive resilience but unrelated to Alzheimer disease and Alzheimer disease-related dementia (AD/ADRD) pathologies. Posttranslational modifications of proteins with glycans can modify protein function. In this study, we identified glycopeptiforms associated with cognitive resilience. METHODS:We studied brains from adults with annual cognitive testing with postmortem indices of 10 AD/ADRD pathologies and proteome-wide data from dorsal lateral prefrontal cortex (DLPFC). We quantified 11, 012 glycopeptiforms from DLPFC using liquid chromatography with tandem mass spectrometry. We used linear mixed-effects models to identify glycopeptiforms associated with cognitive decline correcting for multiple comparisons (p < 5 × 10-6). Then, we regressed out the effect of AD/ADRD pathologies to identify glycopeptiforms that may provide cognitive resilience. RESULTS:We studied 366 brains, average age at death 89 years, and 70% female with no cognitive impairment = 152, mild cognitive impairment = 93, and AD = 121 cognitive status at death. In models adjusting for age, sex and education, 11 glycopeptiforms were associated with cognitive decline. In further modeling, 8 of these glycopeptiforms remained associated with cognitive decline after adjusting for AD/ADRD pathologies: NPTX2a (Est., 0.030, SE, 0.005, p = 1 × 10-4); NPTX2b (Est.,0.019, SE, 0.005, p = 2 × 10-4) NECTIN1(Est., 0.029, SE, 0.009, p = 9 × 10-4), NPTX2c (Est., 0.015, SE, 0.004, p = 9 × 10-4), HSPB1 (Est., -0.021, SE, 0.006, p = 2 × 10-4), PLTP (Est., -0.027, SE, 0.009, p = 4.2 × 10-3), NAGK (Est., -0.027, SE, 0.008, p = 1.4 × 10-3), and VAT1 (Est., -0.020, SE, 0.006, p = 1.1 × 10-3). Higher levels of 4 resilience glycopeptiforms derived through glycosylation were associated with slower decline and higher levels of 4 derived through glycation were related to faster decline. Together, these 8 glycopeptiforms accounted for an additional 6% of cognitive decline over the 33% accounted for the 10 brain pathologies and demographics. All 8 resilience glycopeptiforms remained associated with cognitive decline after adjustments for the expression level of their corresponding protein. Exploratory gene ontology suggested that molecular mechanisms of glycopeptiforms associated with cognitive decline may involve metabolic pathways including pyruvate and NADH pathways and highlighted the importance of molecular mechanisms involved in glucose metabolism. DISCUSSION:Glycopeptiforms in aging brains may provide cognitive resilience. Targeting these glycopeptiforms may lead to therapies that maintain cognition through resilience.

Alzheimer's disease (AD) has recently been associated with diverse cell states1-11, yet when and how these states affect the onset of AD remains unclear. Here we used a data-driven approach to reconstruct the dynamics of the brain's cellular environment and identified a trajectory leading to AD that is distinct from other ageing-related effects. First, we built a comprehensive cell atlas of the aged prefrontal cortex from 1.65 million single-nucleus RNA-sequencing profiles sampled from 437 older individuals, and identified specific glial and neuronal subpopulations associated with AD-related traits. Causal modelling then prioritized two distinct lipid-associated microglial subpopulations-one drives amyloid-β proteinopathy while the other mediates the effect of amyloid-β on tau proteinopathy-as well as an astrocyte subpopulation that mediates the effect of tau on cognitive decline. To model the dynamics of cellular environments, we devised the BEYOND methodology, which identified two distinct trajectories of brain ageing, each defined by coordinated progressive changes in certain cellular communities that lead to (1) AD dementia or (2) alternative brain ageing. Thus, we provide a cellular foundation for a new perspective on AD pathophysiology that informs personalized therapeutic development, targeting different cellular communities for individuals on the path to AD or to alternative brain ageing.

Psychosocial experiences affect brain health and aging trajectories, but the molecular pathways underlying these associations remain unclear. Normal brain function relies on energy transformation by mitochondria oxidative phosphorylation (OxPhos). Two main lines of evidence position mitochondria both as targets and drivers of psychosocial experiences. On the one hand, chronic stress exposure and mood states may alter multiple aspects of mitochondrial biology; on the other hand, functional variations in mitochondrial OxPhos capacity may alter social behavior, stress reactivity, and mood. But are psychosocial exposures and subjective experiences linked to mitochondrial biology in the human brain? By combining longitudinal antemortem assessments of psychosocial factors with postmortem brain (dorsolateral prefrontal cortex) proteomics in older adults, we find that higher well-being is linked to greater abundance of the mitochondrial OxPhos machinery, whereas higher negative mood is linked to lower OxPhos protein content. Combined, positive and negative psychosocial factors explained 18 to 25% of the variance in the abundance of OxPhos complex I, the primary biochemical entry point that energizes brain mitochondria. Moreover, interrogating mitochondrial psychobiological associations in specific neuronal and nonneuronal brain cells with single-nucleus RNA sequencing (RNA-seq) revealed strong cell-type-specific associations for positive psychosocial experiences and mitochondria in glia but opposite associations in neurons. As a result, these “mind-mitochondria” associations were masked in bulk RNA-seq, highlighting the likely underestimation of true psychobiological effect sizes in bulk brain tissues. Thus, self-reported psychosocial experiences are linked to human brain mitochondrial phenotypes.

The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.

Background:Depression is a common psychiatric illness and global public health problem. However, our limited understanding of the biological basis of depression has hindered the development of novel treatments and interventions. Methods:To identify new candidate genes for therapeutic development, we examined single-nucleus RNA sequencing (snucRNAseq) data from the dorsolateral prefrontal cortex (N=424) in relation to ante-mortem depressive symptoms. To complement these direct analyses, we also used genome-wide association study (GWAS) results for depression (N=500,199) along with genetic tools for inferring the expression of 22,159 genes in 7 cell types and 55 cell subtypes to perform transcriptome-wide association studies (TWAS) of depression followed by Mendelian randomization (MR). Results:Our single-nucleus TWAS analysis identified 71 causal genes in depression that have a role in specific neocortical cell subtypes; 59 of 71 genes were novel compared to previous studies. Depression TWAS genes showed a cell type specific pattern, with the greatest enrichment being in both excitatory and inhibitory neurons as well as astrocytes. Gene expression in different neuron subtypes have different directions of effect on depression risk. Compared to lower genetically correlated traits (e.g. body mass index) with depression, higher correlated traits (e.g., neuroticism) have more common TWAS genes with depression. In parallel, we performed differential gene expression analysis in relation to depression in 55 cortical cell subtypes, and we found that genes such as ANKRD36, MADD, TAOK3, SCAI and CHUK are associated with depression in specific cell subtypes. Conclusions:These two sets of analyses illustrate the utility of large snucRNAseq data to uncover both genes whose expression is altered in specific cell subtypes in the context of depression and to enhance the interpretation of well-powered GWAS so that we can prioritize specific susceptibility genes for further analysis and therapeutic development.

Human microglia play a pivotal role in neurological diseases, but we still have an incomplete understanding of microglial heterogeneity, which limits the development of targeted therapies directly modulating their state or function. Here, we use single-cell RNA sequencing to profile 215,680 live human microglia from 74 donors across diverse neurological diseases and CNS regions. We observe a central divide between oxidative and heterocyclic metabolism and identify microglial subsets associated with antigen presentation, motility and proliferation. Specific subsets are enriched in susceptibility genes for neurodegenerative diseases or the disease-associated microglial signature. We validate subtypes in situ with an RNAscope-immunofluorescence pipeline and high-dimensional MERFISH. We also leverage our dataset as a classification resource, finding that induced pluripotent stem cell model systems capture substantial in vivo heterogeneity. Finally, we identify and validate compounds that recapitulate certain subtypes in vitro, including camptothecin, which downregulates the signature of disease-enriched subtypes and upregulates a signature previously associated with Alzheimer's disease.

Supplementary Materials. Additional Material and Methods section and clinical data of the Ponatib treated patient.