Biology subjects

Schneider, J. A.

Publications and source records attributed to Schneider, J. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Differential Associations of Microglial Inflammation on LATE-NC and Tangle-Related Hippocampal Atrophy

BACKGROUND: Accumulations of AD and LATE-NC both contribute to changes in hippocampal volume, possibly via distinct and/or overlapping mechanisms. Microglia-driven inflammation is a shared pathway associated with both AD and LATE-NC. However, the extent to which microglia inflammation is associated with hippocampal volume is less understood. OBJECTIVE: Examine the relationship between AD and LATE-NC with hippocampal volume in persons with differing levels of microglia inflammation. METHODS: Cerebral hemispheres from 441 older adults who came to autopsy were studied. All hemispheres underwent ex-vivo MRI and detailed neuropathologic examination for neurodegenerative and cerebrovascular pathologies. Microglia were quantified in the hippocampal CA1/subiculum region using machine learning-based classifiers trained on digitized CR3-43-stained images via the HALO digital pathology platform. First, linear regression models examined the association of microglia with hippocampal volume, adjusting for demographics, postmortem interval (PMI), and common age-related pathologies. Second, linear regression models were employed to examine whether microglia density modified associations of {beta}-amyloid, tangle, or LATE-NC on hippocampal volume. RESULTS: Participants had a mean age of 90 years at death with 75% being women. Intermediate or high likelihood ADNC was present in 64% and LATE-NC (stage 2/3) was present in 52%. In linear regression models, adjusting for demographics and PMI, higher microglia density was associated with a lower hippocampal volume to hemisphere ratio (estimate = -0.021 SE=0.01, p=0.002); however, after adjusting for common age-related pathologies the association was attenuated (p=0.70). {beta}-amyloid, tangles, and LATE-NC remained independently associated with a lower hippocampal volume. The association of LATE-NC with hippocampal volume was stronger in brains with greater microglia burden (estimate for the interaction term = -0.016; SE=0.01, p=0.002). No interactions were seen between {beta}-amyloid or tangles with microglia on hippocampal volume. In stratified analyses, microglial density modified the association between LATE-NC and hippocampal volume, independent of AD neuropathologic status. CONCLUSION: Microglia-driven inflammation strengthens the association of LATE-NC, but not AD pathology, on hippocampal volume loss. These findings emphasize the importance of inflammatory pathways [when interpreting MRI-based neurodegeneration markers] in aging and mixed pathology.

pathology↗

bioRxiv2026

Post-translational modifications in the brain are critical contributors to Alzheimers disease neuropathology and cognitive decline

Post-translational modifications (PTMs) in APP and MAPT contribute to plaques and tangles in Alzheimers disease (AD). Yet broader proteome-wide PTMs in the AD brain are relatively unexplored. Therefore, this study highlights associations between PTMs, quantified by mass spectrometry in prefrontal cortex tissue, and Alzheimers disease neuropathology and cognition. Leveraging PTMs quantified from prefrontal cortices in 101 Rush Memory and Aging Project participants. We assessed associations with post-mortem amyloid-{beta} and tau burden, global cognition, and cognitive decline. First, APP and MAPT PTM associations were assessed on these outcomes given their known relevance in AD, followed by assessment of protein-wide effects of PTMs. Then, kinase enrichment analysis was performed on each outcome to assess which kinases might contribute to the results. We observed a novel association of APP-K687 acetylation, a known mutation hotspot driving pathology, with amyloid-{beta} load ({beta}=0.44, P=3.9e-8), while confirming known MAPT PTMs with tangle burden. Further, we identified 20+ novel PTMs associations with AD neuropathology, including ENO2-K256 ubiquitination ({beta}=0.353, P=1.13e-6), PSMD13-K31 ubiquitination ({beta}=0.568, P=1.34e-6), and PLXND1-K1826 ubiquitination ({beta}=0.577, P=7.08e-8) for tangle burden and SYP-K23 ubiquitination ({beta}=1.50, P=4.7e-8), TMEFF2-C80 cysteine oxidation ({beta}=1.64, P=1.1e-8), and STX1B-T121 phosphorylation ({beta}=0.898, P=3.3e-7) for amyloid-{beta} load. Further, kinase enrichment analyses highlight the complexity of disease-related proteome changes with some kinases like CDK5 showing expected over-enrichment (amyloid z=3.44, P=3.0e-4; tau z=4.98, P=3.3e-7) but others like PKC family kinases showing divergent enrichment between amyloid (z=8.98-11.55, P<1.0e-18) and tau (z=-2.83--3.88, P<0.006). This study provides an atlas of brain PTMs within crucial proteins like MAPT and APP and at the proteome-wide level, that impact AD neuropathology and clinical presentation. Further, we explored what kinases might be driving phosphorylation results, emphasizing the complex proteome changes which impact AD. In sum, these results highlight robust post-translational alterations in the AD brain and provide novel targets for future mechanistic studies.

neuroscience↗

bioRxiv2026

Multi-omics characterization of vascular, neurodegenerative, and mixed neuropathology in the aging human brain

Late-life cognitive impairment most commonly occurs in the setting of mixed neurodegenerative and cerebrovascular pathology, yet the molecular programs distinguishing vascular, neurodegenerative, and mixed pathology in the aging human brain remain incompletely defined. We performed neuropathology-stratified proteomic and transcriptomic profiling of postmortem brain tissue from participants in the Religious Orders Study and Rush Memory and Aging Project. Dorsolateral prefrontal cortex proteomics (n = 733) were analyzed alongside bulk RNA sequencing from dorsolateral prefrontal cortex (n = 938), posterior cingulate cortex (n = 569), and anterior caudate (n = 632). Participants were classified into vascular, neurodegenerative, and mixed pathology groups based on comprehensive autopsy assessment. Neurodegenerative and mixed pathology, relative to vascular pathology, showed coordinated upregulation of immune and inflammatory pathways and downregulation of mitochondrial and oxidative phosphorylation programs across molecular layers. Although few individual proteins differed between mixed and neurodegenerative groups, pathway-level analyses identified additional remodeling programs in mixed pathology, including extracellular matrix organization and vesicle-mediated transport. Proteomic co-expression network analysis identified immune-stress modules associated with amyloid burden, tau pathology, and cognitive decline, whereas a mitochondrial bioenergetic module showed relative preservation in vascular pathology. Cross-omics concordance was robust at the pathway level but limited at the level of individual genes and proteins. These findings define conserved molecular programs distinguishing vascular, neurodegenerative, and mixed pathology and demonstrate that pathway-level organization provides a stable framework for interpreting molecular heterogeneity in late-life dementia.

genomics↗

bioRxiv2026

Blood-brain barrier dysfunction predicts cognitive trajectory after ischemic stroke

Ischemic stroke doubles the risk of dementia.1-4 Stroke severity and location affect cognition early,5,6 but late dementia risk is not related to infarct characteristics, nor is it reduced by preventing additional strokes,3,6,7 and its mechanism is unknown. We identified a plasma proteomic signature of chronic stroke that was consistent with blood-brain barrier (BBB) dysfunction, including a 58% decrease in plasma levels of platelet-derived growth factor B and downregulation of its pathway compared to healthy controls. During 2 years of follow-up, the stroke-specific proteome was accentuated in stroke survivors who subsequently declined in the processing speed/executive function cognitive domain. To test BBB function, we performed dynamic contrast-enhanced MRI 6-9 months after stroke in an additional cohort and found 1.7-fold higher whole brain BBB leakage compared to controls. Finally, we compared autopsy tissue from people with infarcts and dementia at death to those with infarcts and no dementia. Those who died with dementia had dramatic loss of vascular mural cell coverage compared to those without dementia (median 0.7% vs. 27%). Thus, our proteomic, functional, and structural data implicate chronic BBB dysfunction in cognitive decline late after stroke, revealing potential proteomic and imaging biomarkers and, importantly, a novel target for intervention.

neuroscience↗

bioRxiv2025

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity

The molecular correlates of Alzheimers disease (AD) are increasingly being defined by omics. Yet, the findings from different data types or cohorts are often difficult to reconcile. Collecting multiple omics from the same individuals allows a comprehensive view of disease-related molecular mechanisms, while addressing conflicting findings derived from single omics. Such same-sample multi-omics can reveal, for instance, when changes observed in the transcriptome share distinct but coordinated signals in epigenetics and proteomics, relationships otherwise unclear. Here, we apply a data-driven multi-omic framework to integrate epigenomic, transcriptomic, proteomic, metabolomic, and cell-type-specific population data from up to 1,358 aged human brain samples from the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP). We demonstrate the existence of sprawling cross-omics cross-system biological factors that also relate to AD phenotypes. The strongest AD-associated factor (factor 8) involved elevated immune activity at the epigenetic level, decreased expression of heat shock genes in the transcriptome, and disrupted energy metabolism and cytoskeletal dynamics in the proteome. We also showed immune-related factors (factors 2 and 3) with discordant enrichments, reflecting reactive-like glial subpopulations and protective contributions from surveillance microglia. Both were negatively associated with AD pathology, suggesting potential immune resilience mechanisms. Finally, unsupervised clustering of participants revealed eleven molecular subtypes of the aging brain, including three clusters strongly associated with AD but displaying distinct molecular signatures and phenotypic characteristics. Our findings provide a comprehensive map of molecular mechanisms underlying AD heterogeneity, highlighting the complex role of neuroinflammatory processes, and yielding potential novel biomarkers and therapeutic targets for precision medicine approaches to AD treatment.

molecular biology↗

bioRxiv2025

Automated image segmentation uncovers the role of CD74high human microglia in cognitive decline

The role of activated microglia in Alzheimers disease (AD) is well established; the proportion of stage III activated microglia has been associated with AD and cognitive decline, but this morphologically defined subtype is relatively uncommon (1-2% of microglia) and its cellular function is unknown. Single-cell RNA-sequencing revealed CD74 as a marker gene that is enriched in immunologically active microglial subtypes associated with AD. Here, we evaluated the relationship between CD74 expression, AD- related traits, and microglial morphology using dorsolateral prefrontal cortex samples from two brain collections (ROSMAP: n=63, NYBB: n=91). An image segmentation pipeline using CellProfiler was developed to extract features from entire tissue sections. The pipeline automatically delineated gray and white matter regions and segmented 1,120,780 gray matter microglia. In a meta-analysis of the two datasets, we find an increase in frequency of microglia with high CD74 expression (CD74high) in relation to AD dementia (p = 0.038), particularly in the phase of terminal, accelerated cognitive decline before death. These microglia have a more rounded, amoeboid shape (ROSMAP: p = 1.4x10-6; NYBB: p = 2x10-13) which is a characteristic morphology of activated stage III microglia. Results were consistent across both datasets, highlighting the robustness of our cellular segmentation approach. This study identifies a potential role for CD74high microglia and the CD74 ligand MIF in cognitive decline, and it provides evidence for a partially overlapping but distinct role for CD74high microglia and morphologically defined stage III microglia, whose functional properties have remained poorly understood. These CD74high microglia appear to be enriched for genes involved in cytokine response for class I and II antigen presentation, as well as regulation of T cell proliferation. These findings begin to link microglial subtypes defined by single-cell transcriptomic data with those characterized by classical morphological criteria to resolve the roles of different microglial functions to distinct stages in the trajectory to AD.

neuroscience↗

bioRxiv2025

Cytokine expression profile in the human brain of older adults

Alzheimers disease (AD) is a complex neurodegenerative condition linked to chronic neuroinflammation. This study investigates the cytokine gene expression profile in cortical tissue samples from elderly individuals with and without AD to identify potential biomarkers and enhance our understanding of disease pathogenesis. Utilizing high-depth RNA sequencing data, we identified a set of cytokines whose expression significantly associated with different aspects of the AD phenotype, including measures of neurofibrillary tangles, amyloid-{beta} deposition, and a person-specific rate of cognitive decline. Single-nucleus transcriptomics data facilitated the identification of specific cell types, such as microglia and oligodendrocytes, that significantly contribute to the inflammatory response in AD. Additionally, we observed a strong correlation between the expression of certain cytokines and genetic risk for the disease. Our findings indicate that cytokine-mediated neuroinflammation plays a vital role in AD progression and that modulating the immune response may offer a promising strategy for developing new therapies.

molecular biology↗

bioRxiv2025

Single Cell Landscape of Sex-specific Drivers of Alzheimers Disease

BackgroundSex differences in Alzheimers disease (AD) have been documented for decades, and many sex-specific molecular contributors to AD have been discovered through bulk omics analysis of brain tissues. RNA sequencing (RNAseq) at single cell resolution provides an opportunity to characterize transcript associations with AD in a cell type-specific matter. Here, we investigated sex-specific gene expression associations with neuropathology and cognitive manifestation of AD (endophenotypes) leveraging a large single-nucleus transcriptomic dataset consisting of 1.64 million nuclei from dorsolateral prefrontal cortex (DLPFC) tissue of 424 unique donors from the Religious Orders Study and Memory and Aging Project (ROS/MAP; AD Knowledge Portal syn2580853). MethodsROS/MAP single-nucleus RNAseq data (snRNA-seq) were processed through a rigorous pipeline. In total, eight major cell types from DLPFC were identified. We first performed sex-stratified and sex-interaction association analyses by fitting negative binomial mixed models in relation to {beta}-amyloid load (A{beta}), paired helical filament tau tangle density (tau), global cognitive performance at last visit, and longitudinal cognitive trajectory. We then conducted gene-set enrichment analysis to identify functional signaling pathways enriched for sex-specific associations. Lastly, we compared differential gene expression patterns and intercellular communication profiles between sexes and diagnostic groups among major cell types. For replication, sex-specific associations were examined using snRNA-seq derived from DLPFC tissue-derived of an independent set of 84 donors from The Seattle Alzheimers Disease Brain Cell Atlas (SEA-AD) study. Results68% of the ROS/MAP participants were female, and 52% were diagnosed with AD dementia. We first identified several disease-dependent or sex-dependent cell subpopulations. Then we identified 2,660 sex-specific associations involving 2,110 genes with A{beta} (51%), tau (21%), and cognitive performance (29%). 60% female-specific associations were for A{beta}, and 49% male-specific associations were with tau. The vast majority (93%) of female protective associations were from neurons, and most (76%) of female risk associations were from glial cells. Nine of the female-specific associations involving eight unique genes were replicated in the SEA-AD cohort, including ADGRV1 and OR3A3 with A{beta}; IFI27L1, LYRM1, STAP2, and TSTD2 with tau; PDYN with global cognition; and TMEM50B with longitudinal cognitive decline. All replicated associations except TMEM50B were observed in neurons. Furthermore, the preponderance of protective female-specific associations in neurons was also recapitulated in the SEA-AD cohort. Sex-specific associations were enriched for genes in the immune, inflammation, and damage-related stress response pathways, and microglia presented the most sex-specific enriched pathways. Finally, we identified six ITGB1-mediated microglia-specific incoming signals that may play a role in female-specific risk for A{beta} accumulation. ConclusionOur study highlights the transcriptome-wide, single-cell landscape of sex-specific molecular associations with AD neuropathology and cognitive decline. We delineate the full scope of sex-specific transcript associations, differential expression, signaling pathway, and cell-cell communication network changes in each major DLPFC cell type, while identifying and replicating several female-specific gene associations in neurons to help direct future mechanistic studies.

neuroscience↗

bioRxiv2025

A proteogenomic tool uncovers protein markers for human microglial states

Human microglial heterogeneity has been largely described using transcriptomic data. Here, we introduce a microglial proteomic data resource and a Cellular Indexing of Transcriptomes and Epitopes by Sequencing panel enhanced with antibodies targeting 17 microglial cell surface proteins (mCITE-Seq). We evaluated mCITE-Seq on HMC3 microglia-like cells, induced-pluripotent stem cell-derived microglia (iMG), and freshly isolated primary human microglia. We identified novel protein microglial markers such as CD51 and relate expression of 101 cell surface proteins to transcriptional programs. This results in the identification and validation of three protein marker combinations with which to purify microglia enriched with each of 23 transcriptional programs; for example, CD49D, HLA-DR and CD32 enrich for GPNMBhigh ("disease associated") microglia. Further, we identify and validate proteins - SIRPA, PDPN and CD162 - that differentiate microglia from infiltrating macrophages. The mCITE-Seq panel enables the transition from RNA-based classification and facilitates the functional characterization and harmonization of model systems.

neuroscience↗

bioRxiv2025

A factor-based analysis of individual human microglia uncovers regulators of an Alzheimer-related transcriptional signature

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 Alzheimers 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.

neuroscience↗

bioRxiv2025

Translating the Post-Mortem Brain Multi-Omics Molecular Taxonomy of Alzheimer's Dementia to Living Humans

Alzheimers disease (AD) dementia is characterized by significant molecular and phenotypic heterogeneity, which confounds its mechanistic understanding, diagnosis, and effective treatment. In this study, we harness the most comprehensive dataset of paired ante-mortem blood omics, clinical, psychological, and post-mortem brain multi-omics data and neuroimaging to extensively characterize and translate the molecular taxonomy of AD dementia to living individuals. First, utilizing a comprehensive integration of eight complementary molecular layers from brain multi-omics data (N = 1,189), we identified three distinct molecular AD dementia subtypes exhibiting strong associations with cognitive decline, sex, psychological traits, brain morphology, and characterized by specific cellular and molecular drivers involving immune, vascular, and oligodendrocyte precursor cells. Next, in a significant translational effort, we developed predictive models to convert these advanced brain-derived molecular profiles (AD dementia pseudotimes and subtypes) into blood-, MRI- and psychological traits-based markers. The translation results underscore both the promise of these models and the opportunities for further enhancement. Our findings enhance the understanding of AD heterogeneity, underscore the value of multi-scale molecular approaches for elucidating causal mechanisms, and lay the groundwork for the development of novel therapies in living persons that target multi-level brain molecular subtypes of AD dementia.

neuroscience↗

bioRxiv2025

Multi-omic subtypes of Alzheimer's dementia are differentially associated with psychological traits

ImportancePsychological traits reflecting neuroticism, depressive symptoms, loneliness, and purpose in life are risk factors of AD dementia; however, the underlying biologic mechanisms of these associations remain largely unknown. ObjectiveTo examine whether one or more multi-omic brain molecular subtypes of AD is associated with neuroticism, depressive symptoms, loneliness, and/or purpose in life. DesignTwo cohort-based studies; Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP), both ongoing longitudinal clinical pathological studies that began enrollment in 1994 and 1997. SettingOlder priests, nuns, and brothers from across the U.S. (ROS) and older adults from across the greater Chicago metropolitan area (MAP). Participants822 decedents with multi-omic data from the dorsolateral prefrontal cortex. Exposure(s)Pseudotime, representing molecular distance from no cognitive impairment (NCI) to AD dementia, and three multi-omic brain molecular subtypes of AD dementia representing 3 omic pathways from no cognitive impairment (NCI) to AD dementia that differ by their omic constituents. Main outcome(s) and measure(s)We first ran four separate linear regressions with neuroticism, depressive symptoms, loneliness, purpose in life as the outcomes, and pseudotime as the predictor, adjusting for age, sex and education. We then ran four separate analyses of covariance (ANCOVAs) with Bonferroni-corrected post-hoc tests to test whether the three multi-omic AD subtypes are differentially associated with the four traits, adjusting for the same covariates. ResultPseudotime was positively associated (p<0.05) with neuroticism and loneliness. AD subtypes were differentially associated with the traits: AD subtypes 1 and 3 were associated with neuroticism; AD subtype 2 with depressive symptoms; AD subtype 3 with loneliness, and AD subtype 2 with purpose in life. Conclusions and RelevanceThree multi-omic brain molecular subtypes of AD dementia differentially share omic features with four psychological risk factors of AD dementia. Our data provide novel insights into the biology underlying well-established associations between psychological traits and AD dementia. Key pointsO_ST_ABSQuestionC_ST_ABSAre three distinct multi-omic brain molecular subtypes of Alzheimers disease (AD) dementia associated with four well-established psychological AD risk factors (neuroticism, depressive symptoms, loneliness and purpose in life)? FindingsWe found differential associations: AD subtypes 1 and 3 were associated with neuroticism, AD subtype 2 was associated with depressive symptoms, AD subtype 3 was associated with loneliness; and AD subtype 2 was associated with purpose in life. MeaningPsychological risk factors might be associated with AD dementia via shared multi-omic molecular pathways.

molecular biology↗

bioRxiv2025

PLXNB1 and other signaling drives a pathologic astrocyte state contributing to cognitive decline in Alzheimer's Disease

Alzheimers 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 SLC38A2highSMTNhighCACNA1Dhighastrocyte subset, Astrocyte 10 (Ast10), in AD and aging-related cognitive decline. We then investigated the signaling drivers of Ast10s 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.

neuroscience↗

bioRxiv2025

Gene module-trait network analysis uncovers cell type specific systems and genes relevant to Alzheimers Disease

Alzheimers Disease (AD) is marked by the accumulation of pathology, neuronal loss, and gliosis and frequently accompanied by cognitive decline. Understanding brain cell interactions is key to identifying new therapeutic targets to slow its progression. Here, we used systems biology methods to analyze single-nucleus RNA sequencing (snRNASeq) data generated from dorsolateral prefrontal cortex (DLPFC) tissues of 424 participants in the Religious Orders Study or the Rush Memory and Aging Project (ROSMAP). We identified modules of co-regulated genes in seven major cell types, assigned them to coherent cellular processes, and assessed which modules were associated with AD traits such as cognitive decline, tangle density, and amyloid-{beta} deposition. Coexpression network structure was conserved in the majority of modules across cell types, but we also found distinct communities with altered connectivity, especially when compared to bulk RNASeq, suggesting cell-specific gene co-regulation. These coexpression modules can also capture signatures of cell subpopulations and be influenced by cell proportions. Using a Bayesian network framework, we modeled the direction of relationships between the modules and AD progression. We highlight two key modules, a microglia module (mic_M46), associated with tangles; and an astrocyte module (ast_M19), associated with cognitive decline. Our work provides cell-specific molecular networks modeling the molecular events leading to AD.

systems biology↗

bioRxiv2025

Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance

The biological mechanisms underlying womens increased Alzheimers disease (AD) prevalence remain undefined. Previous case/control studies have identified sex-biased molecular pathways, but sex-specific relationships between gene expression and AD endophenotypes, particularly sex chromosomes, are underexplored. With bulk transcriptomic data across 3 brain regions from 767 decedents, we investigated sex-specific associations between gene expression and post-mortem {beta}-amyloid and tau as well as antemortem longitudinal cognition. Of 23,118 significant gene associations, 10% were significant in one sex and not the other (sex-specific). Most sex-specific gene associations were identified in females (73%) and associated with tau tangles and longitudinal cognition (90%). Four X-linked genes, MCF2, HDAC8, FTX, and SLC10A3, demonstrated significant sex differences in their associations with AD endophenotypes (i.e., significant sex x gene interaction). Our results also uncovered sex-specific biological pathways, including a female-specific role of neuroinflammation and neuronal development, reinforcing the potential for sex-aware analyses to enhance precision medicine approaches in AD.

neuroscience↗

bioRxiv2024

Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord

Development of therapeutic approaches that target specific microglia responses in amyotrophic lateral sclerosis (ALS) is crucial due to the involvement of microglia in ALS progression. Our study identifies the predominant microglia subset in human ALS primary motor cortex and spinal cord as an undifferentiated phenotype with dysregulated respiratory electron transport. Moreover, we find that the interferon response microglia subset is enriched in donors with aggressive disease progression, while a previously described potentially protective microglia phenotype is depleted in ALS. Additionally, we observe an enrichment of non-microglial immune cell, mainly NK/T cells, in ALS central nervous system, primarily in the spinal cord. These findings pave the way for the development of microglia subset-specific therapeutic interventions to slow or even stop ALS progression.

neuroscience↗

bioRxiv2024

HEXIM1 is correlated with Alzheimer's disease pathology and regulates immediate early gene dynamics in neurons

Cognitive processes require de novo gene transcription in neurons. Memory requires the rapid and robust transcription of a class of genes called immediate early genes (IEGs). IEG transcription is facilitated by the formation of a poised basal state, in which RNA polymerase II (RNAP2) initiates transcription, but remains paused downstream of the promoter. Upon neuronal depolarization, the paused RNAP2 is released to complete the synthesis of messenger RNA (mRNA) transcripts, a process stimulated by positive transcription elongation factor b (P-TEFb). In many cell types, P-TEFb is sequestered into a large inactive complex containing Hexamethylene bisacetamide inducible 1 (HEXIM1), but the impact of this interaction on neuronal gene transcription is not yet fully understood. In this study, we found that neuronal expression levels of HEXIM1 mRNA are highly correlated with impaired cognition in Alzheimers disease. It is also induced in the hippocampus during memory formation, and following depolarization in neurons. The role of HEXIM1 in neuronal gene transcription was then explored in murine neuronal cultures where we found that calcium frees P-TEFb from the HEXIM1 inhibitory complex. Modulation of P-TEFb by inhibiting the activity of the cyclin-dependent kinase 9 (CDK9) subunit of this complex significantly impacts IEG induction, particularly during repeated depolarization. Our findings indicate that HEXIM1 in complex with P-TEFb plays an important role in establishing and resetting the poised RNAP2 state, enabling efficient activation of genes necessary for synaptic plasticity.

neuroscience↗

bioRxiv2024

Association of 10 VEGF Family Genes with Alzheimer's Disease Pathology at Single Cell Resolution

The cell-type specific role of the vascular endothelial growth factors (VEGFs) in the pathogenesis of Alzheimers disease (AD) is not well characterized. In this study, we utilized a single-nucleus RNA sequencing dataset from Dorsolateral Prefrontal Cortex (DLFPC) of 424 donors from the Religious Orders Study and Memory and Aging Project (ROS/MAP) to investigate the effect of 10 VEGF genes (VEGFA, VEGFB, VEGFC, VEGFD, PGF, FLT1, FLT4, KDR, NRP1, and NRP2) on AD endophenotypes. Mean age of death was 89 years, among which 68% were females, and 52% has AD dementia. Negative binomial mixed models were used for differential expression analysis and for association analysis with {beta}-amyloid load, PHF tau tangle density, and both cross-sectional and longitudinal global cognitive function. Intercellular VEGF-associated signaling was profiled using CellChat. We discovered prefrontal cortical FLT1 expression was upregulated in AD brains in both endothelial and microglial cells. Higher FLT1 expression was also associated with worse cross-sectional global cognitive function, longitudinal cognitive trajectories, and {beta}-amyloid load. Similarly, higher endothelial FLT4 expression was associated with more {beta}-amyloid load. In contrast to the receptors, VEGFB showed opposing effects on {beta}-amyloid load whereby higher levels in oligodendrocytes was associated with high amyloid burden, while higher levels in inhibitory neurons was associated with lower amyloid burden. Finally, AD cells showed significant reduction in overall VEGF signaling comparing to those from cognitive normal participants. Our results highlight key changes in VEGF receptor expression in endothelial and microglial cells during AD, and the potential protective role of VEGFB in neurons.

neuroscience↗