Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology

The temporal onset of associations of cortical proteins with cognitive resilience vary during late life

BACKGROUND

Cortical proteins associated with cognitive resilience have been identified but their temporal onset in older adults is unknown. We present a multistage approach to first identify cortical proteins associated with cognitive resilience and then examine their associated temporal onset.

METHODS

We used data from a subset of 1088 decedents from two cohort-studies who had selected reaction monitoring proteomics from the dorsolateral prefrontal cortex, and at least 3 cognitive assessments. Cognition was assessed using a composite derived from 19 tests. We first used linear mixed-effects models to identify cortical proteins associated with cognitive resilience. We then used functional mixed-effects models to examine non-linear associations between proteins and cognitive resilience to identify their temporal onset.

RESULTS

Mean age at death was 90 years (SD = 6.4); 69 % were female. On average, cognition started to decline at around 15 years before death, with accelerated decline in the last 7 years. We identified 40 proteins associated with cognitive resilience, of which 17 proteins also showed non-linear associations. Non-linear associations indicated that higher levels of 10 proteins were associated with slower cognitive decline between 23 and 4 years before death. In contrast, higher levels of 7 proteins were associated with faster decline only within the last 7 years before death.

CONCLUSIONS

Cognitive resilience proteins are differentially related to late-life cognitive aging; the onset of proteins that maintain cognition may begin many years before the onset of proteins that hasten cognitive decline. The temporal onset of cognitive resilience proteins may be crucial for timing efficacious interventions.

Brief sleep disruption alters synaptic structures among hippocampal and neocortical somatostatin-expressing interneurons

STUDY OBJECTIVES

Brief sleep loss alters cognition and synaptic structures of principal neurons in the hippocampus and neocortex. However, while in vivo recording and bioinformatic data suggest that inhibitory interneurons are more strongly affected by sleep loss, it is unclear how sleep and sleep deprivation (SD) affect interneurons' synapses. Disruption of the somatostatin-expressing (SST+) interneuron population seems to be a critical early sign of neuropathology in Alzheimer's dementia, schizophrenia, and bipolar disorder-and the risk of developing all three is increased by habitual sleep loss. We aimed to test how the synaptic structures of SST+ interneurons in various brain regions are affected by brief sleep disruption.

METHODS

We used Brainbow 3.0 to label SST+ interneurons in the dorsal hippocampus, prefrontal cortex, and visual cortex of male SST-CRE transgenic mice, then compared synaptic structures in labeled neurons after a 6-hour period of ad lib sleep, or gentle handling SD starting at lights on.

RESULTS

Dendritic spine density among SST+ interneurons in both hippocampus and neocortex was altered in a subregion-specific manner, with increased overall and thin spine density in CA1, dramatic increases in spine volume and surface area in CA3, and small but significant changes (primarily decreases) in spine size in CA1, PFC, and V1.

CONCLUSIONS

We suggest that the synaptic connectivity of SST+ interneurons is significantly altered in a brain region-specific manner by a few hours of sleep loss. This suggests a cell type-specific mechanism by which sleep loss disrupts cognition and alters excitatory-inhibitory balance in brain networks.

Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution

Neurodegenerative diseases and serious mental illnesses often exhibit overlapping characteristics, highlighting the potential for shared underlying mechanisms. To facilitate a deeper understanding of these diseases and pave the way for more effective treatments, we have generated a population-scale multi-omics dataset consisting of genotype and single-nucleus transcriptome data from the prefrontal cortex of frozen human brain specimens. Encompassing over 6.3 million nuclei from 1,494 donors, our dataset represents a diverse range of neurodegenerative and serious mental illnesses, including Alzheimer's and Parkinson's diseases, schizophrenia, bipolar disorder and diffuse Lewy body dementia, as well as neurotypical controls. Our dataset offers a unique opportunity to study disease interactions, as 21% of donors had comorbid diagnoses of two or more major brain disorders. Additionally, it includes detailed phenotypic information on neuropsychiatric symptoms, such as apathy and weight loss, which commonly accompany Alzheimer's disease and related dementias. We have performed stringent preprocessing and quality controls, ensuring the reliability and usability of the data. As a commitment to fostering collaborative research, we provide this valuable resource as an online repository, enabling widespread analyses across the scientific community.

Rewired m6A of promoter antisense RNAs in Alzheimer's disease regulates neuronal genes in 3D nucleome

N6-methyladenosine (m6A) is an abundant internal RNA modification that can impact gene expression at both post-transcriptional and transcriptional levels. However, the landscapes and functions of m6A in human brains and neurodegenerative diseases, including Alzheimer's disease (AD), are under-explored. Here, we examined RNA m6A methylome using total RNA-seq and meRIP-seq in middle frontal cortex of post-mortem brains from individuals with or without AD, which revealed m6A alteration on both mRNAs and various noncoding RNAs. Notably, many promoter-antisense RNAs (paRNAs) displayed cell-type-specific expression and changes in AD, including one produced adjacent to MAPT that encodes the Tau protein. MAPT-paRNA is highly expressed in neurons, and m6A positively controls its expression. In iPSC-derived human excitatory neurons, MAPT-paRNA does not impact the nearby MAPT mRNA, but instead promotes expression of hundreds of neuronal and synaptic genes, and is protective against excitotoxicity. Analysis of single nuclei RNA-DNA interactome in human brains supports that brain paRNAs interact with both cis- and trans-chromosomal target genes to impact their transcription. These data reveal landscapes and functions of noncoding RNAs and m6A in brain gene regulation and AD pathogenesis.

Advances in gait research related to Alzheimer's disease

Introduction

Alzheimer's disease (AD) represents a degenerative condition affecting the nervous system, characterized by the absence of a definitive cause and a lack of a precise therapeutic intervention. Extensive research efforts are being conducted worldwide to enhance early detection methods for AD and to develop medications capable of effectively halting the initiation and progression of the disease during its early stages. Some current detection methods for early diagnosis are expensive and require invasive procedures. More and more evidence shows that gait is related to cognition. A deeper investigation into the intricate interplay between gait and cognition is necessary to elucidate their reciprocal influences and the temporal sequence of these interactions. In the future, it is hoped that with the results of clinical manifestations, neuroimaging, and electrophysiology, simple and objective gait analysis results can be used as an alternative biomarker for cognitive decline to diagnose dementia early.

Research objective

This research offers a comprehensive scoping review of the contemporary landscape of clinical gait evaluation. It delineates the pertinent concepts of gait analysis and machine learning in AD and elucidates the intricate interplay between gait patterns and cognitive status.

Methods

A comprehensive literature search was conducted within PubMed for all articles published until march 18, 2024, using a set of keywords, including "machine learning and gait "and "gait and Alzheimer." original articles that met the selection criteria were included.

Results and significance

A strong correlation exists between autonomous gait and cognitive attributes, necessitating further investigation into the selective interplay between gait and mental factors. Conversely, the gait information of Alzheimer's disease (AD) patients can be captured using a 3D gait analysis system. Numerous gait characteristics can be derived from this gait data, and the early identification of AD can be facilitated by applying a graph neural network-based machine learning approach.

Contributions of Genetic Variation in Astrocytes to Cell and Molecular Mechanisms of Risk and Resilience to Late-Onset Alzheimer's Disease

Reactive astrocytes are associated with Alzheimer's disease (AD), and several AD genetic risk variants are associated with genes highly expressed in astrocytes. However, the contribution of genetic risk within astrocytes to cellular processes relevant to the pathogenesis of AD remains ill-defined. Here, we present a resource for studying AD genetic risk in astrocytes using a large collection of induced pluripotent stem cell (iPSC) lines from deeply phenotyped individuals with a range of neuropathological and cognitive outcomes. IPSC lines from 44 individuals were differentiated into astrocytes followed by unbiased molecular profiling using RNA sequencing and tandem mass tag-mass spectrometry. We demonstrate the utility of this resource in examining gene- and pathway-level associations with clinical and neuropathological traits, as well as in analyzing genetic risk and resilience factors through parallel analyses of iPSC-astrocytes and brain tissue from the same individuals. Our analyses reveal that genes and pathways altered in iPSC-derived astrocytes from individuals with AD are concordantly dysregulated in AD brain tissue. This includes increased levels of prefoldin proteins, extracellular matrix factors, COPI-mediated trafficking components and reduced levels of proteins involved in cellular respiration and fatty acid oxidation. Additionally, iPSC-derived astrocytes from individuals resilient to high AD neuropathology show elevated basal levels of interferon response proteins and increased secretion of interferon gamma. Correspondingly, higher polygenic risk scores for AD are associated with lower levels of interferon response proteins in astrocytes. This study establishes an experimental system that integrates genetic information with a matched iPSC lines and brain tissue data from a large cohort of individuals to identify genetic contributions to molecular pathways affecting AD risk and resilience.

Sex-specific GABAergic microcircuits that switch vulnerability into resilience to stress and reverse the effects of chronic stress exposure

Clinical and preclinical studies have identified somatostatin (SST)-positive interneurons as critical elements that regulate the vulnerability to stress-related psychiatric disorders. Conversely, disinhibition of SST neurons in mice results in resilience to the behavioral effects of chronic stress. Here, we established a low-dose chronic chemogenetic protocol to map these changes in positively and negatively motivated behaviors to specific brain regions. AAV-hM3Dq-mediated chronic activation of SST neurons in the prelimbic cortex (PLC) had antidepressant drug-like effects on anxiety- and anhedonia-like motivated behaviors in male but not female mice. Analogous manipulation of the ventral hippocampus (vHPC) had such effects in female but not male mice. Moreover, the activation of SST neurons in the PLC of male mice and the vHPC of female mice resulted in stress resilience. Activation of SST neurons in the PLC reversed prior chronic stress-induced defects in motivated behavior in males but was ineffective in females. Conversely, activation of SST neurons in the vHPC reversed chronic stress-induced behavioral alterations in females but not males. Quantitation of c-Fos+ and FosB+ neurons in chronic stress-exposed mice revealed that chronic activation of SST neurons leads to a paradoxical increase in pyramidal cell activity. Collectively, these data demonstrate that GABAergic microcircuits driven by dendrite targeting interneurons enable sex- and brain-region-specific neural plasticity that promotes stress resilience and reverses stress-induced anxiety- and anhedonia-like motivated behavior. The data provide a rationale for the lack of antidepressant efficacy of benzodiazepines and superior efficacy of dendrite-targeting, low-potency GABAA receptor agonists, independent of sex and despite striking sex differences in the relevant brain substrates.

IGF1R/ARRB1 Mediated Regulation of ERK and cAMP Pathways in Response to Aβ Unfolds Novel Therapeutic Avenue in Alzheimer's Disease

IGF1R/INSR signaling is crucial for understanding Alzheimer's disease (AD) and may aid in the development of potent therapeutic strategies. This study investigated the expression and activity of these receptors and their potential to form functional hybrids in response to amyloid beta (Aβ). IGF1R, INSR, and ARRB1 were found to be upregulated in AD. The propensity for functional hybrid formation was also greater in the presence of Aβ. The association of IGF1R with ARRB1 reached a maximum at 60 min of Aβ treatment, which coincided with increased pERK activity at approximately the same time, indicating the importance of this association in pERK regulation. Knocking down IGF1R, INSR, and ARRB1 independently reduced cAMP, whereas overexpressing IGF1R significantly increased cAMP. Knocking down ARRB1 in IGF1R-overexpressing cells led to a reduction in cAMP, indicating that the interaction of ARRB1 and IGF1R possibly contributes to cAMP dysregulation. Since cAMP plays a crucial role in cognition and memory, alterations in cAMP after receptor hybridization could be significant in AD. Additionally, we noted hyperactivation of MAPK, which is associated with aberrant cellular activity, transcriptional control, and stress pathways. This finding highlights the importance of IGF1R and INSR dysregulation, which plays a major role in addition to conventional RTK signaling through multiple pathways. Here, we focused on the ARRB1 and IGF1R interaction and showed that picropodophyllin (PPP), an IGF1R-specific inhibitor, blocks this interaction and alters the ERK and cAMP status under disease conditions. Cell viability studies further revealed that the PPP substantially improved cell viability in the presence of Aβ. This highlights the role of the PPP in regulating these cascades and opens the arena for further therapeutic development for AD.

Drug-targeted Mendelian randomization analysis combined with transcriptome sequencing to explore the molecular mechanisms associated with cognitive impairment

BackgroundCurrent therapies for cognitive impairment, including Alzheimer's disease (AD) and mild cognitive impairment, are limited by a lack of universal treatment and adverse effects associated with polypharmacy. Investigating genetic and molecular mechanisms underlying cognitive decline is critical for the development of targeted therapeutics.ObjectiveTo identify causal genes and potential therapeutic targets for cognitive impairment through integrative genomic analyses.MethodsGenome-wide association study data on cognitive impairment were combined with the expression quantitative trait loci (eQTL) data from the eQTLGen consortium. Mendelian randomization (MR) and colocalization analyses were employed to infer causal relationships. Gene Set Enrichment Analysis and Gene Set Variation Analysis evaluated the pathway and functional differences. Immune cell infiltration patterns and the immunometabolic pathways were assessed, followed by drug target prediction.ResultsMR analysis identified seven gene-eQTL pairs significantly associated with cognitive impairment. SMR colocalization prioritized three key genes: HNMT (histamine metabolism), TNFSF8 (inflammatory signaling), and S1PR5 (sphingolipid signaling). HNMT, TNFSF8, and S1PR5 had 39, 24, and 30 predicted targeted drugs, respectively, including arsenic trioxide, aspirin, and immunomodulators.ConclusionsThis study implicates HNMT, TNFSF8, and S1PR5 as potential therapeutic targets for cognitive impairment. Further validation is required to confirm their clinical relevance.

Psychiatric Genomics 2025: State of the Art and the Path Forward

Psychiatric genetics has evolved from candidate-gene studies to whole-genome sequencing efforts. With hundreds of disease-associated loci now identified, functional interpretation of the associated loci becomes the critical next step toward translational applications. The article discusses achievements, challenges, and opportunities in psychiatric genomics associated with complexity and heterogeneity. Brain expression quantitative trait loci, single-cell ribonucleic acid-sequence, and functional genomics technologies are highlighted. It also covers newly developed techniques with improved spatiotemporal resolution, quality and sensitivity, coupled with advanced analytical methods and artificial intelligence. The power of collaborative research and inclusion of diverse populations will ensure a bright future for precision psychiatry.

Integrative single-cell and cell-free plasma RNA transcriptomics identifies biomarkers for early non-invasive AD screening

Introduction

Data-driven omics approaches have rapidly advanced our understanding of the molecular heterogeneity of Alzheimer's disease (AD). However, limited by the unavailability of brain tissue, there is an urgent need for a non-invasive tool to detect alterations in the AD brain. Cell-free RNA (cfRNA), which crosses the blood-brain barrier, could reflect AD brain pathology and serve as a diagnostic biomarker.

Methods

Here, we integrated plasma-derived cfRNA-seq data from 337 samples (172 AD patients and 165 age-matched controls) with brain-derived single cell RNA-seq (scRNA-seq) data from 88 samples (46 AD patients and 42 controls) to explore the potential of cfRNA profiling for AD diagnosis. A systematic comparative analysis of cfRNA and brain scRNA-seq datasets was conducted to identify dysregulated genes linked to AD pathology. Machine learning models-including support vector machine, random forest, and logistic regression-were trained using cfRNA expression patterns of the identified gene set to predict AD diagnosis and classify disease progression stages. Model performance was rigorously evaluated using area under the receiver operating characteristic curve (AUC), with robustness assessed through cross-validation and independent validation cohorts.

Results

Notably, we identified 34 dysregulated genes with consistent expression changes in both cfRNA and scRNA-seq. Machine learning models based on the cfRNA expression patterns of these 34 genes can accurately predict AD patients (the highest AUC = 89%) and effectively distinguish patients at early stage of AD. Furthermore, classifiers developed based on the expression of 34 genes in brain transcriptome data demonstrated robust predictive performance for assessing the risk of AD in the population (the highest AUC = 94%).

Discussion

This multi-omics approach overcomes limitations of invasive brain biomarkers and noisy blood-based signatures. The 34-gene panel provides non-invasive molecular insights into AD pathogenesis and early screening. While cfRNA stability challenges clinical translation, our framework highlights the potential for precision diagnostics and personalized therapeutic monitoring in AD.

Cell-death pathways and tau-associated neuronal vulnerability in Alzheimer's disease

Neuronal loss is the ultimate driver of neural system dysfunction in Alzheimer's disease (AD). We used single-nucleus RNA sequencing and neuropathological phenotyping to elucidate mechanisms of neurodegeneration in AD by identifying vulnerable neuronal populations and probing for their differentially expressed genes. Evidenced by transcriptomic analyses and quantitative tau immunoassays of human AD and non-AD brain tissue, we identified a neuronal population especially vulnerable to tau pathology. Multiplexed immunohistochemistry and in situ hybridization (CBLN2 and LINC00507) validated the presence of the tau-vulnerable neuronal population and revealed a propensity of this population to bear tau pathology. Differentially expressed genes associated with phospho-tau pathology in these neurons revealed genes involved in apoptosis, cell-component dissociation (e.g., autophagosome maturation and actin filament depolymerization), and regulation of vesicle-mediated transport.

White matter dysfunction in Alzheimer's disease is associated with disease-related transcriptomic signatures

While anatomical white matter (WM) alterations in Alzheimer's disease (AD) are well-established, functional WM dysregulation remains rarely investigated. The current study examines WM functional connectivity and network properties alterations in AD and mild cognitive impairment (MCI) and further describes their spatially correlated genes. AD and MCI shared decreased functional connectivity, clustering coefficient, and local efficiency within WM regions involved in impaired sensory-motor, visual-spatial, language, or memory functions. AD-specific dysfunction (i.e., AD vs. MCI and cognitively unimpaired participants) was predominantly located in WM, including anterior and posterior limb of internal capsule, corona radiata, and left tapetum. This WM dysfunction spatially correlates with specific genes, which are enriched in multiple biological processes related to synaptic function and development, and are mostly active in neurons and astrocytes. These findings may contribute to understanding molecular, cellular, and functional signatures associated with WM damage in AD.

Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer's disease and a cumulative effects model for risk liability

Genome-wide association studies (GWAS) on Alzheimer's disease (AD) have predominantly focused on identifying common variants in Europeans. Here, we performed whole-genome sequencing (WGS) of 1,559 individuals from a Korean AD cohort to identify various genetic variants and biomarkers associated with AD. Our GWAS analysis identified a previously unreported locus for common variants (APCDD1) associated with AD. Our WGS analysis was extended to explore the less-characterized genetic factors contributing to AD risk. We identified rare noncoding variants located in cis-regulatory elements specific to excitatory neurons associated with cognitive impairment. Moreover, structural variation analysis showed that short tandem repeat expansion was associated with an increased risk of AD, and copy number variant at the HPSE2 locus showed borderline statistical significance. APOE ε4 carriers with high polygenic burden or structural variants exhibited severe cognitive impairment and increased amyloid beta levels, suggesting a cumulative effects model of AD risk.

Synapse vulnerability and resilience across the clinical spectrum of dementias

Preservation of synapses is crucial for healthy cognitive ageing, and synapse loss is one of the closest anatomical correlates of cognitive decline in Alzheimer disease, dementia with Lewy bodies and frontotemporal dementia. In these conditions, some synapses seem particularly vulnerable to degeneration whereas others are resilient and remain preserved. Evidence has highlighted that vulnerability and resilience are intrinsically distinct phenomena linked to specific brain structural and/or functional signatures, yet the key features of vulnerable and resilient synapses in the dementias remain incompletely understood. Defining the characteristics of vulnerable and resilient synapses in each form of dementia could offer novel insight into the mechanisms of synapse preservation and of synapse loss that underlies cognitive decline, thereby facilitating the discovery of targeted biomarkers and disease-modifying therapies. In this Review, we consider the concepts of synapse vulnerability and resilience, and provide an overview of our current understanding of the associations between synaptic protein changes, neuropathology and cognitive decline. We also consider how understanding of the underlying mechanisms could identify novel strategies to mitigate the cognitive dysfunction associated with dementias.

An integrative systems-biology approach defines mechanisms of Alzheimer's disease neurodegeneration

Despite years of intense investigation, the mechanisms underlying neuronal death in Alzheimer's disease, remain incompletely understood. To define relevant pathways, we conducted an unbiased, genome-scale forward genetic screen for age-associated neurodegeneration in Drosophila. We also measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer's disease and identified Alzheimer's genetic variants that modify gene expression in disease-vulnerable neurons in humans. We then used a network model to integrate these data with previously published Alzheimer's disease proteomics, lipidomics and genomics. Here, we computationally predict and experimentally confirm how HNRNPA2B1 and MEPCE enhance toxicity of the tau protein, a pathological feature of Alzheimer's disease. Furthermore, we demonstrated that the screen hits CSNK2A1 and NOTCH1 regulate DNA damage in Drosophila and human stem cell-derived neural progenitor cells. Our study identifies candidate pathways that could be targeted to ameliorate neurodegeneration in Alzheimer's disease.

hiPSC-neurons recapitulate the subtype-specific cell intrinsic nature of susceptibility to neurodegenerative disease-relevant aggregation

Alzheimer's disease (AD) is characterized by the accumulation and spread of Tau intraneuronal inclusions throughout most of the telencephalon, leaving hindbrain regions like the cerebellum and spinal cord largely spared. These neuropathological observations, along with the identification of specific vulnerable sub-populations from AD brain-derived single nuclei transcriptomics, suggest that a subset of brain regions and neuronal subtypes possess a selective vulnerability to Tau pathology. Given the inability to culture neurons from patient brains, a disease-relevant in vitro model which recapitulates these features would serve as a critical tool to validate modulators of vulnerability and resilience. Using our recently established platform for inducing endogenous Tau aggregation in human induced pluripotent stem cell (hiPSC)-derived cortical excitatory neurons via application of AD brain-derived exogenous Tau aggregates, we explored whether Tau aggregates preferentially induce aggregation in specific neuronal subtypes. We compared Tau seeding in hiPSC-derived neuron subtypes representing regional identities across the forebrain, midbrain, and hindbrain. Higher susceptibility (i.e. more Tau aggregation) was consistently observed among cortical neuron subtypes, with CTIP2-positive, somatostatin (SST)-positive cortical inhibitory neurons showing the greatest aggregation levels across hiPSC lines from multiple donors. hiPSC-neurons also delineated between the disease-specific vulnerabilities of different protein aggregates, as α-synuclein preformed fibrils showed an increased propensity to induce aggregates in midbrain dopaminergic (mDA)-like neurons, mimicking Parkinson's disease (PD)-specific susceptibility. Aggregate uptake and degradation rates were insufficient to explain differential susceptibility. The absence of a consistent transcriptional response following aggregate seeding further indicated that intrinsic neuronal subtype-specific properties could drive susceptibility. The present data provides evidence that hiPSC-neurons exhibit features of selective neuronal vulnerability which manifest in a cell autonomous manner, suggesting that mining intrinsic (or basal) transcriptomic signatures of more vulnerable compared to more resilient hiPSC-neurons could uncover the molecular underpinnings of differential susceptibility to protein aggregation found in a variety of neurodegenerative diseases.

Enhanced differentiation of neural progenitor cells in Alzheimer's disease into vulnerable immature neurons

Focusing on the early stages of Alzheimer's disease (AD) holds great promise. However, the specific events in neural cells preceding AD onset remain elusive. To address this, we utilized human-induced pluripotent stem cells carrying APPswe mutation to explore the initial changes associated with AD progression. We observed enhanced neural activity and early neuronal differentiation in APPswe cerebral organoids cultured for one month. This phenomenon was also evident when neural progenitor cells (NPCs) were differentiated into neurons. Furthermore, transcriptomic analyses of NPCs and neurons confirmed altered expression of neurogenesis-related genes in APPswe NPCs. We also found that the upregulation of reactive oxygen species (ROS) is crucial for early neuronal differentiation in these cells. In addition, APPswe neurons remained immature after initial differentiation with increased susceptibility to toxicity, providing valuable insights into the premature exit from the neural progenitor state and the increased vulnerability of neural cells in AD.

Transcriptomic signatures of oxytosis/ferroptosis are enriched in Alzheimer's disease

BACKGROUND

Oxytosis/ferroptosis is a form of non-apoptotic regulated cell death characterized by specific changes in the redox balance that lead to lethal lipid peroxidation. It has been hypothesized recently that aging predisposes the brain to the activation of oxytosis/ferroptosis in Alzheimer's disease (AD), and consequently that inhibition of oxytosis/ferroptosis offers a path to develop a new class of therapeutics for the disease. The goal of the present study was to investigate the occurrence of oxytosis/ferroptosis in the AD brain by examining transcriptomic signatures of oxytosis/ferroptosis in cellular and animal models of AD as well as in human AD brain samples.

RESULTS

Since oxytosis/ferroptosis has been poorly defined at the RNA level, the publicly available datasets are limited. To address this limitation, we developed TrioSig, a gene signature generated from transcriptomic data of human microglia, astrocytes, and neurons treated with inducers of oxytosis/ferroptosis. It is shown that the different signatures of oxytosis/ferroptosis are enriched to varying extents in the brains of AD mice and human AD patients. The TrioSig signature was the most frequently found enriched, and bioinformatic analysis of its composition identified genes involved in the integrated stress response (ISR). It was confirmed in nerve cell culture that oxytosis/ferroptosis induces the ISR via phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2α) and activating transcription factor 4 (ATF4) signaling.

CONCLUSIONS

Our data support the involvement of oxytosis/ferroptosis in AD. The implications of the ISR for the progression and prevention of AD are discussed.

Distinct systemic impacts of Aβ42 and Tau revealed by whole-organism snRNA-seq

Both neuronal and peripheral tissues become disrupted in Alzheimer's disease (AD). However, a comprehensive understanding of how AD impacts different tissues across the whole organism is lacking. Using Drosophila, we generated an AD Fly Cell Atlas (AD-FCA) based on whole-organism single-nucleus transcriptomes of 219 cell types from flies expressing AD-associated proteins, either human amyloid-β 42 peptide (Aβ42) or Tau, in neurons. We found that Aβ42 primarily affects the nervous system, including sensory neurons, while Tau induces accelerated aging in peripheral tissues. We identified a neuronal cluster enriched in Aβ42 flies, which has high lactate dehydrogenase (LDH) expression. This LDH-high cluster is conserved in 5XFAD mouse and human AD datasets. We found a conserved defect in fat metabolism from both fly and mouse tauopathy models. The AD-FCA offers new insights into how Aβ42 or Tau systemically and differentially affects a whole organism and provides a valuable resource for understanding brain-body communication in neurodegeneration.

APOE genotype determines cell-type-specific pathological landscape of Alzheimer's disease

The apolipoprotein E (APOE) gene is the strongest genetic risk modifier for Alzheimer's disease (AD), with the APOE4 allele increasing risk and APOE2 decreasing it compared with the common APOE3 allele. Using single-nucleus RNA sequencing of the temporal cortex from APOE2 carriers, APOE3 homozygotes, and APOE4 carriers, we found that AD-associated transcriptomic changes were highly APOE genotype dependent. Comparing AD with controls, APOE2 carriers showed upregulated synaptic and myelination-related pathways, preserving synapses and myelination at the protein level. Conversely, these pathways were downregulated in APOE3 homozygotes, resulting in reduced synaptic and myelination proteins. In APOE4 carriers, excitatory neurons displayed reduced synaptic pathways similar to APOE3, but oligodendrocytes showed upregulated myelination pathways like APOE2. However, their synaptic and myelination protein levels remained unchanged or increased. APOE4 carriers also showed increased pro-inflammatory signatures in microglia but reduced responses to amyloid-β pathology. These findings reveal APOE genotype-specific molecular alterations in AD across cell types.

The intersection of delirium and long-term cognition in older adults: the critical role of delirium prevention

Delirium, a neuropsychiatric syndrome characterized by an acute and usually reversible state of confusion, while dementia is a chronic, acquired cognitive impairment that significantly reduces a patient's ability to perform daily tasks, learn, work, and engage in social interactions. Previous studies indicates that individuals with dementia are more susceptible to delirium than the general population, and that delirium serves as an independent risk factor for the subsequent onset of dementia. However, a major controversy in this field concerns whether delirium is merely a marker of vulnerability to dementia, or whether delirium-induced adverse outcomes such as falls and functional decline contribute to dementia, or whether delirium directly causes permanent neuronal damage and lead to dementia. It is possible that all these hypotheses hold some truth. In this review, we examine the shared and distinct mechanisms of delirium and dementia by reviewing their clinical features, epidemiology, clinicopathological, biomarkers, neuroimaging, and recent experimental studies, and we discuss the importance of targeting delirium to explore new preventive and therapeutic strategies for reducing long-term cognitive impairment.

Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease

Oligodendroglia are the responsible cells for myelination in the central nervous system and their involvement in Parkinson's disease (PD) is poorly understood. We performed sn-RNA-seq and image-based spatial transcriptomics of human caudate nucleus and putamen (dorsal striatum) from PD and control brain donors to elucidate the diversity of oligodendroglia and how they are affected by the disease. We profiled a total of ~ 200.000 oligodendroglial nuclei, defining 15 subclasses, from precursor to mature cells, 4 of which are disease-associated. These PD-specific populations are characterized by the overexpression of heat shock proteins, as well as distinct expression signatures related to immune responses, myelination alterations, and disrupted cell signaling pathways. We have also identified impairments in cell communication and oligodendrocyte development, evidenced by changes in neurotransmitter receptors expression and cell adhesion molecules. In addition, we observed significant disruptions in oligodendrocyte development, with aberrant differentiation trajectories and shifts in cell proportions, particularly in the transition from mature oligodendrocytes to disease-associated states. Quantitative immunohistochemical analysis revealed decreased myelin levels in the PD striatum, which correlated with transcriptomic alterations. Furthermore, spatial transcriptomics mapping revealed the distinct localization of disease-associated populations within the striatum, with evidence of impaired myelin integrity. Thus, we uncover oligodendroglia as a critical cell type in PD and a potential new therapeutic target for myelin-based interventions.

Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes

Spatial transcriptomics (ST) data provide spatially informed gene expression profiles. However, power is limited for spatially informed differential gene expression (DGE) of complex diseases such as Alzheimer disease (AD), due to small sample sizes of ST data. Conversely, single-nucleus RNA sequencing (snRNA-seq) data offer larger sample sizes for cell-type-specific (CTS) analyses but lack spatial information. Here, we integrated ST and snRNA-seq data to enhance the power of spatially informed CTS DGE analysis of AD-related phenotypes. We first utilized the CeLEry tool to infer six cortical layers of ∼1.5 million cells in the snRNA-seq data that were profiled from the dorsolateral prefrontal cortex (DLPFC) tissue of 436 postmortem brains. Then, we conducted cortical layer- and cell-type-specific (LCS) and CTS DGE analyses based on the linear mixed model, for β-amyloid, tangle density, and cognitive decline. We identified 138 LCS significant genes with false discovery rate (FDR) q <0.05, including 103 for β-amyloid, 24 for tangle density, and 25 for cognitive decline. The majority of these LCS significant genes, including known AD risk genes such as APOE, KCNIP3, and CTSD, cannot be detected by CTS analyses. We also identified 2 genes shared across all 3 phenotypes and 10 shared between 2 phenotypes. Gene set enrichment analyses with the LCS DGE results of microglia in cortical layer 6 of β-amyloid identified 12 significant AD-related pathways. In conclusion, incorporating spatial information with snRNA-seq data enhanced the power of spatially informed DGE analyses. These identified LCS significant genes not only help illustrate the pathogenesis of AD but they also provide potential targets for developing therapeutics of AD.

Computational and functional prioritization identifies genes that rescue behavior and reduce tau protein in fly and human cell models of Alzheimer disease

Genome-wide association studies (GWASs) in Alzheimer disease (AD) have uncovered over 70 loci significantly associated with AD risk, but identifying the true causal gene(s) at these loci requires systematic functional validation that is rarely performed due to limitations of time and cost. Here, we integrate transcriptome-wide association study (TWAS) with colocalization analysis, fine-mapping, and additional annotation of AD GWAS variants to identify 123 genes at known and suggestive AD risk loci. A comparison with human AD brain transcriptome data confirmed that many of these candidate genes are dysregulated in human AD and correlate with neuropathology. We then tested all available orthologs in two well-established Drosophila AD models that express either wild-type tau or secreted β-amyloid (β42). Experimental perturbation of the 60 available candidates pinpointed 46 that modulated neuronal dysfunction in one or both fly models. The effects of 18 of these genes were concordant with the TWAS prediction, such that the direction of misexpression predicted to increase AD risk in humans exacerbated behavioral impairments in the AD fly models. Reversing the aberrant down- or upregulation of 11 of these genes (MTCH2, ELL, TAP2, HDC, DMWD, MYCL, SLC4A9, ABCA7, CSTF1, PTK2B, and CD2AP) proved neuroprotective in vivo. We further studied MTCH2 and found that it regulates steady-state tau protein levels in the Drosophila brain and reduces tau accumulation in human neural progenitor cells. This systematic, integrative approach effectively prioritizes genes at GWAS loci and reveals promising AD-relevant candidates for further investigation as risk factors or targets for therapeutic intervention.

Neuroinflammation in Alzheimer disease

Increasing evidence points to a pivotal role of immune processes in the pathogenesis of Alzheimer disease, which is the most prevalent neurodegenerative and dementia-causing disease of our time. Multiple lines of information provided by experimental, epidemiological, neuropathological and genetic studies suggest a pathological role for innate and adaptive immune activation in this disease. Here, we review the cell types and pathological mechanisms involved in disease development as well as the influence of genetics and lifestyle factors. Given the decade-long preclinical stage of Alzheimer disease, these mechanisms and their interactions are driving forces behind the spread and progression of the disease. The identification of treatment opportunities will require a precise understanding of the cells and mechanisms involved as well as a clear definition of their temporal and topographical nature. We will also discuss new therapeutic strategies for targeting neuroinflammation, which are now entering the clinic and showing promise for patients.

Transcriptome signatures of the medial prefrontal cortex underlying GABAergic control of resilience to chronic stress exposure

Analyses of postmortem human brains and preclinical studies of rodents have identified somatostatin (SST)-positive, dendrite-targeting GABAergic interneurons as key elements that regulate the vulnerability to stress-related psychiatric disorders. Conversely, genetically induced disinhibition of SST neurons (induced by Cre-mediated deletion of the γ2 GABAA receptor subunit gene selectively from SST neurons, SSTCre:γ2f/f mice) results in stress resilience. Similarly, chronic chemogenetic activation of SST neurons in the medial prefrontal cortex (mPFC) results in stress resilience but only in male and not in female mice. Here, we used RNA sequencing of the mPFC of SSTCre:γ2f/f mice to characterize the transcriptome changes underlying GABAergic control of stress resilience. We found that stress resilience of male but not female SSTCre:γ2f/f mice is characterized by resilience to chronic stress-induced transcriptome changes in the mPFC. Interestingly, the transcriptome of non-stressed SSTCre:γ2f/f (stress-resilient) male mice resembled that of chronic stress-exposed SSTCre (stress-vulnerable) mice. However, the behavior and the serum corticosterone levels of non-stressed SSTCre:γ2f/f mice showed no signs of physiological stress. Most strikingly, chronic stress exposure of SSTCre:γ2f/f mice was associated with an almost complete reversal of their chronic stress-like transcriptome signature, along with pathway changes suggesting stress-induced enhancement of mRNA translation. Behaviorally, the SSTCre:γ2f/f mice were not only resilient to chronic stress-induced anhedonia - they also showed an inversed, anxiolytic-like behavioral response to chronic stress exposure that mirrored the chronic stress-induced reversal of the chronic stress-like transcriptome signature. We conclude that GABAergic dendritic inhibition by SST neurons exerts bidirectional control over behavioral vulnerability and resilience to chronic stress exposure that is mirrored in bidirectional changes in the expression of putative stress resilience genes, through a sex-specific brain substrate.

A cerebrospinal fluid synaptic protein biomarker for prediction of cognitive resilience versus decline in Alzheimer's disease

Rates of cognitive decline in Alzheimer's disease (AD) are extremely heterogeneous. Although biomarkers for amyloid-beta (Aβ) and tau proteins, the hallmark AD pathologies, have improved pathology-based diagnosis, they explain only 20-40% of the variance in AD-related cognitive impairment (CI). To discover novel biomarkers of CI in AD, we performed cerebrospinal fluid (CSF) proteomics on 3,397 individuals from six major prospective AD case-control cohorts. Synapse proteins emerged as the strongest correlates of CI, independent of Aβ and tau. Using machine learning, we derived the CSF YWHAG:NPTX2 synapse protein ratio, which explained 27% of the variance in CI beyond CSF pTau181:Aβ42, 11% beyond tau positron emission tomography, and 28% beyond CSF neurofilament, growth-associated protein 43 and neurogranin in Aβ+ and phosphorylated tau+ (A+T1+) individuals. CSF YWHAG:NPTX2 also increased with normal aging and 20 years before estimated symptom onset in carriers of autosomal dominant AD mutations. Regarding cognitive prognosis, CSF YWHAG:NPTX2 predicted conversion from A+T1+ cognitively normal to mild cognitive impairment (standard deviation increase hazard ratio = 3.0, P = 7.0 × 10-4) and A+T1+ mild cognitive impairment to dementia (standard deviation increase hazard ratio = 2.2, P = 8.2 × 10-16) over a 15-year follow-up, adjusting for CSF pTau181:Aβ42, CSF neurofilament, CSF neurogranin, CSF growth-associated protein 43, age, APOE4 and sex. We also developed a plasma proteomic signature of CI, which we evaluated in 13,401 samples, which partly recapitulated CSF YWHAG:NPTX2. Overall, our findings underscore CSF YWHAG:NPTX2 as a robust prognostic biomarker for cognitive resilience versus AD onset and progression, highlight the potential of plasma proteomics in replacing CSF measurement and further implicate synapse dysfunction as a core driver of AD dementia.

Integrated analysis of molecular atlases unveils modules driving developmental cell subtype specification in the human cortex

Human brain development requires generating diverse cell types, a process explored by single-cell transcriptomics. Through parallel meta-analyses of the human cortex in development (seven datasets) and adulthood (16 datasets), we generated over 500 gene co-expression networks that can describe mechanisms of cortical development, centering on peak stages of neurogenesis. These meta-modules show dynamic cell subtype specificities throughout cortical development, with several developmental meta-modules displaying spatiotemporal expression patterns that allude to potential roles in cell fate specification. We validated the expression of these modules in primary human cortical tissues. These include meta-module 20, a module elevated in FEZF2+ deep layer neurons that includes TSHZ3, a transcription factor associated with neurodevelopmental disorders. Human cortical chimeroid experiments validated that both FEZF2 and TSHZ3 are required to drive module 20 activity and deep layer neuron specification but through distinct modalities. These studies demonstrate how meta-atlases can engender further mechanistic analyses of cortical fate specification.

Decoding Alzheimer's Disease: Single-Cell Sequencing Uncovers Brain Cell Heterogeneity and Pathogenesis

Alzheimer's disease (AD) is a complex neurodegenerative disorder marked by progressive cognitive decline and diverse neuropathological features. Recent advances in single-cell sequencing technologies have provided unprecedented insights into the cellular and molecular heterogeneity of the AD brain. This review systematically summarizes the applications of single-cell transcriptomic and epigenomic approaches in AD research, with a focus on the characterization of cell type- and subtype-specific transcriptomic alterations. This review highlights key discoveries related to selectively vulnerable neuronal and glial subpopulations, as well as transcriptional dysregulation associated with genetic risk loci such as APOE and TREM2. This review also discusses how the integration of single-cell RNA sequencing (scRNA-seq), assays for transposase-accessible chromatin using sequencing (ATAC-seq), and spatial transcriptomics elucidates disease trajectories and cellular communication networks across pathological stages. These insights not only enhance the understanding of the pathogenesis of AD but also pave the way for precision medicine through the identification of novel therapeutic targets and biomarkers.

A molecular brain atlas reveals cellular shifts during the repair phase of stroke

Ischemic stroke triggers a cascade of pathological events that affect multiple cell types and often lead to incomplete functional recovery. Despite advances in single-cell technologies, the molecular and cellular responses that contribute to long-term post-stroke impairment remain poorly understood. To gain better insight into the underlying mechanisms, we generated a single-cell transcriptomic atlas from distinct brain regions using a mouse model of permanent focal ischemia at one month post-injury. Our findings reveal cell- and region-specific changes within the stroke-injured and peri-infarct brain tissue. For instance, GABAergic and glutamatergic neurons exhibited upregulated genes in signaling pathways involved in axon guidance and synaptic plasticity, and downregulated pathways associated with aerobic metabolism. Using cell-cell communication analysis, we identified increased strength in predicted interactions within stroke tissue among both neural and non-neural cells via signaling pathways such as those involving collagen, protein tyrosine phosphatase receptor, neuronal growth regulator, laminin, and several cell adhesion molecules. Furthermore, we found a strong correlation between mouse transcriptome responses after stroke and those observed in human nonfatal brain stroke lesions. Common molecular features were linked to inflammatory responses, extracellular matrix organization, and angiogenesis. Our findings provide a detailed resource for advancing our molecular understanding of stroke pathology and for discovering therapeutic targets in the repair phase of stroke recovery.

Transcriptomic and morphologic vascular aberrations underlying FCDIIb etiology

Focal cortical dysplasia type II (FCDII) is a major cause of drug-resistant epilepsy, but genetic factors explain only some cases, suggesting other mechanisms. In this study, we conduct a molecular analysis of brain lesions and adjacent areas in FCDIIb patients. By analyzing over 217,506 single-nucleus transcriptional profiles from 15 individuals, we find significant changes in smooth muscle cells (SMCs) and astrocytes. We identify abnormal vascular malformations and a unique type of SMC that we call "Firework cells", which migrate from blood vessels into the brain parenchyma and associate with VIM+ cells. These abnormalities create localized ischemic-hypoxic (I/H) microenvironments, as confirmed by clinical data, further impairing astrocyte function, activating the HIF-1α/mTOR/S6 pathway, and causing neuronal loss. Using zebrafish models, we demonstrate that vascular abnormalities resulting in I/H environments promote seizures. Our results highlight vascular malformations as a factor in FCDIIb pathogenesis, suggesting potential therapeutic avenues.

Photobiomodulation modulates mitochondrial energy metabolism and ameliorates neurological damage in an APP/PS1 mousmodel of Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is a neurodegenerative disease. Amyloid β-protein (Aβ) is one of the key pathological features of AD, which is cytotoxic and can damage neurons, thereby causing cognitive dysfunction. Photobiomodulation (PBM) is a non-invasive physical therapy that induces changes in the intrinsic mechanisms of cells and tissues through low-power light exposure. Although PBM has been employed in the treatment of AD, the effect and precise mechanism of PBM on AD-induced neurological damage are still unclear.

METHODS

In vivo experiments, PBM (808 nm, 20 mW/cm2) was used to continuously interfere with APP/PS1 mice for 6 weeks, and then their cognitive function and AD pathological changes were evaluated. In vitro experiments, lipopolysaccharide (LPS) was used to induce microglia to model inflammation, and the effect of PBM treatment on microglia polarization status and phagocytic Aβ ability was evaluated. Hexokinase 2 (HK2) inhibitor 3-bromopyruvate (3BP) was used to study the effect of PBM treatment on mitochondrial energy metabolism in microglia.

RESULTS

PBM further ameliorates AD-induced cognitive impairment by alleviating neuroinflammation and neuronal apoptosis, thereby attenuating nerve damage. In addition, PBM can also reduce neuroinflammation by promoting microglial anti-inflammatory phenotypic polarization; Promotes Aβ clearance by enhancing the ability of microglia to engulf Aβ. Among them, PBM regulates microglial polarization and inhibits neuronal apoptosis, which may be related to its regulation of mitochondrial energy metabolism, promotion of oxidative phosphorylation, and inhibition of glycolysis.

CONCLUSION

PBM regulates neuroinflammatory response and inhibits neuronal apoptosis, thereby repairing Aβ-induced neuronal damage and cognitive dysfunction. Mitochondrial energy metabolism plays an important role in PBM in improving nerve injury in AD mice. This study provides theoretical support for the subsequent application of PBM in the treatment of AD.

Integrative network analysis reveals novel moderators of Aβ-Tau interaction in Alzheimer's disease

BACKGROUND

Although interactions between amyloid-beta and tau proteins have been implicated in Alzheimer's disease (AD), the precise mechanisms by which these interactions contribute to disease progression are not yet fully understood. Moreover, despite the growing application of deep learning in various biomedical fields, its application in integrating networks to analyze disease mechanisms in AD research remains limited. In this study, we employed BIONIC, a deep learning-based network integration method, to integrate proteomics and protein-protein interaction data, with an aim to uncover factors that moderate the effects of the Aβ-tau interaction on mild cognitive impairment (MCI) and early-stage AD.

METHODS

Proteomic data from the ROSMAP cohort were integrated with protein-protein interaction (PPI) data using a Deep Learning-based model. Linear regression analysis was applied to histopathological and gene expression data, and mutual information was used to detect moderating factors. Statistical significance was determined using the Benjamini-Hochberg correction (p < 0.05).

RESULTS

Our results suggested that astrocytes and GPNMB + microglia moderate the Aβ-tau interaction. Based on linear regression with histopathological and gene expression data, GFAP and IBA1 levels and GPNMB gene expression positively contributed to the interaction of tau with Aβ in non-dementia cases, replicating the results of the network analysis.

CONCLUSIONS

These findings suggest that GPNMB + microglia moderate the Aβ-tau interaction in early AD and therefore are a novel therapeutic target. To facilitate further research, we have made the integrated network available as a visualization tool for the scientific community (URL: https://igcore.cloud/GerOmics/AlzPPMap ).

Astrocyte and oligodendrocyte pathology in Alzheimer's disease

Astrocytes and oligodendrocytes, once considered passive support cells, are now recognized as active participants in the pathogenesis of Alzheimer's disease. Emerging evidence highlights the critical role that these glial cells play in the pathological features of Alzheimer's, including neuroinflammation, excitotoxicity, synaptic dysfunction, and myelin degeneration, which contribute to neurodegeneration and cognitive decline. Here, we review the current understanding of astrocyte and oligodendrocyte pathology in Alzheimer's disease and highlight research that supports the therapeutic potential of modulating astrocyte and oligodendrocyte functions to treat Alzheimer's disease.

Stress tests and biomarkers of resilience: Proceedings of the second state of resilience science conference

The "Stress Tests and Biomarkers of Resilience" conference, hosted by the American Geriatrics Society and the National Institute on Aging, marks the second in a series aimed at advancing the field of resilience science. Held on March 4-5, 2024, in Bethesda, Maryland, this conference built upon the foundational work from the first conference, which focused on defining resilience across various domains-physical, cognitive, and psychosocial. This year's gathering centered around three factors: the biology that underlies resilient outcomes; the social, environmental, genetic, and psychosocial factors that impact that resilience biology; and the biomarker testing and imaging that predicts resilient outcomes for older adults. The presentations and discussions around these topics were underscored by considerations around the many impacts of social determinants of health on resiliency interventions, and by advances in the modern training and research methodologies that influence data collection and experiment design.

Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease

Alzheimer's disease (AD) presents significant challenges in drug discovery and development due to its complex and poorly understood pathology and etiology. Digital twins (DTs) are recently developed virtual real-time representations of physical entities that enable rapid assessment of the bidirectional interaction between the virtual and physical domains. With recent advances in artificial intelligence (AI) and the growing accumulation of multi-omics and clinical data, application of DTs in healthcare is gaining traction. Digital twin technology, in the form of multiscale virtual models of patients or organ systems, can track health status in real time with continuous feedback, thereby driving model updates that enhance clinical decision-making. Here, we posit an additional role for DTs in drug discovery, with particular utility for complex diseases like AD. In this review, we discuss salient challenges in AD drug development, including complex disease pathology and comorbidities, difficulty in early diagnosis, and the current high failure rate of clinical trials. We also review DTs and discuss potential applications for predicting AD progression, discovering biomarkers, identifying new drug targets and opportunities for drug repurposing, facilitating clinical trials, and advancing precision medicine. Despite significant hurdles in this area, such as integration and standardization of dynamic medical data and issues of data security and privacy, DTs represent a promising approach for revolutionizing drug discovery in AD.

A Single-Nucleus Transcriptomic Atlas Reveals Cellular and Genetic Characteristics of Alzheimer's-Like Pathology in Aging Tree Shrews

The lack of natural aging-inducing Alzheimer's disease (AD) model presents a significant gap in the current preclinical research. Here, we identified a unique cohort of 10 naturally aging tree shrews (TSs) displaying distinct Alzheimer's-like pathology (ALP) from a population of 324, thereby establishing a novel model that closely mirrors human AD progression. Using single-nucleus RNA sequencing, we generated a comprehensive transcriptome atlas, revealing the cellular diversity and gene expression changes underlying AD pathology in aged TSs. Particularly, distinct differentiation trajectories of neural progenitor cells were highly associated with AD pathology. Intriguingly, cross-species comparisons among humans, TSs, monkeys, and mice highlighted a greater cellular homogeneity of TSs to primates and humans than to mice. Our extended cross-species analysis by including a direct comparison between human and TS hippocampal tissue under AD conditions uncovered conserved cell types, enriched synaptic biological processes, and elevated excitatory/inhibitory imbalance across species. Cell-cell communication analysis unveiled parallel patterns between AD human and ALP TSs, with both showing reduced interaction strength and quantity across most cell types. Overall, our study provides rich, high-resolution resources on the cellular and molecular landscape of the ALP TS hippocampus, reinforcing the utility of TSs as a robust model for AD research.

Therapeutic modulation of neurogenesis to improve hippocampal plasticity and cognition in aging and Alzheimer's disease

Alzheimer's disease is characterized by progressive memory loss and cognitive decline. The hippocampal formation is the most vulnerable brain area in Alzheimer's disease. Neurons in layer II of the entorhinal cortex and the CA1 region of the hippocampus are lost at early stages of the disease. A unique feature of the hippocampus is the formation of new neurons that incorporate in the dentate gyrus of the hippocampus. New neurons form synapses with neurons in layer II of the entorhinal cortex and with the CA3 region. Immature and new neurons are characterized by high level of plasticity. They play important roles in learning and memory. Hippocampal neurogenesis is impaired early in mouse models of Alzheimer's disease and in human patients. In fact, neurogenesis is compromised in mild cognitive impairment (MCI), suggesting that rescuing neurogenesis may restore hippocampal plasticity and attenuate neuronal vulnerability and memory loss. This review will discuss the current understanding of therapies that target neurogenesis or modulate it, for the treatment of Alzheimer's disease.

Molecular Mechanisms of Propofol-Induced Cognitive Impairment: Suppression of Critical Hippocampal Pathways

Propofol, a commonly used anesthetic, is known to cause postoperative cognitive dysfunction (POCD), particularly after prolonged or high-dose administration. Its effects on neural remodeling in the hippocampal region, which is vital for cognitive function, remain poorly understood. This study employs single-cell RNA sequencing (scRNA-seq) and high-throughput transcriptomic analysis to elucidate the molecular mechanisms by which propofol impairs hippocampal neural remodeling. Our findings indicate that propofol suppresses the (5-Hydroxytryptamine Receptor 1A/Glutamate Receptor 2/Phosphoinositide 3-Kinase Regulatory Subunit 1) HTR1A/GRIA2/PIK3R1 signaling pathway, contributing to cognitive dysfunction in mice. In vitro experiments reveal that propofol treatment reduces the expression of HTR1A/GRIA2/PIK3R1-related factors, decreases neuronal activity and synaptic plasticity, and increases apoptosis and inflammation. In vivo experiments demonstrate significant impairments in spatial memory and learning abilities in mice treated with propofol. These results provide new insights into the long-term effects of anesthetic drugs and offer a scientific basis for their judicious use in clinical practice. The study highlights potential strategies and targets for preventing and treating POCD, emphasizing the importance of understanding the molecular mechanisms underlying anesthetic-induced cognitive dysfunction.

Risk of Alzheimer's disease in Down syndrome: Insights gained by multi-omics

Individuals with Down syndrome (DS) are highly susceptible to Alzheimer's disease (AD). The integration of genomics, transcriptomics, epigenomics, proteomics, and metabolomics enables unprecedented understanding of DS-AD, offering a detailed picture of this complex issue. The vast -omics data also present challenges that reflect the complexity of genetic information flow. These studies nonetheless reveal critical mechanisms behind AD risk, including unique observations in DS that differ from those seen in the general population and familial dominant AD. In addition, the correlations between the AD polygenic risk score and proteins related to female infertility and autoimmune thyroiditis corroborate clinical observations. Metabolomic data reveal disrupted metabolic networks, offering prospects for a dynamic score to create specialized nutritional interventions. By adopting a multidimensional perspective with integrated reductionism, the evolving landscape presents an opportunity to identify promising directions for developing precision strategies to mitigate the impact of AD in the DS population. HIGHLIGHTS: Individuals with Down syndrome (DS) are highly susceptible to Alzheimer's disease (AD). DS-AD is characterized by its polygenic nature, extending beyond chromosome 21 with significant contributions from various chromosomes. DS-AD also presents unique features that differ from those observed in the general population and familial dominant AD. Our review consolidates key findings from genomics, transcriptomics, epigenomics, proteomics, and metabolomics, providing a comprehensive view of the molecular mechanisms underlying DS-AD. We highlight promising research directions to further elucidate the pathogenesis of DS-AD.

Association of RDoC dimensions with post mortem brain transcriptional profiles in Alzheimer's disease

INTRODUCTION

Neuropsychiatric symptoms are common in people with Alzheimer's disease (AD) across all severity stages. Their heterogeneous presentation and variable temporal association with cognitive decline suggest shared and distinct biological mechanisms. We hypothesized that specific patterns of gene expression associate with distinct National Institute of Mental Health Research Domain Criteria (RDoC) domains in AD.

METHODS

Post-mortem bulk RNA sequencing of the insula and anterior cingulate cortex from 60 brain donors, representing the spectrum of canonical Alzheimer's disease neuropathology, was combined with natural language processing approaches based on the RDoC Clinical Domains to uncover transcriptomic patterns linked to disease progression.

RESULTS

Distinct sets of >100 genes (P false discovery rate < 0.05) were specifically associated with at least one clinical domain (cognitive, social, negative, positive, arousal). In addition, dysregulation of immune response pathways was shared across domains and brain regions.

DISCUSSION

Our findings provide evidence for distinct transcriptional profiles associated with RDoC domains suggesting that each dimension is characterized by sets of genes providing insight into the underlying mechanisms.

Highlights

Post mortem brain tissue investigations are critically important for Alzheimer's disease (AD) research.Neuropsychiatric symptoms in AD are common and an important aspect of AD.Categorical phenotypes are commonly used, but insufficiently describe the heterogenous presentation of AD.Using natural language processing (NLP) of post mortem brain donor health records provides insight into dimensional phenotypes of AD.We provide evidence for distinct RNA expression profiles associated with NLP-derived Research Domain Criteria clinical domain scores.

Molecular pathways and diagnosis in spatially resolved Alzheimer's hippocampal atlas

We employed Stereo-seq combined with single-nucleus RNA sequencing (snRNA-seq) to investigate the gene expression and cell composition changes in human hippocampus with or without Alzheimer's disease (AD). The transcriptomic map, with single-cell precision, unveiled AD-associated alterations with spatial specificity, which include the following: (1) elevated synapse pruning gene expression in the fimbria of AD, with disrupted microglia-astrocyte communication likely leading to disorganized synaptic structure; (2) a globally increased energy generation in the cornu ammonis (CA) region, with varying degrees across its subregions; (3) a significant reduction in the number of CA1 neurons in AD, while CA4 neurons remained largely unaffected, potentially due to gene alterations in CA4 conferring resilience to AD; and (4) aggravated amyloid-beta (Aβ) plaques in CA1 and stratum lucidum, radiatum, and moleculare (SLRM), and integration of Stereo-seq map with Aβ staining revealed a sequential enrichment of microglia and astrocytes around Aβ plaques. Finally, reduced brain-derived extracellular vesicles carrying cholecystokinin (CCK) and peripheral myelin protein 2 (PMP2) in AD plasma highlighted their diagnostic potential for clinical applications.

Transcriptional signatures of hippocampal tau pathology in primary age-related tauopathy and Alzheimer's disease

In primary age-related tauopathy (PART) and Alzheimer's disease (AD), tau aggregates share a similar structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, transcriptional similarities between PART and AD and gene expression changes within tau-pathology-bearing neurons are largely unknown. Using GeoMx spatial transcriptomics, mRNA was quantified in hippocampal neurons with and without tau pathology in PART and AD. Synaptic genes were down-regulated in disease overall but up-regulated in tau-pathology-positive neurons. Two transcriptional signatures were associated with intraneuronal tau, both validated in a cortical AD dataset. Genes in the up-regulated signature were enriched in calcium regulation and synaptic function. Notably, transcriptional changes associated with intraneuronal tau in PART and AD were similar, suggesting a possible mechanistic relationship. These findings highlight the power of molecular analysis stratified by pathology and provide insight into common pathways associated with tau pathology in PART and AD.

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

Alzheimer's 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.

Rewired m6A methylation of promoter antisense RNAs in Alzheimer's disease regulates global gene transcription in the 3D nucleome

N6-methyladenosine (m6A) is the most prevalent internal RNA modification that can impact mRNA expression post-transcriptionally. Recent progress indicates that m6A also acts on nuclear or chromatin-associated RNAs to impact transcriptional and epigenetic processes. However, the landscapes and functional roles of m6A in human brains and neurodegenerative diseases, including Alzheimer's disease (AD), have been under-explored. Here, we examined RNA m6A methylome using total RNA-seq and meRIP-seq in middle frontal cortex tissues of post-mortem human brains from individuals with AD and age-matched counterparts. Our results revealed AD-associated alteration of m6A methylation on both mRNAs and various noncoding RNAs. Notably, a series of promoter antisense RNAs (paRNAs) displayed cell-type-specific expression and changes in AD, including one produced adjacent to the MAPT locus that encodes the Tau protein. We found that MAPT-paRNA is enriched in neurons, and m6A positively controls its expression. In iPSC-derived human excitatory neurons, MAPT-paRNA promotes expression of hundreds of genes related to neuronal and synaptic functions, including a key AD resilience gene MEF2C, and plays a neuroprotective role against excitotoxicity. By examining RNA-DNA interactome in the three-dimensional (3D) nuclei of human brains, we demonstrated that brain paRNAs can interact with both cis- and trans-chromosomal target genes to impact their transcription. These data together reveal previously unexplored landscapes and functions of noncoding RNAs and m6A methylome in brain gene regulation, neuronal survival and AD pathogenesis.

Parvalbumin interneurons regulate rehabilitation-induced functional recovery after stroke and identify a rehabilitation drug

Motor disability is a critical impairment in stroke patients. Rehabilitation has a limited effect on recovery; but there is no medical therapy for post-stroke recovery. The biological mechanisms of rehabilitation in the brain remain unknown. Here, using a photothrombotic stroke model in male mice, we demonstrate that rehabilitation after stroke selectively enhances synapse formation in presynaptic parvalbumin interneurons and postsynaptic neurons in the rostral forelimb motor area with axonal projections to the caudal forelimb motor area where stroke was induced (stroke-projecting neuron). Rehabilitation improves motor performance and neuronal functional connectivity, while inhibition of stroke-projecting neurons diminishes motor recovery. Stroke-projecting neurons show decreased dendritic spine density, reduced external synaptic inputs, and a lower proportion of parvalbumin synapse in the total GABAergic input. Parvalbumin interneurons regulate neuronal functional connectivity, and their activation during training is necessary for recovery. Furthermore, gamma oscillation, a parvalbumin-regulated rhythm, is increased with rehabilitation-induced recovery in animals after stroke and stroke patients. Pharmacological enhancement of parvalbumin interneuron function improves motor recovery after stroke, reproducing rehabilitation recovery. These findings identify brain circuits that mediate rehabilitation-recovery and the possibility for rational selection of pharmacological agents to deliver the first molecular-rehabilitation therapeutic.

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

Most genetic risk variants for neurological diseases are located in non-coding regulatory regions, where they may often act as expression quantitative trait loci (eQTLs), modulating gene expression and influencing disease susceptibility. However, eQTL studies in bulk brain tissue or specific cell types lack the resolution to capture the brain's cellular diversity. Single-nucleus RNA sequencing (snRNA-seq) offers high-resolution mapping of eQTLs across diverse brain cell types. Here, we performed a meta-analysis, "SingleBrain," integrating publicly available snRNA-seq and genotype data from four cohorts, totaling 5.8 million nuclei from 983 individuals. We mapped cis-eQTLs across major brain cell types and subtypes and employed statistical colocalization and Mendelian randomization to identify genes mediating neurological disease risk. We observed up to a 10-fold increase in cis-eQTLs compared to previous studies and uncovered novel cell type-specific genes linked to Alzheimer's disease, Parkinson's disease, and schizophrenia that were previously undetectable in bulk tissue analyses. Additionally, we prioritized putative causal variants for each locus through fine-mapping and integration with cell type-specific enhancer and promoter regulatory elements. SingleBrain represents a comprehensive single-cell eQTL resource, advancing insights into the genetic regulation of brain disorders.

The glamor of and insights regarding hydrotherapy, from simple immersion to advanced computer-assisted exercises: A narrative review

Water-based therapy has been gaining attention in recent years and is being widely used in clinical settings. Hydrotherapy is the most important area of water-based therapy, and it has distinct advantages and characteristics compared to conventional land-based exercises. Several new techniques and pieces of equipment are currently emerging with advances in computer technologies. However, comprehensive reviews of hydrotherapy are insufficient. Hence, this study reviewed the status quo, mechanisms, adverse events and contraindications, and future prospects of the use of hydrotherapy. This study aims to comprehensively review the latest information regarding the application of hydrotherapy to musculoskeletal diseases, neurological diseases, and COVID-19. We have attempted to provide a "take-home message" regarding the clinical applications and mechanisms of hydrotherapy based on the latest evidence available.

Nanopore Long-Read Sequencing Unveils Genomic Disruptions in Alzheimer's Disease

Studies in laboratory models and postmortem human brain tissue from patients with Alzheimer's disease have revealed disruption of basic cellular processes such as DNA repair and epigenetic control as drivers of neurodegeneration. While genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark regions," are difficult to resolve using traditional sequencing approaches, long-read technologies offer promising new avenues to explore previously inaccessible regions of the genome. In the current study, we leverage nanopore-based long-read whole-genome sequencing of DNA extracted from postmortem human frontal cortex at early and late stages of Alzheimer's disease, as well as age-matched controls, to analyze retrotransposon insertion events, non-allelic homologous recombination (NAHR), structural variants and DNA methylation within retrotransposon loci and other repetitive/dark regions of the human genome. Interestingly, we find that retrotransposon insertion events and repetitive element-associated NAHR are particularly enriched within centromeric and pericentromeric regions of DNA in the aged human brain, and that ribosomal DNA (rDNA) is subject to a high degree of NAHR compared to other regions of the genome. We detect a trending increase in potential somatic retrotransposition events of the small interfering nuclear element (SINE) AluY in late-stage Alzheimer's disease, and differential changes in methylation within repetitive elements and retrotransposons according to disease stage. Taken together, our analysis provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, NAHR, structural variants, and DNA methylation in the aged brain, and points toward transposable elements, centromeric/pericentromeric regions and rDNA as hotspots for genomic variation.