Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression

Neuronal guidance signaling in neurodegenerative diseases: Key regulators that function at neuron-glia and neuroimmune interfaces

The nervous system processes a vast amount of information, performing computations that underlie perception, cognition, and behavior. During development, neuronal guidance genes, which encode extracellular cues, their receptors, and downstream signal transducers, organize neural wiring to generate the complex architecture of the nervous system. It is now evident that many of these neuroguidance cues and their receptors are active during development and are also expressed in the adult nervous system. This suggests that neuronal guidance pathways are critical not only for neural wiring but also for ongoing function and maintenance of the mature nervous system. Supporting this view, these pathways continue to regulate synaptic connectivity, plasticity, and remodeling, and overall brain homeostasis throughout adulthood. Genetic and transcriptomic analyses have further revealed many neuronal guidance genes to be associated with a wide range of neurodegenerative and neuropsychiatric disorders. Although the precise mechanisms by which aberrant neuronal guidance signaling drives the pathogenesis of these diseases remain to be clarified, emerging evidence points to several common themes, including dysfunction in neurons, microglia, astrocytes, and endothelial cells, along with dysregulation of neuron-microglia-astrocyte, neuroimmune, and neurovascular interactions. In this review, we explore recent advances in understanding the molecular and cellular mechanisms by which aberrant neuronal guidance signaling contributes to disease pathogenesis through altered cell-cell interactions. For instance, recent studies have unveiled two distinct semaphorin-plexin signaling pathways that affect microglial activation and neuroinflammation. We discuss the challenges ahead, along with the therapeutic potentials of targeting neuronal guidance pathways for treating neurodegenerative diseases. Particular focus is placed on how neuronal guidance mechanisms control neuron-glia and neuroimmune interactions and modulate microglial function under physiological and pathological conditions. Specifically, we examine the crosstalk between neuronal guidance signaling and TREM2, a master regulator of microglial function, in the context of pathogenic protein aggregates. It is well-established that age is a major risk factor for neurodegeneration. Future research should address how aging and neuronal guidance signaling interact to influence an individual's susceptibility to various late-onset neurological diseases and how the progression of these diseases could be therapeutically blocked by targeting neuronal guidance pathways.

The Citron homology domain of MAP4Ks improves outcomes of traumatic brain injury

JOURNAL/nrgr/04.03/01300535-202511000-00027/figure1/v/2024-12-20T164640Z/r/image-tiff The mitogen-activated protein kinase kinase kinase kinases (MAP4Ks) signaling pathway plays a pivotal role in axonal regrowth and neuronal degeneration following insults. Whether targeting this pathway is beneficial to brain injury remains unclear. In this study, we showed that adeno-associated virus-delivery of the Citron homology domain of MAP4Ks effectively reduces traumatic brain injury-induced reactive gliosis, tauopathy, lesion size, and behavioral deficits. Pharmacological inhibition of MAP4Ks replicated the ameliorative effects observed with expression of the Citron homology domain. Mechanistically, the Citron homology domain acted as a dominant-negative mutant, impeding MAP4K-mediated phosphorylation of the dishevelled proteins and thereby controlling the Wnt/β-catenin pathway. These findings implicate a therapeutic potential of targeting MAP4Ks to alleviate the detrimental effects of traumatic brain injury.

Large-scale proteomic analyses of incident Alzheimer's disease reveal new pathophysiological insights and potential therapeutic targets

Pathophysiological evolutions in early-stage Alzheimer's disease (AD) are not well understood. We used data of 2923 Olink plasma proteins from 51,296 non-demented middle-aged adults. During a follow-up of 15 years, 689 incident AD cases occurred. Cox-proportional hazard models were applied to identify AD-associated proteins in different time intervals. Through linking to protein categories, changing sequences of protein z-scores can reflect pathophysiological evolutions. Mendelian randomization using blood protein quantitative loci data provided causal evidence for potentially druggable proteins. We identified 48 AD-related proteins, with CEND1, GFAP, NEFL, and SYT1 being top hits in both near-term (HR:1.15-1.77; P:9.11 × 10-65-2.78 × 10-6) and long-term AD risk (HR:1.20-1.54; P:2.43 × 10-21-3.95 × 10-6). These four proteins increased 15 years before AD diagnosis and progressively escalated, indicating early and sustained dysfunction in synapse and neurons. Proteins related to extracellular matrix organization, apoptosis, innate immunity, coagulation, and lipid homeostasis showed early disturbances, followed by malfunctions in metabolism, adaptive immunity, and final synaptic and neuronal loss. Combining CEND1, GFAP, NEFL, and SYT1 with demographics generated desirable predictions for 10-year (AUC = 0.901) and over-10-year AD (AUC = 0.864), comparable to full model. Mendelian randomization supports potential genetic link between CEND1, SYT1, and AD as outcome. Our findings highlight the importance of exploring the pathophysiological evolutions in early stages of AD, which is essential for the development of early biomarkers and precision therapeutics.

Development of a brain-penetrant G9a methylase inhibitor to target Alzheimer's disease-associated proteopathology

Current Aβ-targeting therapeutics for Alzheimer's disease (AD) only slow cognitive decline due to poor understanding of AD pathogenesis. Here we describe a mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of hippocampal proteins associated with AD pathology. Correspondingly, we developed a brain-penetrant inhibitor of G9a, MS1262, which restored both age-related learning & memory and noncognitive functions in multiple AD mouse models. Further, comparison of AD pathology-correlated mouse proteomes with those of AD patients found G9a regulates pathological pathways that promote Aβ and neurofibrillary tangles. This mouse-to-human overlap of G9a regulated AD-associated pathologic proteins supports at the molecular level the efficacy of targeting G9a translational mechanism for treating AD patients. Additionally, MS1262 treatment reversed the AD-characteristic expression or phosphorylation of multiple clinically validated biomarkers of AD that have the potential to be used for early-stage AD diagnosis and companion diagnosis of individualized drug effects.

Alzheimer's disease patient brain extracts induce multiple pathologies in novel vascularized neuroimmune organoids for disease modeling and drug discovery

Alzheimer's Disease (AD) is the most common cause of dementia, afflicting 55 million individuals worldwide, with limited treatment available. Current AD models mainly focus on familial AD (fAD), which is due to genetic mutations. However, models for studying sporadic AD (sAD), which represents over 95% of AD cases without specific genetic mutations, are severely limited. Moreover, the fundamental species differences between humans and animals might significantly contribute to clinical failures for AD therapeutics that have shown success in animal models, highlighting the urgency to develop more translational human models for studying AD, particularly sAD. In this study, we developed a complex human pluripotent stem cell (hPSC)-based vascularized neuroimmune organoid model, which contains multiple cell types affected in human AD brains, including human neurons, microglia, astrocytes, and blood vessels. Importantly, we demonstrated that brain extracts from individuals with sAD can effectively induce multiple AD pathologies in organoids four weeks post-exposure, including amyloid beta (Aβ) plaque-like aggregates, tau tangle-like aggregates, neuroinflammation, elevated microglial synaptic pruning, synapse/neuronal loss, and impaired neural network activity. Proteomics analysis also revealed disrupted AD-related pathways in our vascularized AD neuroimmune organoids. Furthermore, after treatment with Lecanemab, an FDA-approved antibody drug targeting Aβ, AD brain extracts exposed organoids showed a significant reduction of amyloid burden, along with an elevated vascular inflammation response. Thus, the vascularized neuroimmune organoid model provides a unique opportunity to study AD, particularly sAD, under a pathophysiological relevant three-dimensional (3D) human cell environment. It also holds great promise to facilitate AD drug development, particularly for immunotherapies.

Unraveling sex differences in Alzheimer's disease and related endophenotypes with brain proteomes

INTRODUCTION

Sex differences exist in Alzheimer's disease (AD), but the underlying mechanisms remain unclear.

METHODS

We examined brain proteomes profiled from the dorsolateral prefrontal cortex of 770 donors (66.2% female).

RESULTS

Proteome-wide differential expression analysis in males and females jointly identified many significant proteins for AD dementia (n = 1228), amyloid beta (n = 1183), tangles (n = 1309), and global cognitive trajectory (n = 2325) at a false discovery rate of <0.05. Sex-stratified analyses also identified many proteins associated with AD or its endophenotypes. Finally, we found 10 proteins with significant sex-by-trait interactions, including one in AD clinical diagnosis (MARCKS), seven in cognitive trajectories (TOGARAM1, PLCD3, SLC22A5, MTFR1L, DCUN1D5, S100A12, and TRIM46), and two in cerebral pathologies (PANK4 and SOS1).

DISCUSSION

The 10 proteins with sex interaction in AD cover a range of functions likely relevant for AD pathogenesis, including estrogen response, inflammation, and mitochondrial biology, and their specific roles in AD ought to be studied. Future work should test their potential as sex-specific AD biomarkers.

HIGHLIGHTS

At the phenotypic level, we found sex differences in baseline cognitive performance, cognitive trajectories, and AD hallmark pathologies. Proteome-wide differential expression analyses identified many brain proteins associated with AD and its endophenotypes in either sex alone or when considered together. We found 10 brain proteins with significant sex interactions in AD and its endophenotypes, which could be investigated as potential sex-specific biomarkers of AD.

Plasma proteomic analysis of intermuscular fat links muscle integrity with processing speed in older adults

INTRODUCTION

More intermuscular fat (IMF) has been associated with lower cognitive performance through mechanisms that are not fully elucidated.

METHODS

The associations of 7628 plasma proteins with IMF were assessed in the Baltimore Longitudinal Study on Aging (n = 941, mean age = 66.7 ± 15.2) and validated in the Coronary Artery Risk Development in Young Adults Study (n = 2451, mean age = 50.2 ± 3.6). Processing speed was assessed by Digit Symbol Substitution Test (DSST). Associations between the main exposures, outcome, and mediators were evaluated using linear regression, and mediating effects were assessed by causal mediation analysis.

RESULTS

There were 722 plasma proteins associated with IMF in both the discovery and replication cohorts (false discovery rate [FDR] adjusted p ≤ 0.05). Of these, 26 mediated the relationship between IMF and DSST, with effects ranging from 2.8% to 20.9% (p ≤ 0.05). These proteins represented synaptic function and organization, and growth factor binding (FDR adjusted p ≤ 0.05).

DISCUSSION

Reducing IMF may improve processing speed through effects on growth factor and synaptic activity.

HIGHLIGHTS

Higher intermuscular fat is associated with lower processing speed, consistently across populations that represent different demographic characteristics. There is a robust plasma proteomic profile of intermuscular fat that is assessed in the abdominal and thigh skeletal muscle. The proteins associated with intermuscular fat reflect signals that are reflective of synaptic function and organization, as well as other molecular pathways such as growth factor binding. Circulating proteins partially explain the association between higher intermuscular fat and lower processing speed, suggesting that higher intermuscular fat effects processing speed through pathways including synaptic functions and growth factor binding.

Involvement of the VGF/BDNF axis in the neuropathology of Alzheimer's disease and its potential role in diagnosis and treatment

The brain is a highly plastic organ that continually receives and integrates signals to generate functional and structural changes and homeostatic adaptations throughout life. Alterations in some signaling pathways that mediate these responses can impact brain plasticity, accelerate brain aging and potentially lead to neurodegeneration. There is substantial evidence that two important signaling pathways activated by neurotrophins, nonacronymic (VGF) and brain-derived neurotrophic factor (BDNF), are involved in substantial functions stimulating neuronal growth, differentiation, and circuit establishment during development and neuronal maintenance and plasticity in the mature brain. In this review, we present evidence that these two pathways and their interactions are central players in cognitive performance and alterations in pathological aging, particularly in conditions such as Alzheimer's disease (AD). Finally, we suggest specific avenues for future research on the basis of recent findings suggesting these molecules are diagnostic biomarkers and putative therapeutic tools to prevent, delay or improve AD neuropathology.

Affinity peptide ligands: new tools for chasing non-canonical N-phosphoproteome

The enrichment of protein N-phosphorylation encounters substantial challenges due to the inherent instability of the N-P bond, severely impeding the manifestation of its biological functions. Traditional enrichment methods often rely on antibodies, organic solvents and metal ion interactions, which are limited by lack of universality, potential degradation of sample integrity, or reduced selectivity for N-phosphorylation. To overcome these challenges, we innovatively capitalized phage display technology to identify affinity peptides that specifically bind to the N-PO3 group. By functionalizing magnetic nanoparticles with the affinity peptide, we developed a novel, organic solvent- and metal-free enrichment strategy that enhanced both the selectivity and efficiency for all three types of N-phosphopeptide capture under neutral conditions, ensuring superior preservation of sample integrity and allowing more accurate proteomic analysis. This strategy has demonstrated robust enrichment capabilities for both prokaryotic and eukaryotic samples. In HeLa cells, 1995 novel N-phosphorylation sites were identified, representing a substantial increase of 2- to 5-fold in detection depth over previous approaches and significantly expanding the scale of the N-phosphoproteome database. Additionally, it was discovered that N-phosphorylation modification was highly concentrated in the nucleus. By integrating the nuclear isolation technique, 1296 N-phosphorylation sites were identified for the first time, offering new leads for uncovering the functions of N-phosphorylation in nuclear proteins. Finally, in conjunction with the quantitative proteomics method, the dynamic changes in N-phosphorylation modification during the progression of Alzheimer's disease were investigated, providing fresh perspectives on the research of AD pathogenesis. Overall, this work not only presents a new approach for efficient enrichment of N-phosphopeptides but also advances the functional study of N-phosphorylated proteins in physiological and pathological processes.

Multiomics from Alzheimer's Brains and Mesenchymal Stem Cell-Derived Extracellular Vesicles Identifies Therapeutic Potential of Specific Subpopulations to Target Mitochondrial Proteostasis

Background

Alzheimer's disease (AD) is characterized by complex molecular alterations that complicate its pathogenesis and contribute to the lack of effective treatments. Mesenchymal stem cell-derived extracellular vesicles (EVs) have shown promise in AD models, but results across different EV subpopulations remain inconsistent.

Objectives

This study investigates proteomic and transcriptomic data from publicly available postmortem AD brain datasets to identify molecular changes at both the gene and protein levels. These findings are then compared with the proteomes of various EV subpopulations, differing in size and distribution, to determine the most promising subtype for compensating molecular degeneration in AD.

Design

We conducted a comprehensive analysis of 788 brain samples, including 481 AD cases and 307 healthy controls, examining protein and mRNA levels to uncover AD-associated molecular changes. These findings were then compared with the proteomes of different EV subpopulations to identify potential therapeutic candidates.

Methods

A multi-omics approach was employed, integrating proteomic and transcriptomic data analysis, miRNA and transcription factor profiling, protein-protein network construction, hub gene identification, and enrichment analyses. This approach aimed to explore molecular changes in AD brains and pinpoint the most relevant EV subpopulations for therapeutic intervention.

Results

We identified common alterations in the cAMP signaling pathway and coagulation cascade at both the protein and mRNA levels. Distinct changes in energy metabolism were observed at the protein level but not at the mRNA level. A specific EV subtype, characterized by a broader size distribution obtained through high-speed centrifugation, was identified as capable of compensating for dysregulated mitochondrial proteostasis in AD brains. Network biology analyses further highlighted potential regulators of key therapeutic proteins within this EV subtype.

Conclusion

This study underscores the critical role of proteomic alterations in AD and identifies a promising EV subpopulation, enriched with proteins targeting mitochondrial proteostasis, as a potential therapeutic strategy for AD.

Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis

Neurons dynamically regulate their proteome in response to sensory input, a key process underlying experience-dependent plasticity. We characterized the visual experience-dependent nascent proteome in mice within a brief, defined time window after stimulation using an optimized metabolic labeling approach. Visual experience induced cell-type-specific and age-dependent alterations in the nascent proteome, including proteostasis-related proteins. Emerin is the top activity-induced candidate plasticity protein. Activity-induced neuronal Emerin synthesis is rapid and transcription independent. Emerin broadly inhibits protein synthesis, decreasing translation regulators and synaptic proteins. Decreasing Emerin shifted the dendritic spine population from a predominantly mushroom morphology to filopodia and decreased network connectivity. Blocking visual experience-induced Emerin reduced visually evoked electrophysiological responses and impaired behaviorally assessed visual information processing. Our findings support a proteostatic model in which visual experience-induced Emerin provides a feedforward block on further protein synthesis, refining temporal control of activity-induced plasticity proteins and optimizing visual system function.

SFRP1 upregulation causes hippocampal synaptic dysfunction and memory impairment

Impaired neuronal and synaptic function are hallmarks of early Alzheimer's disease (AD), preceding other neuropathological traits and cognitive decline. We previously showed that SFRP1, a glial-derived protein elevated in AD brains from preclinical stages, contributes to disease progression, implicating glial factors in early pathogenesis. Here, we generate and analyze transgenic mice overexpressing astrocytic SFRP1. SFRP1 accumulation causes early dendritic and synaptic defects in adult mice, followed by impaired synaptic long-term potentiation and cognitive decline, evident only when the animals age, thereby mimicking AD's structural-functional temporal distinction. This phenotype correlates with proteomic changes, including increased structural synaptic proteins like neurexin, which localizes in close proximity with SFRP1 in cultured hippocampal neurons. We conclude that excessive SFRP1 hinders synaptic protein turnover, reducing synaptic plasticity-a mechanism that may underlie the synaptopathy observed in the brains of prodromal AD patients.

Cerebrospinal fluid proteomics identification of biomarkers for amyloid and tau PET stages

Accurate staging of Alzheimer's disease (AD) pathology is crucial for therapeutic trials and prognosis, but existing fluid biomarkers lack specificity, especially for assessing tau deposition severity, in amyloid-beta (Aβ)-positive patients. We analyze cerebrospinal fluid (CSF) samples from 136 participants in the Alzheimer's Disease Neuroimaging Initiative using more than 6,000 proteins. We apply machine learning to predict AD pathological stages defined by amyloid and tau positron emission tomography (PET). We identify two distinct protein panels: 16 proteins, including neurofilament heavy chain (NEFH) and SPARC-related modular calcium-binding protein 1 (SMOC1), that distinguished Aβ-negative/tau-negative (A-T-) from A+ individuals and nine proteins, such as HCLS1-associated protein X-1 (HAX1) and glucose-6-phosphate isomerase (GPI), that differentiated A+T+ from A+T- stages. These signatures outperform the established CSF biomarkers (area under the curve [AUC]: 0.92 versus 0.67-0.70) and accurately predicted disease progression over a decade. The findings are validated in both internal and external cohorts. These results underscore the potential of proteomic-based signatures to refine AD diagnostic criteria and improve patient stratification in clinical trials.

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 ).

Cerebrospinal fluid VGF is associated with the onset and progression of Alzheimer's disease

BackgroundIt remains unclear whether cerebrospinal fluid (CSF) VGF (non-acronymic) is associated with the onset and progression of Alzheimer's disease (AD).ObjectiveTo assess the levels of CSF VGF throughout the AD continuum, and its association with primary AD pathology, cognition, brain atrophy, and brain metabolism.MethodsWe studied a total of 526 individuals including 377 amyloid-positive individuals (76 preclinical AD, 200 prodromal AD, and 101 AD dementia) and 149 amyloid-negative cognitively normal individuals. VGF peptide in CSF was analyzed using mass spectrometry.ResultsWe observed decreased CSF VGF in preclinical, prodromal, and AD dementia individuals than amyloid-negative cognitively normal individuals. Reduced CSF VGF was associated with cognitive decline, hippocampal atrophy, ventricle enlargement, and glucose hypometabolism at baseline, and it predicted a more marked deterioration over time.ConclusionsOur findings support the important contributions of VGF to disease pathogenesis and progression in the early stages of AD. Exploring the biologics modulating VGF might be a promising approach for AD prevention and early treatment.

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.

Downregulation of Hmox1 and Rpgrip1l Expression Linked to Risk-Taking Behavior, Reduced Depressive Symptoms, and Diminished Novelty Socialization in SUMO1 Knockout Mice

SUMO1 is involved in the normal physiological functions of the nervous system and is also associated with the development of neurodegenerative diseases. Whereas, the effects and underling mechanisms of SUMO1 knockout (SUMO1- KO) on emotion- and cognition -related behaviors remain unexplored. We investigated changes in depression-like behaviors, social interaction, and cognition in SUMO1-KO mice compared to wild-type (WT) controls using the open-field test, tail suspension test, three-chamber test and novel object recognition test, respectively. To explore the underlying mechanisms of these behavioral differences, we performed Gene Ontology (GO) analysis of proteomics data and subsequently validated the findings through experimental verification. The results showed that SUMO1-KO mice exhibited increased risk-taking behavior, reduced depressive symptoms, and diminished novelty socialization compared to WT mice. Mass spectrometry-based proteomics analysis revealed 370 upregulated proteins and downregulated 84 proteins. GO annotation analysis identified significant enrichment of amino acid transmembrane transporter activities and ion channel. We further investigated two behavior-associated proteins, Hmox1 and Rpgrip1l, and validated their downregulated expression. We concluded that decreased expression of Hmox1 and Rpgrip1l associated with the risk-taking behavior, reduced depressive symptoms, and diminished novelty socialization observed in SUMO1-KO mice.

Heparin treatment is associated with a delayed diagnosis of Alzheimer's dementia in electronic health records from two large United States health systems

Recent studies suggest that heparan sulfate proteoglycans (HSPG) contribute to the predisposition to, protection from, and potential treatment and prevention of Alzheimer's disease (AD). Here, we used electronic health records (EHR) from two different health systems to examine whether heparin therapy was associated with a delayed diagnosis of AD dementia. Longitudinal EHR data from 15,183 patients from the Mount Sinai Health System (MSHS) and 6207 patients from Columbia University Medical Center (CUMC) were used in separate survival analyses to compare those who did or did not receive heparin therapy, had a least 5 years of observation, were at least 65 years old by their last visit, and had subsequent diagnostic code or drug treatment evidence of possible AD dementia. Analyses controlled for age, sex, comorbidities, follow-up duration and number of inpatient visits. Heparin therapy was associated with significant delays in age of clinical diagnosis of AD dementia, including +1.0 years in the MSMS cohort (P < 0.001) and +1.0 years in the CUMC cohort (P < 0.001). While additional studies are needed, this study supports the potential roles of heparin-like drugs and HSPGs in the protection from and prevention of AD dementia.

Cocaine perturbs neurodevelopment and increases neuroinflammation in a prenatal cerebral organoid model

Prenatal exposure to cocaine causes abnormalities in foetal brain development, which are linked to later development of anxiety, depression and cognitive dysfunction. Previous studies in rodent models have indicated that prenatal cocaine exposure affects proliferation, differentiation and connectivity of neural cell types. Here, using cerebral organoids derived from the human iPSC cell line HPSI1213i-babk_2, we investigated cocaine-induced changes of the gene expression regulatory landscape at an early developmental time point, leveraging recent advances in single cell RNA-seq and single cell ATAC-seq. iPSC-cerebral organoids replicated well-established cocaine responses observed in vivo and provided additional information about the cell-type specific regulation of gene expression following cocaine exposure. Cocaine altered gene expression patterns, in part through epigenetic landscape remodelling, and revealed disordered neural plasticity mechanisms in the cerebral organoids. Perturbed neurodevelopmental cellular signalling and an inflammatory-like activation of astrocyte populations were also evident following cocaine exposure. The combination of altered neuroplasticity, neurodevelopment and neuroinflammatory signalling suggests cocaine exposure can mediate substantial disruption of normal development and maturation of the brain. These findings offer new insights into the cellular mechanism underlying the adverse effects of cocaine exposure on neurodevelopment and point to the possible pathomechanisms of later neuropsychiatric disturbances.

Midkine Attenuates Aβ Fibril Assembly and Amyloid Plaque Formation

Proteomic profiling of Alzheimer's disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with Aβ since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates Aβ assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both Aβ40 and Aβ42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdk gene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and detergent-insoluble proteome in these mouse models indicates significant accumulation of Aβ and Aβ-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimer's disease.

Proteomic Subtyping of Alzheimer's Disease CSF links Blood-Brain Barrier Dysfunction to Reduced levels of Tau and Synaptic Biomarkers

Alzheimer's disease (AD) is characterized by significant clinical and molecular heterogeneity, influenced by genetic and demographic factors. Using an unbiased, network-driven approach, we analyzed the cerebrospinal fluid (CSF) proteome from 431 individuals (483 samples), including 111 African American participants, to identify core protein modules associated with AD, race, sex, and age. Our analysis revealed ten co-expression modules linked to distinct biological pathways and cell types, many of which correlated with established AD biomarkers such as β-amyloid, tau, and phosphorylated tau. To further resolve disease heterogeneity, we applied a proteomic subtyping approach, identifying six distinct CSF subtypes spanning the clinical and pathological spectrum. These subtypes were validated across independent cohorts, with many aligning with previously defined AD subtypes, including those linked to neuronal hyperplasticity, immune activation, and blood-brain barrier (BBB) integrity. Notably, the BBB subtype, enriched with African Americans and men, was characterized by low CSF tau, high CSF/serum albumin ratios, and reduced synaptic protein levels. This subtype also exhibited increased levels of proteolytic enzymes, including thrombin and matrix metalloproteases, that cleave tau. Plasma dilution into the neuronal hyperplastic AD subtype CSF led to reduced tau and synaptic protein module levels, indicating that plasma protease activity contributes to tau and synaptic protein depletion independent of underlying brain pathology. These findings highlight the impact of BBB integrity on CSF tau levels, particularly in men and African Americans, and underscore the need for diversity-informed AD biomarker strategies to improve diagnostics and therapeutic targeting across populations.

Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies

BACKGROUND

Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the mechanisms underlying the diversity of neuronal and glial tau pathology in different tauopathies are poorly understood. While there is a growing understanding of tauopathy-specific differences in tau isoforms and fibrillar structures, the specific composition of heterogenous tau lesions remains unknown. Here we study the protein composition of tau aggregates in four major tauopathies: Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP).

METHODS

We developed an approach for in situ proximity labeling and isolation of aggregate-associated proteins using glass slides with formalin-fixed paraffin-embedded (FFPE) human postmortem brain tissue, termed Probe-dependent Proximity Profiling (ProPPr). We used ProPPr for the analysis of proteomes associated with AT8-positive cellular lesions from frontal cortices. Isolated proximity proteomes were analyzed by data-independent acquisition mass spectrometry. Co-immunofluorescence staining and quantitative data analysis for selected proteins in human brain tissue was performed to further investigate associations with diverse tau pathologies.

RESULTS

Proteomics data analysis identified numerous common and tauopathy-specific proteins associated with phospho-tau aggregates. Extensive validations of candidates through quantitative immunofluorescence imaging of distinct aggregates across disease cases demonstrate successful implementation of ProPPr for unbiased discovery of aggregate-associated proteins in in human brain tissue. Our results reveal the association of retromer complex component vacuolar protein sorting-associated protein 35 (VPS35) and lysosome-associated membrane glycoprotein 2 (LAMP2) with specific types of phospho-tau lesions in tauopathies. Furthermore, we discovered a disease-specific association of certain proteins with distinct pathological lesions, including glycogen synthase kinase alpha (GSK3α), ferritin light chain (FTL), and the neuropeptide precursor VGF. Notably, the identification of FTL-positive microglia in CBD astrocytic plaques indicate their potential role in the pathogenesis of these lesions.

CONCLUSIONS

Our findings demonstrate the suitability of the ProPPr approach in FFPE brain tissue for unbiased discovery of local proteomes that provide valuable insights into the underlying proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes in a range of distinct tauopathies enhances our understanding of disease heterogeneity and mechanisms, informing strategies for the development of diagnostic biomarkers and targeted therapies.

Application of the Human Proteome in Disease, Diagnosis, and Translation into Precision Medicine: Current Status and Future Prospects

This review summarizes the existing studies of human proteomics technology in the medical field with a focus on the development mechanism of a disease and its potential in discovering biomarkers. Through a systematic review of the relevant literature, we found the significant advantages and application scenarios of proteomics technology in disease diagnosis, drug development, and personalized treatment. However, the review also identifies the challenges facing proteomics technologies, including sample preparation of low-abundance proteins, massive amounts of data analysis, and how research results can be better used in clinical practice. Finally, this work discusses future research directions, including the development of more effective proteomics technologies, strengthening the integration of multi-source omics technologies, and promoting the application of AI in the human proteome.

Superhydrophilic Nanostructured Microparticles for Enhanced Phosphoprotein Enrichment from Alzheimer's Disease Brain

Alzheimer's disease (AD) is an incurable neurodegenerative disorder and closely related to abnormal phosphoproteoforms. The analysis of low-abundance phosphoproteoforms relies heavily on the enrichment of phosphoproteins. However, existing phosphoprotein enrichment materials suffer from either low selectivity or low coverage due to the unavoidable unspecific adsorption of background proteins. Here, we propose a strategy of nanostructure-enabled superhydrophilic surfaces and synthesize Ti4+-functionalized superhydrophilic nanostructured microparticles (SNMs-Ti4+) via an emulsion interfacial polymerization process. In this process, hydrophilic and hydrophobic monomers assemble into a stable oil-in-water emulsion, producing microparticles with abundant hydrophilic phosphate nanoprotrusions on the surface. The microparticles are subsequently functionalized with Ti4+. SNMs-Ti4+ exhibit enormous nanoprotrusions and abundant Ti4+ modifications, which allow SNMs-Ti4+ to effectively adsorb the phosphoproteins and suppress the unspecific adsorption of background proteins. Using these SNMs-Ti4+, we identified 2256 phosphoproteins from HeLa cells, twice the number of those enriched with commercial kits. From AD mouse brains, 2603 phosphoproteins were successfully enriched, and 10 times of AD-related differentially regulated phosphoproteins were discovered than those without enrichment. These microparticles show great prospects for biomarker detection, disease diagnosis, and downstream biological process disclosure.

Insulin-Like Growth Factor Signaling in Alzheimer's Disease: Pathophysiology and Therapeutic Strategies

Alzheimer's disease (AD) is the leading cause of dementia among the elderly population, posing a significant public health challenge due to limited therapeutic options that merely delay cognitive decline. AD is associated with impaired energy metabolism and reduced neurotrophic signaling. The insulin-like growth factor (IGF) signaling pathway, crucial for central nervous system (CNS) development, metabolism, repair, cognition, and emotion regulation, includes IGF-1, IGF-2, IGF-1R, IGF-2R, insulin receptor (IR), and six insulin-like growth factor binding proteins (IGFBPs). Research has identified abnormalities in IGF signaling in individuals with AD and AD models. Dysregulated expression of IGFs, receptors, IGFBPs, and disruptions in downstream phosphoinositide 3-kinase-protein kinase B (PI3K/AKT) and mitogen-activated protein kinase (MAPK) pathways collectively increase AD susceptibility. Studies suggest modulating the IGF pathway may ameliorate AD pathology and cognitive decline. This review explores the CNS pathophysiology of IGF signaling in AD progression and assesses the potential of targeting the IGF system as a novel therapeutic strategy. Further research is essential to elucidate how aberrant IGF signaling contributes to AD development, understand underlying molecular mechanisms, and evaluate the safety and efficacy of IGF-based treatments.

Small Heat Shock Proteins: Protein Aggregation Amelioration and Neuro- and Age-Protective Roles

Protein misfolding, aggregation, and aberrant aggregate accumulation play a central role in neurodegenerative disease progression. The proteotoxic factors also govern the aging process to a large extent. Molecular chaperones modulate proteostasis and thereby impact aberrant-protein-induced proteotoxicity. These chaperones have a diverse functional spectrum, including nascent protein folding, misfolded protein sequestration, refolding, or degradation. Small heat shock proteins (sHsps) possess an ATP-independent chaperone-like activity that prevents protein aggregation by keeping target proteins in a folding-competent state to be refolded by ATP-dependent chaperones. Due to their near-universal upregulation and presence in sites of proteotoxic stress like diseased brains, sHsps were considered pathological. However, gene knockdown and overexpression studies have established their protective functions. This review provides an updated overview of the sHsp role in protein aggregation amelioration and highlights evidence for sHsp modulation of neurodegenerative disease-related protein aggregation and aging.

Human and mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome

Murine models of Alzheimer's disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. Here we present the comprehensive, age-dependent brain proteome and phosphoproteome across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata and prioritized components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Our analysis of the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including Aβ-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identifies potential targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

Cardiac Heterogeneity Prediction by Cardio-Neural Network Simulation

The bidirectional interactions between brain and heart through autonomic nervous system is the prime focus of neuro-cardiology community. The computer models designed to analyze brain and heart signals are either complex in terms of molecular and cellular interactions or not capable of representing the complex ion channel dynamics. Therefore, scientists are unable to extract the overall behavior of organs by electrical response of heterogeneous cells of brain and heart. In this study, a unified model of excitable cells is proposed that can be modulated by adrenergic features. By implementing the proposed model, a network of one thousand sparsely coupled cardio-neural network is simulated. The major findings of study include i. cardiac heterogeneity in electrical behavior of cardiac myocytes is the prime factor of heart rate variability ii. Brain-heart interplay through electrical pulses holds the necessary information of brain and heart signals that can be analyzed through spiking neural networks iii. Heart rate variability can be predicted and monitored by spiking neural networks from electrophysiological recordings of brain and heart iv. Heart rate variability related to tachycardia and bradycardia depends upon the polarization protocols of cardiac myocytes during plateau phase of action potential. This study provides the modeling and simulation phase of brain-heart interface to predict the morbidity at early stages. The recent advancements in nano-electronics will make is possible to develop brain-heart interface as nano-chip to deploy in subject to stimulate the brain-heart interplay through electrophysiological signals.

Plasma proteomic analysis of intermuscular fat links muscle integrity with processing speed in older adults

INTRODUCTION

More intermuscular fat (IMF) has been associated with lower cognitive performance and faster age-associated decline in cognitive function however, the mechanisms driving this relationship have not been fully elucidated. We utilized proteomic analyses to identify the molecular mediators of the association between IMF and cognition to gain further insight into the mechanisms underlying this association.

METHODS

In this cross-sectional study, the plasma proteomic profile of IMF was assessed in the Baltimore Longitudinal Study on Aging (BLSA; n=941, age=66.7±15.2) and validated in the Coronary Artery Risk Development in Young Adults Study (CARDIA; n=2451, age=50.2±3.6). The 7628 plasma proteins were assessed using an aptamer-based assay and tested for association with IMF from the thigh (BLSA) and abdomen (CARDIA). Processing speed assessed by Digit Symbol Substitution Test (DSST). Associations between the main exposures, outcome and mediators were evaluated using linear regression, and mediating effects were assessed by causal mediation analysis adjusting for age, sex, muscle area or muscle volume, self-reported race, and years of education.

RESULTS

Higher IMF was associated with lower DSST performance both in the BLSA and CARDIA studies. There were 722 plasma proteins associated with IMF in both the discovery and replication cohorts (FDR-adjusted p≤0.05). Of the 722 IMF-associated proteins, 26 (24 unique proteins) mediated the relationship between IMF and processing speed with mediation effects ranging from 2.8 to 20.9% (p≤0.05). Overrepresentation analysis of the IMF-associated proteins showed enrichment of proteins in synaptic function and organization, and growth factor binding (FDR-adjusted p≤0.05).

DISCUSSION

There is a robust proteomic signature explaining, at least in part, the link of IMF with DSST. This signature reflected neurological function and growth factor regulation, which are both implicated in lower processing speed. Reducing IMF through behavioral or pharmacological intervention may improve cognition through reduction in growth factor activity and improvements in synaptic activity.

In defence of ferroptosis

Rampant phospholipid peroxidation initiated by iron causes ferroptosis unless this is restrained by cellular defences. Ferroptosis is increasingly implicated in a host of diseases, and unlike other cell death programs the physiological initiation of ferroptosis is conceived to occur not by an endogenous executioner, but by the withdrawal of cellular guardians that otherwise constantly oppose ferroptosis induction. Here, we profile key ferroptotic defence strategies including iron regulation, phospholipid modulation and enzymes and metabolite systems: glutathione reductase (GR), Ferroptosis suppressor protein 1 (FSP1), NAD(P)H Quinone Dehydrogenase 1 (NQO1), Dihydrofolate reductase (DHFR), retinal reductases and retinal dehydrogenases (RDH) and thioredoxin reductases (TR). A common thread uniting all key enzymes and metabolites that combat lipid peroxidation during ferroptosis is a dependence on a key cellular reductant, nicotinamide adenine dinucleotide phosphate (NADPH). We will outline how cells control central carbon metabolism to produce NADPH and necessary precursors to defend against ferroptosis. Subsequently we will discuss evidence for ferroptosis and NADPH dysregulation in different disease contexts including glucose-6-phosphate dehydrogenase deficiency, cancer and neurodegeneration. Finally, we discuss several anti-ferroptosis therapeutic strategies spanning the use of radical trapping agents, iron modulation and glutathione dependent redox support and highlight the current landscape of clinical trials focusing on ferroptosis.

Preferential clustering of microglia and astrocytes around neuritic plaques during progression of Alzheimer's disease neuropathological changes

Neuroinflammation plays an important role in the pathological cascade of Alzheimer's disease (AD) along with aggregation of extracellular amyloid-β (Aβ) plaques and intracellular aggregates of tau protein. In animal models of amyloidosis, local immune activation is centered around Aβ plaques, which are usually of uniform morphology, dependent on the transgenic model used. In postmortem human brains a diversity of Aβ plaque morphologies is seen including diffuse plaques (non-neuritic plaques, non-NP), dense-core plaques, cotton-wool plaques, and NP. In a recent study, we demonstrated that during the progression of Alzheimer's disease neuropathologic changes (ADNC), a transformation of non-NP into NP occurs which is tightly linked to the emergence of cortical, but not hippocampal neurofibrillary tangle (NFT) pathology. This highlights the central role of NP in AD pathogenesis as well as brain region-specific differences in NP formation. In order to correlate the transformation of plaque types with local immune activation, we quantified the clustering and phenotype of microglia and accumulation of astrocytes around non-NP and NP during the progression of ADNC. We hypothesize that glial clustering occurs in response to formation of neuritic dystrophy around NP. First, we show that Iba1-positive microglia preferentially cluster around NP. Utilizing microglia phenotypic markers, we furthermore demonstrate that CD68-positive phagocytic microglia show a strong preference to cluster around NP in both the hippocampus and frontal cortex. A similar preferential clustering is observed for CD11c and ferritin-positive microglia in the frontal cortex, while this preference is less pronounced in the hippocampus, highlighting differences between hippocampal and cortical Aβ plaques. Glial fibrillary acidic protein-positive astrocytes showed a clear preference for clustering around NP in both the frontal cortex and hippocampus. These data support the notion that NP are intimately associated with the neuroimmune response in AD and underscore the importance of the interplay of protein deposits and the immune system in the pathophysiology of AD.

Wnt/β-catenin Signaling in Central Nervous System Regeneration

The Wnt/β-catenin signaling pathway plays a pivotal role in the development, maintenance, and repair of the central nervous system (CNS). This chapter explores the diverse functions of Wnt/β-catenin signaling, from its critical involvement in embryonic CNS development to its reparative and plasticity-inducing roles in response to CNS injury. We discuss how Wnt/β-catenin signaling influences various CNS cell types-astrocytes, microglia, neurons, and oligodendrocytes-each contributing to repair and plasticity after injury. The chapter also addresses the pathway's involvement in CNS disorders such as Alzheimer's and Parkinson's diseases, psychiatric disorders, and traumatic brain injury (TBI), highlighting potential Wnt-based therapeutic approaches. Lastly, zebrafish are presented as a promising model organism for studying CNS regeneration and neurodegenerative diseases, offering insights into future research and therapeutic development.

Fast Declining Prediction in Alzheimer's Disease from Early Clinical Assessment

INTRODUCTION

The heterogenicity in Alzheimer's Disease (AD) progression hinders individual prognosis. The present work is an observational 2-year longitudinal study in patients with mild cognitive impairment due to AD (n = 52, with positive CSF biomarkers). The aim of this study is to predict which patients are at risk of fast progression. For this, 3 neuropsychological tests based on different domains (clinical dementia, cognition, delayed memory) and the sum of them were used.

METHODS

The tests were performed at diagnosis time (T1) and two years after the diagnosis time (T2). Then, the corresponding progression models were developed using each individual test and their sum as a variable response.

RESULTS

As a result, the model based on cognition status to predict fast decline (differences in the Z score (T2-T1) <1.5 were considered fast declining) provided satisfactory performance (AUC 0.74, 83.3% of sensibility and 70.2% of specificity); the models based on clinical dementia and delayed memory to predict fast declining showed low AUC and sensitivity. Nevertheless, the model based on the sum of the 3 tests showed the highest AUC (0.79), low sensitivity (63.6%), and high specificity.

CONCLUSION

The developed progression models could provide useful information to clinicians and AD patients regarding their fast/normal decline in general or specific domains.

Defining conceptual artefacts to manage and design simplicities in complex adaptive systems

The concept of Simplexity has emerged several times in many discourses within different scientific domains: it somehow refers to the intertwined nature of Simplicity and Complexity. To the eye of the scientist beholder, any of these contributions renders different facets. None of those is negligible nor seems to be superior. Starting from this consideration, this paper uses a recent Design Science Research based method to develop a conceptual artefact allowing the entire realm of Complexity Sciences to unravel the Complexity of Simplexity. By moving through an in-depth systematic literature review, this research mined the nuances of Simplexity's meaning from several different research domains throughout seventy years, and then distilled those nuances. The resulting conceptual artefacts are possibly useful any time there is the need for dealing with Complexity - from the design of cyber-socio-technical systems to the analysis of protein networks - paving the way for a shared language for Psychologists, Neuro-linguists, Designers, Resilience Engineers, Biologists, and other Complexity Scientists.

Identifying Hub Genes and miRNAs Associated with Alzheimer's Disease: A Bioinformatics Pathway to Novel Therapeutic Strategies

Alzheimer's disease (AD) is a neurodegenerative disorder that mainly affects the elderly population. It is characterized by cognitive impairment and dementia due to abnormal levels of amyloid beta peptide (Aβ) and axonal Tau protein in the brain. However, the complex underlying mechanisms affecting this disease are not yet known, and there is a lack of standardized biomarkers and therapeutic targets. Therefore, in this study, by means of bioinformatics analysis, AD-affected brain tissue was analyzed using the GSE138260 dataset, identifying 612 differentially expressed genes (DEGs). Functional analysis revealed 388 upregulated DEGs associated with sensory perception and 224 downregulated DEGs linked to the regulation and modulation of synaptic processes. Protein-protein interaction network analysis identified 20 hub genes. Furthermore, miRNA target gene networks revealed 1767 miRNAs linked to hub genes, among which hsa-mir-106a-5p, hsa-mir-17-5p, hsa-mir-26a-5p, hsa-mir-27a-3p and hsa-mir-34a-5p were the most relevant. This study presents novel biomarkers and therapeutic targets for AD by analyzing the information obtained with a comprehensive literature review, providing new potential targets to study their role in AD.

Saliva Proteome, Metabolome and Microbiome Signatures for Detection of Alzheimer's Disease

Background: As the burden of Alzheimer's disease (AD) escalates with an ageing population, the demand for early and accessible diagnostic methods becomes increasingly urgent. Saliva, with its non-invasive and cost-effective nature, presents a promising alternative to cerebrospinal fluid and plasma for biomarker discovery. Methods: In this study, we conducted a comprehensive multi-omics analysis of saliva samples (n = 20 mild cognitive impairment (MCI), n = 20 Alzheimer's disease and age- and n = 40 gender-matched cognitively normal individuals), from the South Australian Neurodegenerative Disease (SAND) cohort, integrating proteomics, metabolomics, and microbiome data with plasma measurements, including pTau181. Results: Among the most promising findings, the protein Stratifin emerged as a top candidate, showing a strong negative correlation with plasma pTau181 (r = -0.49, p < 0.001) and achieving an AUC of 0.95 in distinguishing AD and MCI combined from controls. In the metabolomics analysis, 3-chlorotyrosine and L-tyrosine exhibited high correlations with disease severity progression, with AUCs of 0.93 and 0.96, respectively. Pathway analysis revealed significant alterations in vitamin B12 metabolism, with Transcobalamin-1 levels decreasing in saliva as AD progressed despite an increase in serum vitamin B12 levels (p = 0.008). Microbiome analysis identified shifts in bacterial composition, with a microbiome cluster containing species such as Lautropia mirabilis showing a significant decrease in abundance in MCI and AD samples. The overall findings were reinforced by weighted correlation network analysis, which identified key hubs and enriched pathways associated with AD. Conclusions: Collectively, these data highlight the potential of saliva as a powerful medium for early AD diagnosis, offering a practical solution for large-scale screening and monitoring.

The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

The Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform of every protein-coding gene and (2) to make proteomics an integral part of multiomics studies of human health and disease. The past year has seen major transitions for the HPP. neXtProt was retired as the official HPP knowledge base, UniProtKB became the reference proteome knowledge base, and Ensembl-GENCODE provides the reference protein target list. A function evidence FE1-5 scoring system has been developed for functional annotation of proteins, parallel to the PE1-5 UniProtKB/neXtProt scheme for evidence of protein expression. This report includes updates from neXtProt (version 2023-09) and UniProtKB release 2024_04, with protein expression detected (PE1) for 18138 of the 19411 GENCODE protein-coding genes (93%). The number of non-PE1 proteins ("missing proteins") is now 1273. The transition to GENCODE is a net reduction of 367 proteins (19,411 PE1-5 instead of 19,778 PE1-4 last year in neXtProt). We include reports from the Biology and Disease-driven HPP, the Human Protein Atlas, and the HPP Grand Challenge Project. We expect the new Functional Evidence FE1-5 scheme to energize the Grand Challenge Project for functional annotation of human proteins throughout the global proteomics community, including π-HuB in China.

Berberine modulates microglial polarization by activating TYROBP in Alzheimer's disease

BACKGROUND

Characterized by β-amyloid (Aβ) plaques, neurofibrillary tangles, and aberrant neuroinflammation in the brain, Alzheimer's disease (AD) is the most common neurodegenerative disease. Microglial polarization is a subtle mechanism which maintains immunological homeostasis and has emerged as a putative therapeutic to combat AD. Berberine (BBR) is a natural alkaloid compound with multiple pharmacological effects, and has shown considerable therapeutic potential against inflammatory disorders. However, BBR functions and underlying mechanisms in neuroinflammation remain unclear.

PURPOSE

To examine BBR pharmacological effects and mechanisms in neuroinflammation with a view to treating AD.

METHODS

BBR effects on cognitive performance in 5 × FAD mice were assessed using open field, Y-maze, and Morris Water Maze (MWM) tests. Neuroinflammation-related markers and Aβ pathology were examined in brain sections from mice. Transcriptomic analyses of hippocampus tissues were also conducted. Microglial BV2 cells were also used to verify potential BBR mechanisms in neuroinflammation and microglial polarization.

RESULTS

BBR improved cognitive performance, reduced amyloid pathology, and alleviated aberrant neuroinflammation in an AD mouse model. BBR induced microglial polarization to an M2-like phenotype, which was manifested by lowered and elevated proinflammatory and anti-inflammatory cytokine production, respectively, improved microglial uptake and Aβ clearance. Mechanistically, BBR directly interacted with TYROBP and promoted its activation by stabilizing TYROBP oligomerization. TYROBP knockdown aggravated M1-like polarization and pro-inflammatory gene expression in microglial cells in the presence of lipopolysaccharide (LPS)+Aβ, while blocked microglial M2-like polarization benefited from BBR administration.

CONCLUSIONS

BBR modulated neuroinflammation by regulating microglial polarization via TYROBP activation. Our study provided new insight into BBR pharmacological actions in regulating microglial homeostasis and combating AD.

Associations of plasma SMOC1 and soluble IL6RA levels with the progression from mild cognitive impairment to dementia

Despite the central role attributed to neuroinflammation in the etiology and pathobiology of Alzheimer's disease (AD), the direct link between levels of inflammatory mediators in blood and cerebrospinal fluid (CSF) compartments, as well as their potential implications for AD diagnosis and progression, remains inconclusive. Moreover, there is debate on whether inflammation has a protective or detrimental effect on disease onset and progression. Indeed, distinct immunological mechanisms may govern protective and damaging effects at early and late stages, respectively. This study aims to (i) identify inflammatory mediators demonstrating robust correlations between peripheral and central nervous system (CNS) compartments by means of plasma and CSF analysis, respectively, and (ii) assess their potential significance in the context of AD and disease progression from mild cognitive impairment (MCI) to dementia. To achieve this, we have examined the inflammatory profile of a well-defined subcohort comprising 485 individuals from the Ace Alzheimer Center Barcelona (ACE). Employing a hierarchical clustering approach, we thoroughly evaluated the intercompartmental correlations of 63 distinct inflammation mediators, quantified in paired CSF and plasma samples, using advanced SOMAscan technology. Of the array of mediators investigated, only six mediators (CRP, IL1RAP, ILRL1, IL6RA, PDGFRB, and YKL-40) exhibited robust correlations between the central and peripheral compartments (proximity scores <400). To strengthen the validity of our findings, these identified mediators were subsequently validated in a second subcohort of individuals from ACE (n = 873). The observed plasma correlations across the entire cohort consistently have a Spearman rho value above 0.51 (n = 1,360, p < 1.77E-93). Of the high CSF-plasma correlated proteins, only soluble IL6RA (sIL6RA) displayed a statistically significant association with the conversion from MCI to dementia. This association remained robust even after applying a stringent Bonferroni correction (Cox proportional hazard ratio [HR] = 1.936 per standard deviation; p = 0.0018). This association retained its significance when accounting for various factors, including CSF amyloid (Aβ42) and Thr181-phosphorylated tau (p-tau) levels, age, sex, baseline Mini-Mental State Examination (MMSE) score, and potential sampling biases identified through principal component analysis (PCA) modeling. Furthermore, our study confirmed the association of both plasma and CSF levels of SPARC-related modular calcium-binding protein 1 (SMOC1) with amyloid and tau accumulation, indicating their role as early surrogate biomarkers for AD pathology. Despite the lack of a statistically significant correlation between SMOC1 levels in CSF and plasma, both acted as independent biomarkers of disease progression (HR > 1.3, p < 0.002). In conclusion, our study unveils that sIL6RA and SMOC1 are associated with MCI progression. The absence of correlations among inflammatory mediators between the central and peripheral compartments appears to be a common pattern, with only a few intriguing exceptions.

Oligodendrocytes, the Forgotten Target of Gene Therapy

If the billions of oligodendrocytes (OLs) populating the central nervous system (CNS) of patients could express their feelings, they would undoubtedly tell gene therapists about their frustration with the other neural cell populations, neurons, microglia, or astrocytes, which have been the favorite targets of gene transfer experiments. This review questions why OLs have been left out of most gene therapy attempts. The first explanation is that the pathogenic role of OLs is still discussed in most CNS diseases. Another reason is that the so-called ubiquitous CAG, CBA, CBh, or CMV promoters-widely used in gene therapy studies-are unable or poorly able to activate the transcription of episomal transgene copies brought by adeno-associated virus (AAV) vectors in OLs. Accordingly, transgene expression in OLs has either not been found or not been evaluated in most gene therapy studies in rodents or non-human primates. The aims of the current review are to give OLs their rightful place among the neural cells that future gene therapy could target and to encourage researchers to test the effect of OL transduction in various CNS diseases.

SMOC1 colocalizes with Alzheimer's disease neuropathology and delays Aβ aggregation

SMOC1 has emerged as one of the most significant and consistent new biomarkers of early Alzheimer's disease (AD). Recent studies show that SMOC1 is one of the earliest changing proteins in AD, with levels in the cerebrospinal fluid increasing many years before symptom onset. Despite this clear association with disease, little is known about the role of SMOC1 in AD or its function in the brain. Therefore, the aim of this study was to examine the distribution of SMOC1 in human AD brain tissue and to determine if SMOC1 influenced amyloid beta (Aβ) aggregation. The distribution of SMOC1 in human brain tissue was assessed in 3 brain regions (temporal cortex, hippocampus, and frontal cortex) using immunohistochemistry in a cohort of 73 cases encompassing advanced AD, mild cognitive impairment (MCI), preclinical AD, and cognitively normal controls. The Aβ- and phosphorylated tau-interaction with SMOC1 was assessed in control, MCI, and advanced AD human brain tissue using co-immunoprecipitation, and the influence of SMOC1 on Aβ aggregation kinetics was assessed using Thioflavin-T assays and electron microscopy. SMOC1 strongly colocalized with a subpopulation of amyloid plaques in AD (43.8 ± 2.4%), MCI (32.8 ± 5.4%), and preclinical AD (28.3 ± 6.4%). SMOC1 levels in the brain strongly correlated with plaque load, irrespective of disease stage. SMOC1 also colocalized with a subpopulation of phosphorylated tau aggregates in AD (9.6 ± 2.6%). Co-immunoprecipitation studies showed that SMOC1 strongly interacted with Aβ in human MCI and AD brain tissue and with phosphorylated tau in human AD brain tissue. Thioflavin-T aggregation assays showed that SMOC1 significantly delayed Aβ aggregation in a dose-dependent manner, and electron microscopy confirmed that the Aβ fibrils generated in the presence of SMOC1 had an altered morphology. Overall, our results emphasize the importance of SMOC1 in the onset and progression of AD and suggest that SMOC1 may influence pathology development in AD.

Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA

Alternative polyadenylation (APA) is an important driver of transcriptome diversity that generates messenger RNA isoforms with distinct 3' ends. The rapid development of single-cell and spatial transcriptomic technologies opened up new opportunities for exploring APA data to discover hidden cell subpopulations invisible in conventional gene expression analysis. However, conventional gene-level analysis tools are not fully applicable to APA data, and commonly used unsupervised dimensionality reduction methods often disregard experimentally derived annotations such as cell type identities. Here, we proposed a supervised analytical framework termed spvAPA, specifically used for APA analysis from both single-cell and spatial transcriptomics data. First, an iterative imputation method based on weighted nearest neighbor was designed to recover missing APA signatures, by integrating both gene expression and APA modalities. Second, a supervised feature selection method based on sparse partial least squares discriminant analysis was devised to identify APA features distinguishing cell types or spatial morphologies. Additionally, spvAPA improves the visualization of high-dimensional data for discovering novel cell subtypes, which considers APA features and dual modalities of gene expression and APA. Evaluations across nine single-cell and spatial transcriptomics datasets demonstrate the effectiveness and applicability of spvAPA. spvAPA is available at https://github.com/BMILAB/spvAPA.

An early, novel arginine methylation of KCa3.1 attenuates subsequent T cell exhaustion

T cell receptor (TCR) engagement initiates the activation process, and this signaling event is regulated in multifaceted ways. Nutrient availability in the immediate niche is one such mode of regulation 1-3 . Here, we investigated how the availability of an essential amino acid methionine (Met) and TCR signaling might interplay in the earliest events of T cell activation to affect subsequent T cell fate and function. We found that limiting Met during only the initial 30 minutes of CD8 + T cell activation increased Ca 2+ influx, Ca 2+ -mediated NFAT1 ( Nfatc2 ) activation, NFAT1 promoter occupancy, and T cell exhaustion. We identified changes in the protein arginine methylome during the initial 30 min of TCR engagement and discovered a novel arginine methylation of a Ca 2+ -activated potassium transporter, KCa3.1, which regulates Ca 2+ -mediated NFAT1 signaling to ensure optimal activation. Ablation of arginine methylation in KCa3.1 led to increased NFAT1 activation, rendering T cells dysfunctional in murine tumour and infection models. Furthermore, acute Met supplementation at early stages reduced nuclear NFAT1 in tumour-infiltrating T cells and augmented their anti-tumour activity. Our findings identify a metabolic event occurring early after T cell activation that influences the subsequent fate of the cell.

CRISPR screens unveil nutrient-dependent lysosomal and mitochondrial nodes impacting intestinal tissue-resident memory CD8+ T cell formation

Nutrient availability and organelle biology direct tissue homeostasis and cell fate, but how these processes orchestrate tissue immunity remains poorly defined. Here, using in vivo CRISPR-Cas9 screens, we uncovered organelle signaling and metabolic processes shaping CD8+ tissue-resident memory T (TRM) cell development. TRM cells depended on mitochondrial translation and respiration. Conversely, three nutrient-dependent lysosomal signaling nodes-Flcn, Ragulator, and Rag GTPases-inhibited intestinal TRM cell formation. Depleting these molecules or amino acids activated the transcription factor Tfeb, thereby linking nutrient stress to TRM programming. Further, Flcn deficiency promoted protective TRM cell responses in the small intestine. Mechanistically, the Flcn-Tfeb axis restrained retinoic acid-induced CCR9 expression for migration and transforming growth factor β (TGF-β)-mediated programming for lineage differentiation. Genetic interaction screening revealed that the mitochondrial protein Mrpl52 enabled early TRM cell formation, while Acss1 controlled TRM cell development under Flcn deficiency-associated lysosomal dysregulation. Thus, the interplay between nutrients, organelle signaling, and metabolic adaptation dictates tissue immunity.

Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers

BACKGROUND

Mass spectrometry (MS)-based cerebrospinal fluid (CSF) proteomics is an important method for discovering biomarkers of neurodegenerative diseases. CSF serves as a reservoir for interstitial fluid (ISF), and extensive communication between the two fluid compartments helps to remove waste products from the brain.

NEW METHOD

We performed proteomic analyses of both CSF and ISF fluid compartments using intracerebral microdialysis to validate and detect novel biomarkers of Alzheimer's disease (AD) in APPtg and C57Bl/6J control mice.

RESULTS

We identified up to 625 proteins in ISF and 4483 proteins in CSF samples. By comparing the biofluid profiles of APPtg and C57Bl/6J mice, we detected 37 and 108 significantly up- and downregulated candidates, respectively. In ISF, 7 highly regulated proteins, such as Gfap, Aldh1l1, Gstm1, and Txn, have already been implicated in AD progression, whereas in CSF, 9 out of 14 highly regulated proteins, such as Apba2, Syt12, Pgs1 and Vsnl1, have also been validated to be involved in AD pathogenesis. In addition, we also detected new interesting regulated proteins related to the control of synapses and neurotransmission (Kcna2, Cacng3, and Clcn6) whose roles as AD biomarkers should be further investigated.

COMPARISON WITH EXISTING METHODS

This newly established combined protocol provides better insight into the mutual communication between ISF and CSF as an analysis of tissue or CSF compartments alone.

CONCLUSIONS

The use of multiple fluid compartments, ISF and CSF, for the detection of their biological communication enables better detection of new promising AD biomarkers.

Associations between the multitrajectory neuroplasticity of neuronavigated rTMS-mediated angular gyrus networks and brain gene expression in AD spectrum patients with sleep disorders

INTRODUCTION

The multifactorial influence of repetitive transcranial magnetic stimulation (rTMS) on neuroplasticity in neural networks is associated with improvements in cognitive dysfunction and sleep disorders. The mechanisms of rTMS and the transcriptional-neuronal correlation in Alzheimer's disease (AD) patients with sleep disorders have not been fully elucidated.

METHODS

Forty-six elderly participants with cognitive impairment (23 patients with low sleep quality and 23 patients with high sleep quality) underwent 4-week periods of neuronavigated rTMS of the angular gyrus and neuroimaging tests, and gene expression data for six post mortem brains were collected from another database. Transcription-neuroimaging association analysis was used to evaluate the effects on cognitive dysfunction and the underlying biological mechanisms involved.

RESULTS

Distinct variable neuroplasticity in the anterior and posterior angular gyrus networks was detected in the low sleep quality group. These interactions were associated with multiple gene pathways, and the comprehensive effects were associated with improvements in episodic memory.

DISCUSSION

Multitrajectory neuroplasticity is associated with complex biological mechanisms in AD-spectrum patients with sleep disorders.

HIGHLIGHTS

This was the first transcription-neuroimaging study to demonstrate that multitrajectory neuroplasticity in neural circuits was induced via neuronavigated rTMS, which was associated with complex gene expression in AD-spectrum patients with sleep disorders. The interactions between sleep quality and neuronavigated rTMS were coupled with multiple gene pathways and improvements in episodic memory. The present strategy for integrating neuroimaging, rTMS intervention, and genetic data provide a new approach to comprehending the biological mechanisms involved in AD.

Genetic regulation of human brain proteome reveals proteins implicated in psychiatric disorders

Psychiatric disorders are highly heritable yet polygenic, potentially involving hundreds of risk genes. Genome-wide association studies have identified hundreds of genomic susceptibility loci with susceptibility to psychiatric disorders; however, the contribution of these loci to the underlying psychopathology and etiology remains elusive. Here we generated deep human brain proteomics data by quantifying 11,608 proteins across 268 subjects using 11-plex tandem mass tag coupled with two-dimensional liquid chromatography-tandem mass spectrometry. Our analysis revealed 788 cis-acting protein quantitative trait loci associated with the expression of 883 proteins at a genome-wide false discovery rate <5%. In contrast to expression at the transcript level and complex diseases that are found to be mainly influenced by noncoding variants, we found protein expression level tends to be regulated by non-synonymous variants. We also provided evidence of 76 shared regulatory signals between gene expression and protein abundance. Mediation analysis revealed that for most (88%) of the colocalized genes, the expression levels of their corresponding proteins are regulated by cis-pQTLs via gene transcription. Using summary data-based Mendelian randomization analysis, we identified 4 proteins and 19 genes that are causally associated with schizophrenia. We further integrated multiple omics data with network analysis to prioritize candidate genes for schizophrenia risk loci. Collectively, our findings underscore the potential of proteome-wide linkage analysis in gaining mechanistic insights into the pathogenesis of psychiatric disorders.

Pressure Cycling Technology Combined With MicroLC-SWATH Mass Spectrometry for the Analysis of Sex-Related Differences Between Male and Female Cerebella: A Promising Approach to Investigating Proteomics Differences in Psychiatric and Neurodegenerative Diseases

PURPOSE

Pressure cycling technology (PCT) coupled with data-independent sequential window acquisition of all theoretical mass spectra (SWATH-MS) can be a powerful tool for identifying and quantifying biomarkers (e.g., proteins) in complex biological samples. Mouse models are frequently used in brain studies, including those focusing on different neurodevelopmental and psychiatric disorders. More and more pieces of evidence have suggested that sex-related differences in the brain impact the rates, clinical manifestations, and therapy outcomes of these disorders. However, sex-based differences in the proteomic profiles of mouse cerebella have not been widely investigated.

EXPERIMENTAL DESIGN

In this pilot study, we evaluate the applicability of coupling PCT sample preparation with microLC-SWATH-MS analysis to map and identify differences in the proteomes of two female and two male mice cerebellum samples.

RESULTS

We identified and quantified 174 proteins in mice cerebella. A comparison of the proteomic profiles revealed that the levels of 11 proteins in the female and male mice cerebella varied significantly.

CONCLUSIONS AND CLINICAL RELEVANCE

Although this study utilizes a small sample, our results indicate that the studied male and female mice cerebella possessed differing proteome compositions, mainly with respect to energy metabolism processes.

Age- and Sex-Associated Wnt Signaling Dysregulation is Exacerbated from the Early Stages of Neuropathology in an Alzheimer's Disease Model

Emerging studies suggest that Wnt signaling is dysregulated in the brains of AD patients, suggesting that this pathway may also contribute to disease progression. However, it remains to be determined whether alterations in the Wnt pathway are the cause or consequence of this disease and which elements of Wnt signaling mainly contribute to the appearance of AD histopathological markers early in disease compared to what occurs during normal aging. The present study aimed to describe the status of several canonical Wnt pathway components and the expression of the AD marker p-tau in the hippocampi of female and male 3xTg-AD mice during disease progression compared to those during normal aging. We analyzed the levels of the canonical Wnt components Wnt7a, Dkk-1, LRP6 and GSK3β as well as the levels of p-tau and BDNF at 3, 6, 9-12 and 18 months of age. We found a gradual increase in Dkk-1 levels during aging prior to Wnt7a and LRP5/6 depletion, which was strongly exacerbated in 3xTg-AD mice even at young ages and correlated with GSK3β activation and p-tau-S202/Thr205 expression. Dkk-1 upregulation, as well as the level of p-tau, was significantly greater in females than in males. Our results suggest that Dkk-1 upregulation is involved in the expression of several features of AD at early stages, which supports the possibility of positively modulating the canonical Wnt pathway as a therapeutic tool to delay this disease at early stages.

SMOC1 colocalizes with Alzheimer's disease neuropathology and delays Aβ aggregation

SMOC1 has emerged as one of the most significant and consistent new biomarkers of early Alzheimer's disease (AD). Recent studies show that SMOC1 is one of the earliest changing proteins in AD, with levels in the cerebrospinal fluid increasing many years before symptom onset. Despite this clear association with disease, little is known about the role of SMOC1 in AD or its function in the brain. Therefore, the aim of this study was to examine the distribution of SMOC1 in human AD brain tissue and to determine if SMOC1 influenced amyloid beta (Aβ) aggregation. The distribution of SMOC1 in human brain tissue was assessed in 3 brain regions (temporal cortex, hippocampus, frontal cortex) using immunohistochemistry in a cohort of 73 cases encompassing advanced AD, mild cognitive impairment (MCI), preclinical AD and cognitively normal controls. The Aβ- and phosphorylated tau-interaction with SMOC1 was assessed in control, MCI and advanced AD human brain tissue using co-immunoprecipitation, and the influence of SMOC1 on Aβ aggregation kinetics was assessed using Thioflavin T assays and electron microscopy. SMOC1 strongly colocalized with a subpopulation of amyloid plaques in AD (43.8±2.4%), MCI (32.8±5.4%) and preclinical AD (28.3±6.4%). SMOC1 levels in the brain strongly correlated with plaque load, irrespective of disease stage. SMOC1 also colocalized with a subpopulation of phosphorylated tau aggregates in AD (9.6±2.6%). Co-immunoprecipitation studies showed that SMOC1 strongly interacted with Aβ in human MCI and AD brain tissue and with phosphorylated tau in human AD brain tissue. Thioflavin T aggregation assays showed that SMOC1 significantly delayed Aβ aggregation in a dose-dependent manner, and electron microscopy confirmed that the Aβ fibrils generated in the presence of SMOC1 had an altered morphology. Overall, our results emphasize the importance of SMOC1 in the onset and progression of AD and suggest that SMOC1 may influence pathology development in AD.