Integrated proteomics reveals brain-based cerebrospinal fluid biomarkers in asymptomatic and symptomatic Alzheimer's disease

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.

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.

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.

Protein co-aggregates of dense core amyloid plaques and CSF differ in rapidly progressive Alzheimer's disease and slower sporadic Alzheimer's disease

BACKGROUND

The rapidly progressive phenotype of Alzheimer's disease (rpAD) remains a rare and less-studied entity. Therefore, the replication of key results from the rpAD brain and cerebrospinal fluid (CSF) is lacking.

METHODS

A label-free quantitative LC-MS/MS analysis of proteins co-aggregating with core-amyloid β plaques in fresh frozen tissue (FFT) from medial temporal regions of rpAD ( n = 8 ) neuropathologically characterized at the National Prion Disease Pathology Surveillance Center (NPDPSC), compared with microdissected amyloid plaques from formalin-fixed, paraffin-embedded (FFPE) tissue blocks from patients with rpAD ( n = 22 ) previously published from the NPDPSC cohort, was performed. Matched rpAD CSF from the FFT cases were compared to a previously published proteomic evaluation of CSF in the AD subtype with rapid progression.

RESULTS

A total of 1841 proteins were characterized in the FFT study, of which 463 were consistently identified in every rpAD patient analyzed. One thousand two hundred eighty-three proteins were shared between the FFT and the prior FFPE study. FFT offered a more comprehensive proteomic profile than the prior FFPE study and prominently included the immune system pathways. Thirty-five proteins were shared in the FFT brain tissue, matched CSF from the same subjects, in which biological processes related to immune response were again notable. These results were validated against prior published proteomic CSF AD data with a faster rate of progression to identify the top 5 potential protein biomarkers of rapid progression in AD CSF.

CONCLUSIONS

These results support a distinct immune-related proteomic profile in both the brain and the CSF that can be explored as potential biomarkers in the future for the clinical diagnosis of rpAD.

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.

Network analysis of the cerebrospinal fluid proteome reveals shared and unique differences between sporadic and familial forms of amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic Lateral Sclerosis (ALS), a neurodegenerative disease involving loss of motor neurons, typically results in death within 3-5 years of disease onset. Although roughly 10% of cases can be linked to a specific inherited mutation (e.g., C9orf72 hexanucleotide repeat expansion or SOD1 mutation), the cause(s) of most cases are unknown. Consequently, there is a critical need for biomarkers that reflect disease onset and progression across ALS subgroups.

METHODS

We employed tandem mass tag mass spectrometry (TMT-MS) based proteomics on cerebrospinal fluid (CSF) to identify and quantify 2105 proteins from sporadic, C9orf72, and SOD1 ALS patients, asymptomatic C9orf72 expansion carriers, and controls (N = 101). To verify trends in our Emory University cohort we used data-independent acquisition (DIA-MS) on an expanded, four center cohort. This expanded cohort of 259 individuals included 50 sporadic ALS (sALS), 43 C9orf72 ALS, 22 SOD1 ALS, 72 asymptomatic gene carriers (59 C9orf72 and 13 SOD1) and 72 age-matched controls. We identified 2330 proteins and used differential protein abundance and network analyses to determine how protein profiles vary across disease subtypes in ALS CSF.

RESULTS

Differential abundance and co-expression network analysis identified proteomic differences between ALS and control, as well as differentially abundant proteins between sporadic, C9orf72 and SOD1 ALS. A panel of proteins differentiated forms of ALS that are indistinguishable in a clinical setting. An additional panel differentiated asymptomatic from symptomatic C9orf72 and SOD1 mutation carriers, marking a pre-symptomatic proteomic signature of genetic forms of ALS. Leveraging this large, multicenter cohort, we validated our ALS CSF network and identified ALS-specific proteins and network modules.

CONCLUSIONS

This study represents a comprehensive analysis of the CSF proteome across sporadic and genetic causes of ALS that resolves differences among these ALS subgroups and also identifies proteins that distinguish symptomatic from asymptomatic gene carriers. These new data point to varying pathogenic pathways that result in an otherwise clinically indistinguishable disease.

Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures across the Alzheimer disease continuum

Changes in β-amyloid (Aβ) and hyperphosphorylated tau (T) in brain and cerebrospinal fluid (CSF) precede Alzheimer's disease (AD) symptoms, making the CSF proteome a potential avenue to understand disease pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 analytes (2,029 unique proteins) dysregulated in AD. Of these, 865 (43%) were previously reported, and 1,164 (57%) are novel. The identified proteins cluster in four different pseudo-trajectories groups spanning the AD continuum and were enriched in pathways including neuronal death, apoptosis, and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfunction (mid stages), brain plasticity and longevity (mid stages), and microglia-neuron crosstalk (late stages). Using machine learning, we created and validated highly accurate and replicable (area under the curve [AUC] > 0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD.

Cerebrospinal fluid proteome profiling across the Alzheimer's disease continuum: a step towards solving the equation for 'X'

BACKGROUND

While the temporal profile of amyloid (Aβ) and tau cerebrospinal fluid (CSF) biomarkers along the Alzheimer's disease (AD) continuum is well-studied, chronological changes of CSF proteins reflecting other disease-relevant processes, denoted 'X' in the ATX(N) framework, remain poorly understood.

METHODS

Using an untargeted mass spectrometric approach termed tandem mass tag (TMT), we quantified over 1500 CSF proteins across the AD continuum in three independent cohorts, finely staged by Aβ/tau positron emission tomography (PET), fluid biomarkers, or brain biopsy. Weighted protein co-expression network analysis identified clusters of proteins robustly correlating in all three cohorts which sequentially changed with AD progression. Obtained protein clusters were correlated with fluid biomarker measurements (phosphorylated tau (p-tau) species including p-tau181, p-tau217, and p-tau205, as well as Aβ), Aβ/tau PET imaging, and clinical parameters to discern disease-relevant clusters which were modelled across the AD continuum.

RESULTS

Neurodegeneration-related proteins (e.g., 14-3-3 proteins, PPIA), derived from different brain cell types, strongly correlated with fluid as well as imaging biomarkers and increased early in the AD continuum. Among them, the proteins SMOC1 and CNN3 were highly associated with Aβ pathology, while the 14-3-3 proteins YWHAZ and YWHAE as well as PPIA demonstrated a strong association with both Aβ and tau pathology as indexed by PET. Endo-lysosomal proteins (e.g., HEXB, TPP1, SIAE) increased early in abundance alongside neurodegeneration-related proteins, and were followed by increases in metabolic proteins such as ALDOA, MDH1, and GOT1 at the mild cognitive impairment (MCI) stage. Finally, later AD stages were characterized by decreases in synaptic/membrane proteins (e.g., NPTX2).

CONCLUSIONS

Our study identified proxies of Aβ and tau pathology, indexed by PET, (SMOC1, YWHAE, CNN3) and highlighted the dynamic fluctuations of the CSF proteome over the disease course, identifying candidate biomarkers for disease staging beyond Aβ and tau.

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.

Proteomic profiling in cerebrospinal fluid reveal biomarkers for shunt outcome in idiopathic normal-pressure hydrocephalus

BACKGROUND

The pathophysiology of idiopathic normal pressure hydrocephalus (iNPH) remains unclear, and the treatment strategy remains suboptimal. This study aims to identify biomarkers for shunt prognosis by cerebrospinal fluid (CSF) proteomic profiling.

METHODS

CSF samples collected from 37 iNPH patients from the discovery cohort and 12 iNPH patients from an independent validation cohort (71.9 ± 6.1 years (mean ± SD)), and 16 age-balanced controls (69.9 ± 7.6 years (mean ± SD)) were collected from September 2020 to December 2023. 53 CSF samples were analyzed using a mass spectrometry-based proteomic workflow. Clinical evaluations were performed on all iNPH patients, and 44 patients underwent ventriculoperitoneal shunting. Postoperative CSF were also collected from 10 iNPH patients who underwent shunting surgery. Bioinformatics, machine learning, and enzyme-linked immunosorbent assay (ELISA) were performed to identify CSF proteome changes related to pathophysiology in iNPH, and screen for biomarkers associated with shunt response.

RESULTS

39 and 285 proteins significantly increased and decreased in iNPH CSF compared to the control group. Gene ontology analysis revealed that the noticeably increased proteins were mainly associated with myeloid leukocyte migration and extracellular matrix organization, and significantly decreased proteins were primarily associated with axon development and synapse organization. Machine learning identified 6 candidate biomarkers that potentially predicted the response to shunt surgery. Among these, QPCT levels were found to be elevated in non-responders, while RBP4 levels were decreased, and both of these changes were validated through ELISA.

CONCLUSIONS

Our findings provide support for the hypothesis that the pathophysiology of iNPH is characterized by a state of neuroinflammation, extracellular matrix remodeling, and neurodegeneration, and CSF shunting can reverse such pathological state. Machine learning using preoperative proteomic profiles satisfactorily predicted the clinical outcome of the shunt procedure in iNPH. Future research targeting specific proteins in iNPH may be warranted to better comprehend the disease mechanism and design patient-tailored treatments.

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.

CLU alleviates Alzheimer's disease-relevant processes by modulating astrocyte reactivity and microglia-dependent synaptic density

Genetic studies implicate clusterin (CLU) in the pathogenesis of Alzheimer's disease (AD), yet its precise molecular impact remains unclear. Through unbiased proteomic profiling and functional validation in CLU-deficient astrocytes, we identify increased nuclear factor κB (NF-κB)-dependent signaling and complement C3 secretion. Reduction of astrocyte CLU induced microglia-dependent modulation of extracellular apolipoprotein E (APOE) and phosphorylated tau, as well as increased microglial phagocytosis and reduced synapse numbers. By integrating mouse and human cellular models with comprehensive analyses of human plasma and brain tissue, we demonstrate that CLU AD-risk alleles are associated with reduced CLU protein and heightened inflammatory profiles. These findings establish a mechanistic link between AD genetic risk factors, astrocyte reactivity, and microglia-mediated effects on synaptic integrity. Collectively, these results support a model in which CLU upregulation in response to neuropathology is associated with maintenance of cognitive function, while diminished astrocyte CLU levels heighten disease susceptibility.

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.

Metabolic Alteration in Oxylipins and Endocannabinoids Point to an Important Role for Soluble Epoxide Hydrolase and Inflammation in Alzheimer's Disease - Finding from Alzheimer's Disease Neuroimaging Initiative

Mounting evidence implicates inflammation as a key factor in Alzheimer's disease (AD) development. We previously identified pro-inflammatory soluble epoxide hydrolase (sEH) metabolites to be elevated in plasma and CSF of AD patients and to be associated with lower cognition in non-AD subjects. Soluble epoxide hydrolase is a key enzyme converting anti-inflammatory epoxy fatty acids to pro-inflammatory diols, reported to be elevated in multiple cardiometabolic disorders. Here we analyzed over 700 fasting plasma samples from the baseline of Alzheimer's Disease Neuroimaging Initiative (ADNI) 2/GO study. We applied targeted mass spectrometry method to provide absolute quantifications of over 150 metabolites from oxylipin and endocannabinoids pathway, interrogating the role for inflammation/immune dysregulation and the key enzyme soluble epoxide hydrolase in AD. We provide further insights into the regulation of this pathway in different disease stages, APOE genotypes and between sexes. Additionally, we investigated in mild cognitive impaired (MCI) patients, metabolic signatures that inform about resilience to progression and conversion to AD. Key findings include I) confirmed disruption in this key central pathway of inflammation and pointed to dysregulation of sEH in AD with sex and disease stage differences; II) identified markers of disease progression and cognitive resilience using sex and ApoE genotype stratified analysis highlighting an important role for bile acids, lipid peroxidation and stress response hormone cortisol. In conclusion, we provide molecular insights into a central pathway of inflammation and links to cognitive dysfunction, suggesting novel therapeutic approaches that are based on targeting inflammation tailored for subgroups of individuals based on their sex, APOE genotype and their metabolic profile.

Stratifying risk of Alzheimer's disease in healthy middle-aged individuals with machine learning

Alzheimer's disease has a prolonged asymptomatic phase during which pathological changes accumulate before clinical symptoms emerge. This study aimed to stratify the risk of clinical disease to inform future disease-modifying treatments. Cerebrospinal fluid analysis from participants in the Emory Healthy Brain Study was used to classify individuals based on amyloid beta 42 (Aβ42), total tau (tTau) and phosphorylated tau (pTau) levels. Cognitively normal (CN), biomarker-positive (CN)/BM+individuals were identified using a tTau: Aβ42 ratio > 0.24, determined by Gaussian mixture models. CN/BM+ individuals (n = 134) were classified as having asymptomatic Alzheimer's disease (AsymAD), while CN, biomarker-negative (CN/BM-) individuals served as controls (n = 134). Cognitively symptomatic, biomarker-positive individuals with an Alzheimer's disease diagnosis confirmed by the Emory Cognitive Neurology Clinic were labelled as Alzheimer's disease (n = 134). Study groups were matched for age, sex, race and education. Cerebrospinal fluid samples from these matched Emory Healthy Brain Study groups were analysed using targeted proteomics via selected reaction monitoring mass spectrometry. The targeted cerebrospinal fluid panel included 75 peptides from 58 unique proteins. Machine learning approaches identified a subset of eight peptides (ADQDTIR, AQALEQAK, ELQAAQAR, EPVAGDAVPGPK, IASNTQSR, LGADMEDVCGR, VVSSIEQK, YDNSLK) that distinguished between CN/BM- and symptomatic Alzheimer's disease samples with a binary classifier area under the curve performance of 0.98. Using these eight peptides, Emory Healthy Brain Study AsymAD cases were further stratified into 'Control-like' and 'Alzheimer's disease-like' subgroups, representing varying levels of risk for developing clinical disease. The eight peptides were evaluated in an independent dataset from the Alzheimer's Disease Neuroimaging Initiative, effectively distinguishing CN/BM- from symptomatic Alzheimer's disease cases (area under the curve = 0.89) and stratifying AsymAD individuals into control-like and Alzheimer's disease-like subgroups (area under the curve = 0.89). In the absence of matched longitudinal data, an established cross-sectional event-based disease progression model was employed to assess the generalizability of these peptides for risk stratification. In summary, results from two independent modelling methods and datasets demonstrate that the identified eight peptides effectively stratify the risk of progression from asymptomatic to symptomatic Alzheimer's disease.

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.

SIRPα modulates microglial efferocytosis and neuroinflammation following experimental subarachnoid hemorrhage via the SHP1/STAT6 axis

Subarachnoid hemorrhage induces extensive neuronal cell death, leading to the release of damage-associated molecular patterns (DAMPs). These DAMPs, along with hemoglobin and cell corpses, trigger localized inflammation. Signal regulatory protein alpha (SIRPα) plays a crucial role in efferocytosis by acting as a "don't eat-me" signal, modulating inflammation and tissue homeostasis. However, the precise function and regulatory mechanisms of SIRPα in efferocytosis remain unclear. Proteomic analysis of cerebrospinal fluid (CSF) reveals that SIRPα levels are significantly elevated in the CSF of SAH patients and correlate with clinical outcomes. In vivo and in vitro studies show that microglial knockdown of SIRPα promotes efferocytosis and attenuates neuroinflammation following SAH. SIRPα inhibits efferocytosis by recruiting and phosphorylating SHP1 and SHP2 through phosphorylation of four tyrosine residues in its cytoplasmic domain, with SHP1 playing a particularly critical role. Mutation of these tyrosine residues to non-phosphorylatable alanine residues enhances efferocytosis and reduces neuroinflammation in vitro. RNA-seq analysis suggests that this mutation upregulates the expression of "eat-me" signals, MerTK and CD36, and identifies STAT6 as a key transcription factor involved in this process. In conclusion, SIRPα plays a central role in regulating microglia efferocytosis and neuroinflammation after SAH via the SHP1/STAT6 axis. Targeting this pathway may provide a promising therapeutic approach for SAH.

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.

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.

Multi Layered Omics Approaches Reveal Glia Specific Alterations in Alzheimer's Disease: A Systematic Review and Future Prospects

Alzheimer's disease (AD) is the most common neurodegenerative dementia with multi-layered complexity in its molecular etiology. Multiple omics-based approaches, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, and lipidomics are enabling researchers to dissect this molecular complexity, and to uncover a plethora of alterations yielding insights into the pathophysiology of this disease. These approaches reveal multi-omics alterations essentially in all cell types of the brain, including glia. In this systematic review, we screen the literature for human studies implementing any omics approach within the last 10 years, to discover AD-associated molecular perturbations in brain glial cells. The findings from over 200 AD-related studies are reviewed under four different glial cell categories: microglia, oligodendrocytes, astrocytes and brain vascular cells. Under each category, we summarize the shared and unique molecular alterations identified in glial cells through complementary omics approaches. We discuss the implications of these findings for the development, progression and ultimately treatment of this complex disease as well as directions for future omics studies in glia cells.

Oxidative stress induced protein aggregation via GGCT produced pyroglutamic acid in drug resistant glioblastoma

Drug resistance is a major barrier to cancer therapies and remains poorly understood. Recently, non-mutational mechanisms of drug resistance have been proposed where a more plastic metabolic response can play a major role. Here, we show that upon drug resistance, glioblastoma (GBM) cells have increased oxidative stress, mitochondria function, and protein aggregation. Gamma (γ)-glutamylcyclotranserase (GGCT), an enzyme in the γ-glutamyl cycle for glutathione production, located on chromosome 7 which is commonly amplified in GBM is also increased upon resistance. We further observe that the byproduct of GGCT-pyroglutamic acid-can bind aggregating proteins and that genetic and pharmacological inhibition of GGCT prevents protein aggregation. Finally, we found increased protein aggregation, GGCT expression, and pyroglutamic acid staining in recurrent GBM patient samples, adjacent non-tumor brain, and Alzheimer's brains. These findings suggest a new pathway for protein aggregation within drug resistant brain cancer that should be further studied in other brain disorders.

Quantitative Analysis of Nonhistone Lysine Methylation Sites and Lysine Demethylases in Breast Cancer Cell Lines

Growing evidence shows that lysine methylation is a widespread protein post-translational modification (PTM) that regulates protein function on histone and nonhistone proteins. Numerous studies have demonstrated that the dysregulation of lysine methylation mediators contributes to cancer growth and chemotherapeutic resistance. While changes in histone methylation are well-documented with extensive analytical techniques available, there is a lack of high-throughput methods to reproducibly quantify changes in the abundances of the mediators of lysine methylation and nonhistone lysine methylation (Kme) simultaneously across multiple samples. Recent studies by our group and others have demonstrated that antibody enrichment is not required to detect lysine methylation, prompting us to investigate the use of tandem mass tag (TMT) labeling for global Kme quantification without antibody enrichment in four different breast cancer cell lines (MCF-7, MDA-MB-231, HCC1806, and MCF10A). To improve the quantification of KDMs, we incorporated a lysine demethylase (KDM) isobaric trigger channel, which enabled 96% of all KDMs to be quantified while simultaneously quantifying 326 Kme sites. Overall, 142 differentially abundant Kme sites and eight differentially abundant KDMs were identified among the four cell lines, revealing cell line-specific patterning.

Proteomic analysis reveals distinct cerebrospinal fluid signatures across genetic frontotemporal dementia subtypes

We used an untargeted mass spectrometric approach, tandem mass tag proteomics, for the identification of proteomic signatures in genetic frontotemporal dementia (FTD). A total of 238 cerebrospinal fluid (CSF) samples from the Genetic FTD Initiative were analyzed, including samples from 107 presymptomatic (44 C9orf72, 38 GRN, and 25 MAPT) and 55 symptomatic (27 C9orf72, 17 GRN, and 11 MAPT) mutation carriers as well as 76 mutation-negative controls ("noncarriers"). We found shared and distinct proteomic alterations in each genetic form of FTD. Among the proteins significantly altered in symptomatic mutation carriers compared with noncarriers, we found that a set of proteins including neuronal pentraxin 2 and fatty acid binding protein 3 changed across all three genetic forms of FTD and patients with Alzheimer's disease from previously published datasets. We observed differential changes in lysosomal proteins among symptomatic mutation carriers with marked abundance decreases in MAPT carriers but not other carriers. Further, we identified mutation-associated proteomic changes already evident in presymptomatic mutation carriers. Weighted gene coexpression network analysis combined with gene ontology annotation revealed clusters of proteins enriched in neurodegeneration and glial responses as well as synapse- or lysosome-related proteins indicating that these are the central biological processes affected in genetic FTD. These clusters correlated with measures of disease severity and were associated with cognitive decline. This study revealed distinct proteomic changes in the CSF of patients with genetic FTD, providing insights into the pathological processes involved in the disease. In addition, we identified proteins that warrant further exploration as diagnostic and prognostic biomarker candidates.

Biomarkers of synaptic degeneration in Alzheimer's disease

Synapse has been considered a critical neuronal structure in the procession of Alzheimer's disease (AD), attacked by two pathological molecule aggregates (amyloid-β and phosphorylated tau) in the brain, disturbing synaptic homeostasis before disease manifestation and subsequently causing synaptic degeneration. Recently, evidence has emerged indicating that soluble oligomeric amyloid-β (AβO) and tau exert direct toxicity on synapses, causing synaptic damage. Synaptic degeneration is closely linked to cognitive decline in AD, even in the asymptomatic stages of AD. Therefore, the identification of novel, specific, and sensitive biomarkers involved in synaptic degeneration holds significant promise for early diagnosis of AD, reducing synaptic degeneration and loss, and controlling the progression of AD. Currently, a range of biomarkers in cerebrospinal fluid (CSF), such as synaptosome-associated protein 25 (SNAP-25), synaptotagmin-1, growth-associated protein-43 (GAP-43), and neurogranin (Ng), along with functional brain imaging techniques, can detect variations in synaptic density, offering high sensitivity and specificity for AD diagnosis. However, these methods face challenges, including invasiveness, high cost, and limited accessibility. In contrast, biomarkers found in blood or urine provide a minimally invasive, cost-effective, and more accessible alternative to traditional diagnostic methods. Notably, neuron-derived exosomes in blood, which contain synaptic proteins, show variations in concentration that can serve as indicators of synaptic injury, providing an additional, less invasive approach to AD diagnosis and monitoring.

Lactylation of tau in human Alzheimer's disease brains

INTRODUCTION

Aggregation of hyperphosphorylated tau (tauopathy) is associated with cognitive impairment in patients with Alzheimer's disease (AD). In AD, a metabolic shift due to the Warburg effect results in increased lactate production. Lactate can induce a post-translational modification (PTM) on proteins that conjugates lactyl groups to lysine (K) residues, which is known as lactylation.

METHODS

We analyzed lactylation of tau in control and AD brain tissue and conducted cell-based assays. In addition, we used in vitro assays to determine whether p300 catalyzed tau lactylation.

RESULTS

Quantitative proteomics detected that tau lactylation was elevated in AD brains, with K residue at position 331 (K331) being a prominent site. Lactate induced tau lactylation, which increased tau phosphorylation and cleavage and reduced ubiquitination. Inhibition of lactate production lowered tau lactylation; p300 catalyzed tau lactylation.

DISCUSSION

Our findings suggest that tau lactylation links metabolic dysregulation with tauopathy and could serve as a novel diagnostic and therapeutic target.

HIGHLIGHTS

Elevated tau lactylation, particularly at K331, is evident in in human AD brain samples. Lactate induces tau lactylation, enhancing phosphorylation and cleavage while inhibiting ubiquitination. The acetyl-transferase p300 catalyzes tau lactylation, with K331 being the most prominent site.

Linking Cerebral Malaria Pathogenesis to APOE-Mediated Amyloidosis: Observations and Hypothesis

Although most children with cerebral malaria fully recover, more than a fifth of the survivors develop post-discharge neurodevelopmental sequelae suggestive of advanced neuronal injury. However, the cerebral molecular processes initiating neurological dysfunction in cerebral malaria are still debatable. In this article, we explore available data and hypothesise that cerebral malaria might be linked to APOE-mediated amyloidosis, one of the pathological processes associated with Alzheimer's disease. If our hypothesis is tested and found to be true, it could have far-reaching implications for what we know about cerebral malaria pathogenesis.

Exploratory profiling of metabolites in cerebrospinal fluid using a commercially available targeted LC-MS based metabolomics kit to discriminate leptomeningeal metastasis

BACKGROUND

Leptomeningeal metastasis (LM) is a devastating complication of cancer that is difficult to treat. Thus, early diagnosis is essential for LM patients. However, cerebrospinal fluid (CSF) cytology has low sensitivity, and imaging approaches are ineffective. We explored targeted CSF metabolic profiling to discriminate among LM and other conditions affecting the central nervous system (CNS).

METHODS

We quantitatively measured amino acids, biogenic amines, hexoses, acylcarnitines (AC), cholesteryl esters (CE), glycerides, phosphatidylcholines (PC), lysophosphatidylcholines (LPC), sphingomyelins (SM), and ceramides (Cer) in 117 CSF samples from various groups of healthy controls (HC, n = 10), patients with LM (LM, n = 47), parenchymal brain tumor (PBT, n = 45), and inflammatory disease (ID, n = 13) with internal standards using the Absolute IDQ- p400® targeted mass spectrometry kit. Metabolites detected in > 90% of samples or showing a difference in proportional level between groups ≥ 75% were used in logistic regression models when there was no single metabolite with AUC = 1 for the groups of comparison.

RESULTS

PC and SM had higher levels in LM than in PBT or HC, whereas LPC had lower level in PBT than the other groups. Glycerides and Cer levels were higher in PBT and LM than in HC. Long-chain AC level in PBT was lower than in LM or HC. A regression model including Ala, PC (42:7), PC (30:3), PC (37:0), and Tyr achieved complete discrimination (AUC = 1.0) between LM and HC. In comparison of PBT and HC, twenty-six individual metabolites allowed complete discrimination between two groups, and between ID and HC fourty-six individual lipid metabolites allowed complete discrimination. Twenty-one individual metabolites (18 ACs and 3 PCs) allowed complete discrimination between LM and PBT.

CONCLUSIONS

Using a commercial targeted liquid chromatography-mass spectrometry (LC-MS) metabolomics kit, we were able to differentiate LM from HC and PBT. Most of the discriminative metabolites among different diseases were lipid metabolites, for which their CNS distribution and quantification in different cell types are largely unknown, whereas amino acids, biogenic amines, and hexoses failed to show significant differences. Future validation studies with larger, controlled cohorts should be performed, and hopefully, the kit may expand its metabolite coverage for unique cancer cell glucose metabolism.

Comparison of the amyloid plaque proteome in Down syndrome, early-onset Alzheimer's disease, and late-onset Alzheimer's disease

Down syndrome (DS) is strongly associated with Alzheimer's disease (AD) due to APP overexpression, exhibiting Amyloid-β (Aβ) and Tau pathology similar to early-onset (EOAD) and late-onset AD (LOAD). We evaluated the Aβ plaque proteome of DS, EOAD, and LOAD using unbiased localized proteomics on post-mortem paraffin-embedded tissues from four cohorts (n = 20/group): DS (59.8 ± 4.99 y/o), EOAD (63 ± 4.07 y/o), LOAD (82.1 ± 6.37 y/o), and controls (66.4 ± 13.04). We identified differentially abundant proteins when comparing Aβ plaques and neighboring non-plaque tissue (FDR < 5%, fold-change > 1.5) in DS (n = 132), EOAD (n = 192), and LOAD (n = 128), with 43 plaque-associated proteins shared across all groups. Positive correlations were observed between plaque-associated proteins in DS and EOAD (R2 = .77), DS and LOAD (R2 = .73), and EOAD and LOAD (R2 = .67). Top gene ontology biological processes (GOBP) included lysosomal transport (p = 1.29 × 10-5) for DS, immune system regulation (p = 4.33 × 10-5) for EOAD, and lysosome organization (p = 0.029) for LOAD. Protein networks revealed a plaque-associated protein signature involving APP metabolism, immune response, and lysosomal functions. In DS, EOAD, and LOAD non-plaque vs. control tissue, we identified 263, 269, and 301 differentially abundant proteins, with 65 altered proteins shared across all cohorts. Non-plaque proteins in DS showed modest correlations with EOAD (R2 = .59) and LOAD (R2 = .33) compared to the correlation between EOAD and LOAD (R2 = .79). Top GOBP term for all groups was chromatin remodeling (p < 0.001), with additional terms for DS including extracellular matrix, and protein-DNA complexes and gene expression regulation for EOAD and LOAD. Our study reveals key functional characteristics of the amyloid plaque proteome in DS, compared to EOAD and LOAD, highlighting shared pathways in endo/lysosomal functions and immune responses. The non-plaque proteome revealed distinct alterations in ECM and chromatin structure, underscoring unique differences between DS and AD subtypes. Our findings enhance our understanding of AD pathogenesis and identify potential biomarkers and therapeutic targets.

Cerebrospinal Fluid (CSF) Proteomic Signature in Preclinical and Clinical Alzheimer's disease (AD): Role of Adhesion Molecules

Background

Although Amyloid-beta and Tau are the hallmarks of Alzheimer's Disease (AD), other protein pathways such as endothelial dysfunction may be involved and may precede cognitive symptoms. Our objective was to characterize the cerebrospinal fluid (CSF) proteomic profiles focusing on cardiometabolic-related protein pathways in individuals on the AD spectrum.

Methods

We performed CSF and plasma-targeted proteomics (276 proteins) from 354 participants of the Brain Stress Hypertension and Aging Program (BSHARP), of which 8% had preclinical AD, and 24% had MCI due to AD. We instituted a bioinformatic pipeline to generate data-driven protein modules, used "Hub" and "Critical" proteins within each module to describe protein signatures for each AD stage and then assessed their associations with clinical and biological AD traits. Finally, we completed pathway enrichment analysis to get insight into pathways that might be implicated in AD pathogenesis.

Results

The 276 measured proteins clustered into five modules that were associated with CSF Amyloid-β42, Tau, and pTau. (all p-value <0.05). A CSF protein AD signature was characterized by elevated levels of CSF Hepatocyte Growth Factor (HGF), Intercellular and Vascular Cell Adhesion Molecule 1 (ICAM-1, VCAM-1), Neuropilin 1 and 2 (NRP-1, NRP-2), Scavenger Receptor Class B Member 2(SCARB2), Plasminogen Activator, Urokinase (PLAU). (all <0.05) We also found a significant difference in the CSF/Plasma ratio for the proteins associated with Cognitive Status and the Tau/Aβ42 ratio (TAR) in the CSF. Pathway enrichment analysis revealed that cell adhesion and endothelial dysfunction (all p-value <0.05) were key mechanisms involved in AD pathogenesis, especially in the preclinical stage.

Conclusion

Our results suggest a proteomic signature in the CSF of individuals with preclinical AD that is driven by adhesion molecules and might be implicated in the pathogenesis of AD. Future studies investigating these pathways may provide insights into novel AD biomarkers and therapeutic targets.

Lower expression of BIN1's neuronal isoform in vulnerable excitatory neurons increases risk in Alzheimer's disease

Background

Neurons in Alzheimer's disease (AD) experience elevated DNA damage, with DNA repair sites enriched at enhancer regions of genes essential for neuronal survival. Excitatory neurons in the cortical superficial layers expressing CUX2 and RORB (Cux2+/Rorb+), are selectively vulnerable in AD, but their relationship to single nucleotide polymorphisms (SNPs) in AD genome-wide association studies (GWAS) is unclear.

Objective

This study aimed to identify and characterize functional AD-GWAS SNPs using single-nucleus RNA sequencing data, focusing on selectively vulnerable neurons and DNA repair hotspots.

Methods

Filters were applied to identify candidate SNPs based on overlap with repair hotspots, RNA expression, transcription factor binding, AD association, and epigenetic significance. In vitro assays and analyses of large datasets from bulk RNA-seq (n = 1894), proteomics (n = 400), and single-nucleus RNA-seq (n = 424, 1.6 M cells) were conducted.

Results

BIN1 SNP, rs78710909, met multiple criteria - located in an AD-GWAS locus, repair hotspot, and promoter region. rs78710909C exhibits 1.52× higher AD risk and 5.4× differential transcription factor binding. In vitro, rs78710909C shows greater enhancer activity and weaker p53 but stronger E2F1 binding. BIN1's neuronal isoform is neuroprotective, but its AD expression is lower (p < 0.01). Moreover, only in AD and Cux2+/Rorb + neurons, rs78710909C is associated with a lower average BIN1 neuronal isoform ratio (p < 0.01). The genes upregulated in neurons with lower neuronal isoform ratio were associated with the hallmarks of AD pathology.

Conclusions

In a disease-relevant mechanism, the BIN1 SNP rs78710909C is associated with a lower ratio of BIN1's neuronal isoform which increases the vulnerability of specific excitatory neurons in AD patients.

Proteomic signatures of Alzheimer's disease and Lewy body dementias: A comparative analysis

INTRODUCTION

We aimed to identify unique proteomic signatures of Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia (PDD).

METHODS

We conducted a comparative proteomic analysis of 33 post mortem brains from AD, DLB, and PDD individuals without dementia focusing on prefrontal, cingulate, and parietal cortices, using weighted gene co-expression network analyses with differential enrichment analysis.

RESULTS

Network modules revealed hub proteins common to all dementias. Lewy body dementias differed from AD by reduced levels of the autophagy protein p62 (SQSTM1), whereas DLB was distinguished from both AD and PDD by altered TRIM33 and cysteine/glutamate transporter (SLC7A11) across brain regions. An increase in mitochondrial and synaptic proteins was related to better cognition whereas enrichment in the extracellular matrix, complement system, and autophagy proteins was associated with greater cognitive impairment.

DISCUSSION

Our study offers valuable insights into the network-based biomarker characterization of molecular signatures of AD, DLB, and PDD.

HIGHLIGHTS

Reduced levels of the autophagy protein p62 (SQSTM1) differentiated Lewy body dementias from Alzheimer's disease (AD) across multiple brain regions. Dementia with Lewy bodies (DLB) was distinguished from both AD and Parkinson's disease dementia (PDD) by altered TRIM33 and cysteine/glutamate transporter (SLC7A11) levels across brain regions. Key mitochondrial oxidative phosphorylation proteins (e.g., COX7A2, TOMM40L, NDUFV1), and synaptic proteins (e.g., GABRB3, GABRB2, GLUA3, GLUA4, SNAP47, dynamin1) were more abundant in preserved cognitive states. Extracellular matrix proteins and members of the complement system (decorin, biglycan, C4A, C4B) showed a strong positive correlation with cognitive decline.

CSF proteomics reveals changes in myelin and synaptic biology after Spectris treatment

INTRODUCTION

Brain steady-state gamma oscillations evoked using a non-invasive medical device (Spectris) have shown potential clinical benefits in patients with mild-moderate Alzheimer's disease (AD), including reduced functional and cognitive decline, reduced brain volume and myelin loss, and increased brain functional connectivity. We analyzed changes in cerebrospinal fluid (CSF) proteins after Spectris treatment in mild cognitive impairment (MCI) and their relationship to established biological pathways implicated in AD.

METHODS

Unbiased proteomic analysis of CSF samples from participants with amyloid-positive MCI (n = 10) was conducted from the FLICKER (NCT03543878) clinical trial. Participants used the Cognito Therapeutics medical device (Spectris), confirmed to evoke steady-state gamma oscillations. Participants were instructed to use the device daily for 1 hour each day during the trial. CSF was collected prior to the start of stimulation and after 4 and 8 weeks of treatment. The proteome was analyzed using tandem mass tag mass spectrometry.

RESULTS

Differential expression analysis of proteins at baseline and after 8 weeks of treatment (N = 5) revealed that 110 out of 2951 proteins met the significance threshold (analysis of variance, P < 0.05, no false discovery rate). Sixty proteins were upregulated, and 50 proteins were downregulated after treatment. Changes in protein expression were mapped to the consensus human AD protein network, representing co-expressed and functionally linked modules linked to cell type and biochemical pathways. Treatment altered CSF proteins linked to AD-related brain proteome modules, including those involved in myelination (proteolipid protein 1, ecotropic viral integration site 2A), synaptic and neuroimmune functions, and regulation of cellular lipid transportation. Biological pathway analysis revealed that most impacted pathways were associated with lipoproteins, cholesterol, phospholipids processing, and phosphatidylcholine biosynthesis.

DISCUSSION

The CSF proteomic changes observed in this study suggest pleiotropic effects on multiple pathways involved in AD, including myelination, synaptic and neuroimmune function, and lipid transport. These findings are also consistent with observations of white matter and myelin preservation after Spectris treatment of AD.

Highlights

We analyzed changes in cerebrospinal fluid (CSF) proteins in response to sensory-evoked gamma oscillations in individuals with mild cognitive impairment.Sensory evoked steady-state gamma oscillations were evoked by Spectris medical device.Changes in CSF proteins were observed after 8 weeks of daily 1 hour treatment.Affected proteins were related to myelination, synaptic and neuroimmune functions, and regulation of cellular lipid transportation.Proteomic changes support clinical outcomes and myelin preservation of Spectris treatment.

Scrutinizing neurodegenerative diseases: decoding the complex genetic architectures through a multi-omics lens

Neurodegenerative diseases present complex genetic architectures, reflecting a continuum from monogenic to oligogenic and polygenic models. Recent advances in multi-omics data, coupled with systems genetics, have significantly refined our understanding of how these data impact neurodegenerative disease mechanisms. To contextualize these genetic discoveries, we provide a comprehensive critical overview of genetic architecture concepts, from Mendelian inheritance to the latest insights from oligogenic and omnigenic models. We explore the roles of common and rare genetic variants, gene-gene and gene-environment interactions, and epigenetic influences in shaping disease phenotypes. Additionally, we emphasize the importance of multi-omics layers including genomic, transcriptomic, proteomic, epigenetic, and metabolomic data in elucidating the molecular mechanisms underlying neurodegeneration. Special attention is given to missing heritability and the contribution of rare variants, particularly in the context of pleiotropy and network pleiotropy. We examine the application of single-cell omics technologies, transcriptome-wide association studies, and epigenome-wide association studies as key approaches for dissecting disease mechanisms at tissue- and cell-type levels. Our review introduces the OmicPeak Disease Trajectory Model, a conceptual framework for understanding the genetic architecture of neurodegenerative disease progression, which integrates multi-omics data across biological layers and time points. This review highlights the critical importance of adopting a systems genetics approach to unravel the complex genetic architecture of neurodegenerative diseases. Finally, this emerging holistic understanding of multi-omics data and the exploration of the intricate genetic landscape aim to provide a foundation for establishing more refined genetic architectures of these diseases, enhancing diagnostic precision, predicting disease progression, elucidating pathogenic mechanisms, and refining therapeutic strategies for neurodegenerative conditions.

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.

Temporal changes of neurobehavior in rats following varied blast magnitudes and screening of serum biomarkers in early stage of brain injury

Blast neurotrauma has been linked to impairments in higher-order cognitive functions, including memory, attention, and mood. Current literature is limited to a single overpressure exposure or repeated exposures at the same level of overpressure. In this study, a rodent model of primary blast neurotrauma was employed to determine the pressure at which acute and chronic neurological alterations occurred. Three pressure magnitudes (low, moderate and high) were used to evaluate injury thresholds. A biology shock tube (BST) was used to simulate shock waves with overpressures of 60 kPa, 90 kPa and 120 kPa respectively. Neurological behavior of the rats was assessed by the Multi-Conditioning System (MCS) at 1 d, 7 d, 28 d and 90 d after shock wave exposure. Serum dopamine (DA), 5-hydroxytryptamine (5-HT), brain-derived neurotrophic factor (BDNF) and gamma-aminobutyric acid (GABA) were measured at the same time points. The proteomic analysis was conducted to identify potentially vulnerable cellular and molecule targets of serum in the immediate post-exposure period. Results revealed that: (1) Anxiety-like behavior increased significantly at 1 d post-exposure in the medium and high overpressure (90 kPa, 120 kPa) groups, returned to baseline at 7 days, and anxiety-like behavior in the high overpressure groups re-emerged at 28 d and 90 d. (2) High overpressure (120 kPa) impaired learning and memory in the immediate post-exposure period. (3) The serum DA levels decreased significantly at 1 d post-exposure in the medium and high overpressure groups; The 5-HT levels decreased significantly at 1 d and 90 d in the high overpressure groups; The BDNF levels decreased significantly at 90 d in the high overpressure groups. (4) Proteomic analysis identified 38, 306, and 57 differentially expressed proteins in serum following low, medium and high overpressure exposures, respectively. Two co-expressed proteins were validated. Functional analysis revealed significant enrichment of 1121, 2096, and 1121 Gene Ontology (GO) items and 33, 47, and 26 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, indicating extensive molecular responses to overpressure in the early phase. These findings suggest that exposure, even at moderate levels, can induce persistent neurobehavioral and molecular alterations, highlighting the need for further research into the long-term consequences of blast neurotrauma.

Sleep deprivation leads to non-adaptive alterations in sleep microarchitecture and amyloid-β accumulation in a murine Alzheimer model

Impaired sleep is a common aspect of aging and often precedes the onset of Alzheimer's disease. Here, we compare the effects of sleep deprivation in young wild-type mice and their APP/PS1 littermates, a murine model of Alzheimer's disease. After 7 h of sleep deprivation, both genotypes exhibit an increase in EEG slow-wave activity. However, only the wild-type mice demonstrate an increase in the power of infraslow norepinephrine oscillations, which are characteristic of healthy non-rapid eye movement sleep. Notably, the APP/PS1 mice fail to enhance norepinephrine oscillations 24 h after sleep deprivation, coinciding with an accumulation of cerebral amyloid-β protein. Proteome analysis of cerebrospinal fluid and extracellular fluid further supports these findings by showing altered protein clearance in APP/PS1 mice. We propose that the suppression of infraslow norepinephrine oscillations following sleep deprivation contributes to increased vulnerability to sleep loss and heightens the risk of developing amyloid pathology in early stages of Alzheimer's disease.

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.

Transcriptome Signatures for Cognitive Resilience Among Individuals with Pathologically Confirmed Alzheimer Disease

INTRODUCTION

Limited success to date in development of drugs that target hallmark Alzheimer disease (AD) proteins as a means to slow AD-related cognitive decline has sparked interest in approaches focused on cognitive resilience. We sought to identify transcriptome signatures among brain donors with neuropathologically confirmed AD that distinguish those with cognitive impairment from those that were cognitively intact.

METHODS

We compared gene expression patterns in brain tissue from donors in four cohorts who were cognitively and pathologically normal (controls), met clinical and pathological criteria for AD (SymAD), or were cognitively normal prior to death despite pathological evidence of AD (cognitively resilient or AsymAD). Differentially expressed genes (DEGs) at the transcriptome-wide significance (TWS) level (P<10 -6 ) in the total sample and nominally significant (P<0.05) in at least two datasets were further evaluated in analyses testing association of gene expression with co-calibrated and harmonized cognitive domain scores and AD-related neuropathological traits.

RESULTS

We identified 52 TWS DEGs, including 14 that surpassed a significance threshold of P<5×10 -8 . The three most significant DEGs, ADAMTS2 (Log2 fold change [Log2FC]=0.46, P=2.94×10 -14 ), S100A4 (Log2FC=0.61, P=3.98×10 -11 ) and NRIP2 (Log2FC=0.32, P=9.52×10 -11 ) were up-regulated in SymAD compared to AsymAD brains. ADAMTS2 and SLC6A9 were also significantly and nominally differentially expressed between AsymAD cases and controls (FDR P=0.45 and FDR P=0.57, respectively). Significant associations (P<0.0038) were identified for executive function with expression of ADAMTS2 (P=4.15×10 -8 ) and ARSG (P=1.09×10 -3 ), and for memory with PRELP (P=3.92×10 -5 ) and EMP3 (P=7.75×10 -4 ), and for language with SLC38A2 (P=6.76×10 -5 ) and SLC6A9 (P=2.13 ×10 -3 ). Expression of ARSG and FHIP1B were associated with measures of Tau pathology (AT8: P=1.5×10 -3 , and pTau181: P=3.64×10 -3 , respectively), and SLC6A9 expression was associated with multiple pTau isoforms including pTau181 (P=1.5×10 -3 ) and pTau396 (P=2.05×10 -3 ). PRELP expression was associated with synaptic density (PSD.95: P=6.18 ×10 -6 ). DEGs were significantly enriched in pathways involving E2F targets, cholesterol homeostasis, and oxidative phosphorylation.

CONCLUSION

We identified multiple DEGs that differentiate neuropathologically confirmed AD cases with and without cognitive impairment prior to death. Expression of several of these genes was also associated with measures of cognitive performance and AD-related neuropathological traits, thus providing important insights into cognitive resilience mechanisms and strategies for delaying clinical symptoms of AD.

CSF proteins of inflammation, proteolysis and lipid transport define preclinical AD and progression to AD dementia in cognitively unimpaired individuals

This preclinical AD CSF proteome study identified a panel of 12-CSF markers detecting amyloid positivity and clinical progression to AD with high accuracy; some of these CSF proteins related to immune function, neurotrophic processes, energy metabolism and endolysosomal functioning (e.g., ITGB2, CLEC5A, IGFBP-1, CST3) changed before amyloid positivity is established.

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.

Target modulation of glycolytic pathways as a new strategy for the treatment of neuroinflammatory diseases

Neuroinflammation is an innate and adaptive immune response initiated by the release of inflammatory mediators from various immune cells in response to harmful stimuli. While initially beneficial and protective, prolonged or excessive neuroinflammation has been identified in clinical and experimental studies as a key pathological driver of numerous neurological diseases and an accelerant of the aging process. Glycolysis, the metabolic process that converts glucose to pyruvate or lactate to produce adenosine 5'-triphosphate (ATP), is often dysregulated in many neuroinflammatory disorders and in the affected nerve cells. Enhancing glucose availability and uptake, as well as increasing glycolytic flux through pharmacological or genetic manipulation of glycolytic enzymes, has shown potential protective effects in several animal models of neuroinflammatory diseases. Modulating the glycolytic pathway to improve glucose metabolism and ATP production may help alleviate energy deficiencies associated with these conditions. In this review, we examine six neuroinflammatory diseases-stroke, Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), and depression-and provide evidence supporting the role of glycolysis in their treatment. We also explore the potential link between inflammation-induced aging and glycolysis. Additionally, we briefly discuss the critical role of glycolysis in three types of neuronal cells-neurons, microglia, and astrocytes-within physiological processes. This review highlights the significance of glycolysis in the pathology of neuroinflammatory diseases and its relevance to the aging process.

Neuronal fatty acid-binding protein enhances autophagy and suppresses amyloid-β pathology in a Drosophila model of Alzheimer's disease

Fatty acid-binding proteins (FABPs) are small cytoplasmic proteins involved in intracellular lipid transport and bind free fatty acids, cholesterol, and retinoids. FABP3, the major neuronal FABP in the adult brain, is upregulated in the CSF of patients with Alzheimer's disease (AD). However, the precise role of neuronal FABPs in AD pathogenesis remains unclear. This study investigates the contribution of fabp, the Drosophila homolog of FABP3 and FABP7, to amyloid β (Aβ) pathology using a Drosophila model. Neuronal knockdown of fabp shortened the lifespan of flies and increased age-related protein aggregates in the brain. In an AD model, fabp knockdown in neurons increased Aβ accumulation and Aβ-induced neurodegeneration, whereas fabp overexpression ameliorated Aβ pathology. Notably, fabp overexpression stimulated autophagy, which was inhibited by the knockdown of Eip75B, the Drosophila homolog of the peroxisome proliferator-activated receptor (PPAR). The PPAR activator rosiglitazone restored autophagy impaired by fabp knockdown and reduced fabp knockdown-induced increased Aβ aggregation and cell death. Furthermore, knockdown of either fabp or Eip75B in the wing imaginal disc or adult fly brain reduced the expression of Atg6 and Atg8a. Additionally, treatment of the fabp knockdown AD model flies with polyunsaturated fatty acids, such as docosahexaenoic acid or linoleic acid, partially alleviated cell death in the developing eye, restored impaired autophagy flux, reduced Aβ aggregation, and attenuated Aβ-induced cell death. Our results suggest that Drosophila fabp plays an important role in maintaining protein homeostasis during aging and protects neurons from Aβ-induced cell death by enhancing autophagy through the PPAR pathway. These findings highlight the potential importance of neuronal FABP function in AD pathogenesis.

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.

Network Medicine Approach Unravels Endophenotype Signature in Alzheimer's Disease through Large-Scale Comparative Proteomics Analysis: Vascular Dysfunction as a Prime Example

Alzheimer's disease (AD) is the most common neurodegenerative disease burdening public health. We proposed a network-based infrastructure to identify protein signatures for five AD pathological endophenotypes: amyloidosis, tauopathy, vascular dysfunction, lysosomal dysfunction, and neuroinflammation. We analyzed 23 proteomic data sets from AD patients and transgenic mouse models, using network proximity to measure associations between endophenotype modules and differentially expressed proteins (DEPs) in the integrated AD proteome. We focused on the vascular dysfunction signature with 21 DEPs by integrating RNA-seq, single-cell transcriptomics, GWAS, and literature. Experiments on APP/PS1 and MCAO models highlighted three proteins (SEPT5, SNAP25, STXBP1) as novel AD biomarker candidates. This study demonstrates a network medicine framework for deciphering endophenotype signatures in AD.

Heparin-enriched plasma proteome is significantly altered in Alzheimer's disease

INTRODUCTION

Heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to β-amyloid (Aβ) and tau pathology in Alzheimer's disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry-based proteomic approaches.

METHODS

We employed heparin-affinity chromatography, followed by off-line fractionation and tandem mass tag mass spectrometry (TMT-MS), to enrich HBPs from plasma obtained from AD (n = 62) and control (n = 47) samples. These profiles were then correlated to Aβ, tau and phosphorylated tau (pTau) CSF biomarkers and plasma pTau181 from the same individuals, as well as a consensus brain proteome network to assess the overlap with AD brain pathophysiology.

RESULTS

Heparin enrichment from plasma was highly reproducible, enriched well-known HBPs like APOE and thrombin, and depleted high-abundant proteins such as albumin. A total of 2865 proteins, spanning 10 orders of magnitude in abundance, were measured across 109 samples. Compared to the consensus AD brain protein co-expression network, we observed that specific plasma proteins exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes, highlighting the complex interplay between the two compartments. Elevated proteins in AD plasma, when compared to controls, included members of the matrisome module in brain that accumulate with Aβ deposits, such as SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB, and the APOE4 proteoform. Additionally, heparin-enriched proteins in plasma demonstrated significant correlations with conventional AD CSF biomarkers, including Aβ, total tau, pTau, and plasma pTau181. A panel of five plasma proteins classified AD from control individuals with an area under the curve (AUC) of 0.85. When combined with plasma pTau181, the panel significantly improved the classification performance of pTau181 alone, increasing the AUC from 0.93 to 0.98. This suggests that the heparin-enriched plasma proteome captures additional variance in cognitive dementia beyond what is explained by pTau181.

CONCLUSION

These findings support the utility of a heparin-affinity approach coupled with TMT-MS for enriching amyloid-associated proteins, as well as a wide spectrum of plasma biomarkers that reflect pathological changes in the AD brain.

Physiology of malate dehydrogenase and how dysregulation leads to disease

Malate dehydrogenase (MDH) is pivotal in mammalian tissue metabolism, participating in various pathways beyond its classical roles and highlighting its adaptability to cellular demands. This enzyme is involved in maintaining redox balance, lipid synthesis, and glutamine metabolism and supports rapidly proliferating cells' energetic and biosynthetic needs. The involvement of MDH in glutamine metabolism underlines its significance in cell physiology. In contrast, its contribution to lipid metabolism highlights its role in essential biosynthetic processes necessary for cell maintenance and proliferation. The enzyme's regulatory mechanisms, such as post-translational modifications, underscore its complexity and importance in metabolic regulation, positioning MDH as a potential target in metabolic dysregulation. Furthermore, the association of MDH with various pathologies, including cancer and neurological disorders, suggests its involvement in disease progression. The overexpression of MDH isoforms MDH1 and MDH2 in cancers like breast, prostate, and pancreatic ductal adenocarcinoma, alongside structural modifications, implies their critical role in the metabolic adaptation of tumor cells. Additionally, mutations in MDH2 linked to pheochromocytomas, paragangliomas, and other metabolic diseases emphasize MDH's role in metabolic homeostasis. This review spotlights MDH's potential as a biomarker and therapeutic target, advocating for further research into its multifunctional roles and regulatory mechanisms in health and disease.

CT1812 biomarker signature from a meta-analysis of CSF proteomic findings from two Phase 2 clinical trials in Alzheimer's disease

INTRODUCTION

CT1812 is in clinical development for the treatment of Alzheimer's disease (AD). Cerebrospinal fluid (CSF) exploratory proteomics was employed to identify pharmacodynamic biomarkers of CT1812 in mild to moderate AD from two independent clinical trials.

METHODS

Unbiased analysis of tandem-mass tag mass spectrometry (TMT-MS) quantitative proteomics, pathway analysis and correlation analyses with volumetric magnetic resonance imaging (vMRI) were performed for the SPARC cohort (NCT03493282). Comparative analyses and a meta-analysis with the interim SHINE cohort (NCT03507790; SHINE-A) followed by network analysis (weighted gene co-expression network analysis [WGCNA]) were used to understand the biological impact of CT1812.

RESULTS

CT1812 pharmacodynamic biomarkers and biological pathways were identified that replicate across two clinical cohorts. The meta-analysis revealed novel candidate biomarkers linked to S2R biology and AD, and network analysis revealed treatment-associated networks driven by S2R.  DISCUSSION: Early clinical validation of CT1812 candidate biomarkers replicating in independent cohorts strengthens the understanding of the biological impact of CT1812 in patients with AD, and supports CT1812's synaptoprotective mechanism of action and its continued clinical development.

HIGHLIGHTS

This exploratory proteomics study identified candidate biomarkers of CT1812 in SPARC (NCT03493282) Comparative analyses identified biomarkers replicating across trials/cohorts Two independent Ph2 trial cohorts (SPARC and interim SHINE [NCT03507790; SHINE-A]) were used in a meta-analysis Amyloid beta (Aβ) & synaptic biology impacted by CT1812 and volumetric magnetic resonance imaging (vMRI) treatment-related correlates emerge Network analyses revealed sigma-2 receptor (S2R)-interacting proteins that may be "drivers" of changes.

Alzheimer's disease CSF biomarkers correlate with early pathology and alterations in neuronal and glial gene expression

INTRODUCTION

Normal pressure hydrocephalus (NPH) patients undergoing cortical shunting frequently show early Alzheimer's disease (AD) pathology on cortical biopsy, which is predictive of progression to clinical AD. The objective of this study was to use samples from this cohort to identify cerebrospinal fluid  (CSF) biomarkers for AD-related central nervous system (CNS) pathophysiologic changes using tissue and fluids with early pathology, free of post mortem artifact.

METHODS

We analyzed Simoa, proteomic, and metabolomic CSF data from 81 patients with previously documented pathologic and transcriptomic changes.

RESULTS

AD pathology on biopsy correlates with CSF β-amyloid-42/40, neurofilament light chain (NfL), and phospho-tau-181(p-tau181)/β-amyloid-42, while several gene expression modules correlate with NfL. Proteomic analysis highlights seven core proteins that correlate with pathology and gene expression changes on biopsy, and metabolomic analysis of CSF identifies disease-relevant groups that correlate with biopsy data.

DISCUSSION

As additional biomarkers are added to AD diagnostic panels, our work provides insight into the CNS pathophysiology these markers are tracking.

HIGHLIGHTS

AD CSF biomarkers correlate with CNS pathology and transcriptomic changes. Seven proteins correlate with CNS pathology and gene expression changes. Inflammatory and neuronal gene expression changes correlate with YKL-40 and NPTXR, respectively. CSF metabolomic analysis identifies pathways that correlate with biopsy data. Fatty acid metabolic pathways correlate with β-amyloid pathology.