Molecular Neurodegeneration

Progranulin (PGRN) deficiency is a common hallmark in frontotemporal dementia (FTD) patients with granulin (GRN) mutations (FTD-GRN). Previous studies by our group and others have observed that reduced PGRN perturbs lysosomal function and microglial activation, which is believed to accelerate neurodegeneration in FTD-GRN patients. Lysosomal function is intrinsically linked to lipid metabolism, and evidence suggests that GRN deficiency can alter lipid profiles in the brain. Unfortunately, studies to date have focused on whole brain or cortical extracts, limiting our ability to assess cell type-dependent changes in lipid metabolism under disease conditions. Here, we employed lipidomic analysis specifically within the pontine microglia of Grn knock-out (KO) mice, a cell population that was previously linked to disease phenotypes in this model. We observed a significant reduction in the endolysosomal lipid bis(monoacylglycero)phosphate (BMP) and the lipid metabolite phosphatidylethanolamine (PE); these microglial-specific lipid alterations mirror previous whole-brain findings, suggesting that similar changes may occur across multiple cell types in the brain. We also detected a significant increase in the myelin-composing factor galactosylceramide (GalCer), which may reflect an aberrant accumulation of myelin debris within microglia that arises due to defective lysosomal clearance. Notably, lipid perturbations were exacerbated with age within Grn KO microglia, suggesting that changes in lipid metabolism are both age- and genotype-dependent in this model. Together, our results support our hypothesis that PGRN acts as a master regulator of critical microglial processes - including lysosomal function, lipid metabolism, and the regulation of myelination - in an age-dependent manner.

BackgroundNeuromelanin (NM) is a pigment that progressively accumulates with age in catecholaminergic neurons, particularly in the substantia nigra, ventral tegmental area, and locus coeruleus. These neuronal populations are especially vulnerable to degeneration in Parkinsons disease (PD). Elevated intracellular NM levels have been linked to neurodegeneration and PD-like phenotypes in experimental models. However, the molecular mechanisms underlying NM-induced pathology remain poorly understood, as human studies cannot disentangle the specific effects of NM accumulation from those of normal aging. MethodsWe performed transcriptomic microarray analysis on laser-captured catecholaminergic neurons and regions (substantia nigra, ventral tegmental area, locus coeruleus) from NM-producing transgenic mice (tgNM) and NM-free wild-type controls across different ages, and compared them to data from postmortem human brain tissue. One of the molecular targets identified, GPNMB, was validated in mouse and human tissue, and functionally tested in vivo. ResultsWe identified region- and age-dependent transcriptional changes associated with progressive NM accumulation. NM consistently upregulated neuroinflammatory pathways with enrichment of disease-associated microglial genes, while downregulating transcription, translation, and mitochondrial functions. Locus coeruleus exhibited the earliest and strongest transcriptional alterations, whereas substantia nigra and ventral tegmental area showed a later-onset, age-progressive transcriptional dysfunction. Neuron-specific analyses revealed that many changes originated within NM-containing neurons rather than being solely glial-driven. NM-driven transcriptional profiles in mice strongly correlated with postmortem data from PD patients, underscoring their translational relevance. Among molecular targets, the glycoprotein GPNMB was consistently upregulated in NM-containing neurons and validated at RNA and protein levels in both NM-producing transgenic mice and human PD brains. Functional experiments demonstrated that GPNMB overexpression attenuated NM-linked dopaminergic neurodegeneration and improved motor performance in mice. ConclusionThis study provides a comprehensive in vivo characterization of NM-specific transcriptomic changes in catecholaminergic neurons, showing that NM accumulation drives neuroinflammatory and neurodegenerative programs. Our results support that the neuroinflammatory changes observed in tgNM mice and in human PD represent early pathological events that precede overt neurodegeneration. The disease-associated gene GPNMB emerged as a conserved NM-induced factor with protective properties, highlighting its potential as a therapeutic target in PD and aging-related neurodegeneration.

BackgroundAggregated alpha-synuclein (syn) phosphorylated at serine 129 (PS129) accumulates in synucleinopathies, with the olfactory bulb (OB) being severely affected. Non-aggregated physiological PS129 is abundant in the mammalian OB, where it likely modulates syn-protein interactions. The impact of aggregation on the PS129 interactome in the OB remains unclear. We hypothesized that syn aggregation alters the PS129 interactome, shifting canonical synaptic partners (e.g., SNARE proteins) toward the aggregate-associated network. To test this hypothesis, we mapped PS129 interactions in the OB of PFF-injected WT and SNCAA53T/A53T (M83) mice using biotinylation by antibody recognition (BAR) and pretreated with calf-intestine alkaline phosphatase (CIAP) to distinguish physiological from aggregate-associated PS129 interactomes. Seeding and spread were assessed by immunohistochemistry and in situ seeding immunodetection assay (isSID). ResultsFollowing OB-PFF injections, CIAP-resistant aggregates and seeds were detected throughout the neuroaxis of M83 mice (e.g., OB to brainstem) but less so in WT mice. isSID seeding was concentrated near CIAP-resistant aggregates, but the overlap was only partial. BAR-PS129 identified 2,309 proteins in M83 OBs and 990 proteins in WT OBs. Of these, 357 proteins in M83 mice and 247 proteins in WT mice were associated with the CIAP-resistant, aggregate-enriched PS129 fraction. In both models, the CIAP-resistant interactome largely overlapped with the broader PS129 interactome, suggesting that seeded aggregation primarily affects existing PS129 interactions rather than directing the formation of new pathological ones. A conserved 107-protein CIAP-resistant signature shared between M83, and WT mice was enriched for axon-glia adhesion, myelin-associated, axonal/cytoskeletal, proteostatic, and synaptic vesicle-related proteins. ConclusionAggregated PS129 engages a subset of PS129 networks enriched at axon-glial interfaces. CIAP-resistant aggregates were partially associated with seed competency, indicating that CIAP resistance and seed competency are related but not equivalent. These results provide molecular details of syn seeding and spread from the OB.

Amyotrophic Lateral Sclerosis (ALS) is a phenotypically diverse neurodegenerative disorder characterized by the degeneration of motor neurons, ultimately resulting in loss of motor function. Currently, patients are classified based on clinical factors which does not fully capture the heterogeneity. Using the Olink Explore HT, we pro-filed ~5400 plasma proteins in ALS patients (n = 235) from the ALSrisc Study at Karolinska Institutet, Sweden, and applied consensus clustering, which revealed three patient subgroups significantly differing in survival outcome. Weighted gene correlation network analysis (WGCNA) and gene ontology (GO) analysis identified protein modules related to biological functions including cellular stress response and Rho-GTPase activity for the shorter surviving patient group. Cell-type enrichment analysis indicating a broad cellular origin of the circulating proteome, with contributions from nervous system cells, vascular cells, immune cells, and muscle cells. Our work highlights the potential of plasma proteomics for clinically meaningful patient stratification in ALS.

Lysosomes make key contributions to the maintenance of cellular proteostasis, and their functional compromise has been linked to aging and neurodegenerative disease. A defining characteristic of lysosomes is their relative acidity compared to other subcellular compartments, a quality that enables the efficient breakdown of macromolecules. Evidence suggests that neuronal lysosomal pH becomes dysregulated with aging and neurodegenerative disease, yet the mechanisms by which lysosomal pH is maintained remain incompletely understood. To better understand neuronal lysosomal pH regulation, we conducted a genome-wide CRISPRi-based screen in iPSC-derived iNeurons for modifiers of lysosomal pH. We validated several previously known regulators of lysosomal pH and identified novel pathways capable of modifying lysosomal pH, including protein UFMylation and mitochondrial homeostasis. We demonstrate that loss of the lysosomal cationic amino acid exporter, PQLC2, prevents lysosomal acidification in a manner independent of amino acid transport. A novel, tauopathy-associated mutation in PQLC2 impairs lysosomal acidification and drives tau accumulation. Together, this study reveals novel genes that modify lysosomal pH and highlights potential new targets for ameliorating age-related lysosome dysfunction.

Tauopathies are characterized by the accumulation and spread of pathogenic tau aggregates throughout the brain, a process that is increasingly recognized to involve not only neurons but also microglia. However, whether pathogenic MAPT directly alters microglial degradative capacity remains poorly understood. Here, using isogenic human induced pluripotent stem cell-derived microglia carrying the pathogenic MAPT IVS10+16 mutation, we identify tau as a regulator of microglial lysosomal function. MAPT IVS10+16 microglia exhibited coordinated suppression of lysosomal and autophagic pathways, reduced lysosomal protease abundance and activity, and impaired autophagosome-lysosome fusion. Mutant microglia also showed reduced uptake of extracellular tau aggregates, reduced tau accumulation in acidic compartments, and a blunted lysosomal response to proteopathic stress. Conversely, genetic loss of MAPT increased lysosomal degradative capacity and accumulation of extracellular tau aggregates within acidic compartments, supporting a cell-intrinsic role for endogenous tau in regulating microglial degradative function. Pharmacologic enhancement of the autophagy lysosome pathway in MAPT IVS10+16 microglia increased proteolytic activity and improved tau handling. Together, these findings reveal a reciprocal relationship between tau and microglial lysosome function and identify degradative capacity as a modifiable component of the microglial response to tau pathology.

Tauopathies encompass diverse neurodegenerative diseases unified by aberrant patterns of tau deposition in brain. Although most appear sporadic, some are linked to genetic etiologies that offer unique mechanistic insights. Here we report that X-linked Dystonia-Parkinsonism (XDP), caused by a non-coding retrotransposon-associated repeat insertion in TAF1, involves a significant imbalance of tau isoforms and the accumulation of hyperphosphorylated, four-repeat tau in the brain. In striatal tissue, both misfolded tau accumulation, predominantly in astrocytes, and MAPT exon 10 inclusion correlated with repeat length within the causal insertion. Transcriptomic profiling across brain regions revealed dysregulation of known tau-related pathways. Levels of phosphorylated tau181, glial fibrillary acidic protein, and neurofilament light chain were elevated in patient plasma and discriminated XDP from controls. These findings implicate defective tau proteostasis as a key pathogenic mechanism and position XDP as a genetic model for uncovering cellular drivers that may disrupt tau in other more common neurodegenerative diseases.

BackgroundParkinsons disease (PD) is driven by -synuclein (-syn) aggregation and affects vulnerable dopaminergic and GABAergic neurons, and its incidence rises dramatically with age. In our -syn mouse model, motor impairment required both syn oligomers and the aging milieu, and pharmacological inhibition of the age hyperactivated Rho GTPase CDC42 with CASIN fully restored motor function, yet the underlying transcriptional pathways mediating this rescue remain to be elucidated. MethodsWe used an inducible -syn oligomer PD mouse model across three age groups (6, 16, and 24 months) with four conditions per group: -syn non-induced (OFF), induced (ON), and each with CASIN treatment (OFF-CASIN, ON-CASIN). Brain tissue from one hemisphere (0 to -5 mm Bregma) was sequenced using 10x Genomics 3 Chromium, with 3-4 mice per condition of both male and female mice. ResultssnRNA-seq demonstrated that CASIN robustly reverted PD-related transcriptional alterations at 24 months whereas aging-related changes were strongest at 16 months. Network and pathway analyses identified CASINs mode of action on two major downstream signaling cascades--MAPK and PI3K/AKT-- in the context of aging and MAPK signaling in PD. ConclusionConvergent gene-, transcription factor-, pathway-, and network-level evidence points to EGFR-PI3K-MAPK signaling as the axis through which CASIN may restore mitochondrial and synaptic function in PD and aging

INTRODUCTIONMicroglia regulate amyloid plaque-associated microenvironments that contribute to downstream tau pathology in Alzheimers disease (AD). Variants within the MS4A locus are strongly associated with AD risk and resilience and are linked to microglial biology; however, the functional role of MS4A4A in plaque-associated tau pathology remains poorly understood. METHODSSingle-nucleus RNA sequencing (snRNA-seq) was performed on hippocampi from non-transgenic, Ms4a4a knockout (4A-KO), 5xFAD, and 5xFAD 4A-KO mice at 6 months of age. To assess plaque-associated tau pathology, AD-derived tau aggregates were injected into the hippocampus of 5xFAD and 5xFAD 4A-KO mice at 6 months, and histological analyses were performed 3 months later. RESULTSAmyloid pathology was the dominant driver of microglial state transitions, while Ms4a4a loss selectively remodeled activated microglial transcriptional programs enriched for interferon, lysosomal, autophagic, and proteostatic pathways. Activated microglia from 5xFAD 4A-KO mice exhibited altered expression of genes linked to immune signaling and protein handling. Following AD-tau inoculation, Ms4a4a loss did not significantly alter overall phospho-tau burden but selectively reduced dense-core plaque-associated neuritic plaque tau (NP-tau), particularly in the contralateral hemisphere. This phenotype was strongest surrounding X-34-positive fibrillar plaques and occurred without major changes in plaque-associated microgliosis. DISCUSSIONThese findings identify Ms4a4a as a regulator of plaque-associated microglial programs linked to NP-tau accumulation in the amyloid-bearing brain. More broadly, this work supports a model in which AD resilience-associated microglial pathways selectively shape plaque-associated microenvironments that promote downstream tau pathology.

Frontotemporal lobar degeneration (FTLD), predominantly comprised of tau and TDP-43 proteinopathies, is a common cause of early-onset dementia. Biomarkers that reliably classify FTLD subtypes are limited, thereby hindering in-vivo diagnosis and clinical trial stratification. We conducted large-scale, multi-platform cerebrospinal fluid proteomics in 566 individuals, including 274 FTLD-spectrum (48 autopsy-confirmed FTLD-TDP, 90 autopsy-confirmed FTLD-tau), 171 Alzheimers disease, and 95 controls. In neuropathological subtype contrasts, elevated matrix metalloproteinase MMP10 classified Picks disease (PiD) versus other subtypes with near-perfect accuracy across proteomic platforms. We further validated CSF MMP10 as a potential PiD diagnostic biomarker via a targeted immunoassay in an independent, autopsy-confirmed FTLD cohort. Post-synaptic proteins HOMER1 and DLG4 exhibited elevations across FTLD-TDP subtypes (A, B, and C) versus FTLD-tau. Network analysis identified RNA metabolism and pro-inflammatory signatures in FTLD-TDP, and cytoskeletal and heat shock signatures in progressive supranuclear palsy. These findings reveal candidate diagnostic biomarkers and proteomic pathways underlying FTLD clinico-pathological heterogeneity.

Frontotemporal lobar degeneration (FTLD) encompasses clinically and biologically heterogeneous syndromes that are unlikely to be captured by a single blood biomarker. Although plasma neurofilament light (NfL) chain reflects neuroaxonal injury, multiplex profiling may identify complementary inflammatory, vascular and proteostatic processes relevant to clinical phenotype and progression. We characterised plasma CNS-related and inflammatory proteomic signatures across FTLD-related clinical syndromes and tested their associations with neuroaxonal injury, clinical severity, regional brain atrophy and survival. Plasma samples from 177 participants with behavioural variant frontotemporal dementia (bvFTD), primary progressive aphasia (PPA), progressive supranuclear palsy (PSP) or corticobasal syndrome (CBS) and 67 healthy controls were analysed using the high-sensitivity nucleic acid-linked immuno-sandwich assay (NULISA) platform. We quantified 130 CNS-related and 250 inflammation-related proteins. Differential expression and multivariate classification analyses were complemented by hierarchical clustering, penalised regression and survival analyses. Canonical correlation analysis tested multivariate associations between disease-associated proteins and regional MRI brain volumes. Sixty-one CNS-related and 61 inflammation-related proteins differed between participants with FTLD-related syndromes and controls after false-discovery-rate correction. NfL was the strongest individual discriminator between all patients and controls, with an area under the receiver operating characteristic curve of 0.91. In exploratory full-cohort models, the multivariate CNS signature achieved an area under the curve of 0.93, compared with 0.82 for the multivariate inflammation signature. However, inflammatory proteins provided stronger discrimination for selected syndrome comparisons, including PPA versus PSP. Among inflammation-related proteins, SPP1 and CD276 showed the strongest positive associations with NfL. Higher CD276 and SPP1 were associated with increased mortality, whereas higher amyloid-{beta}42 was associated with lower mortality. A multivariate protein signature weighted towards tumour necrosis factor and immune signalling was associated with lower regional brain volumes across predominantly frontotemporal and limbic regions (canonical correlation 0.43; permutation p=0.018). Plasma multiplex proteomics identified complementary dimensions of neuroaxonal injury and immune dysregulation across frontotemporal lobar degeneration-related syndromes. CNS-related proteins, particularly NfL, predominantly captured case-control neurodegeneration, whereas inflammatory signatures provided additional information about syndrome heterogeneity, structural brain changes and survival. SPP1, CD276 and broader immune-related signatures are candidates for independent biomarker validation and mechanistic investigation.

The complement system, a proteolytic cascade crucial for innate immune system function, is dysregulated in brain aging and neurodegenerative diseases, including Alzheimer Disease (AD). In models of AD, complement proteins, including C1q and C3, are upregulated and mediate microglial clearance of amyloid plaques and pruning of synapses. Among complement genes, C4b, which in mice encodes complement protein C4, is the most highly upregulated in astrocytes in the setting of aging and amyloid pathology. While C4 plays a key role in the complement cascade, there have been no investigations of the direct role of C4 in regulating AD pathology. To probe the function of C4 in amyloid plaque-related pathology, we crossed a germ line C4b knockout mouse (C4 KO) to the 5XFAD mouse model of AD-related amyloidosis. To our surprise, we observed striking reductions in amyloid plaque pathology across multiple brain regions in 5XFAD-C4 KO mice relative to standard 5XFAD controls. This reduction in plaque burden stands in sharp contrast to previous reports of C3 deletion in AD models, which increases plaques. Additionally, we observed a reduction in neuroinflammation and peri-plaque glial clustering in 5XFAD-C4 KO mice, suggestive of a role for C4 in regulating overall neuroinflammatory tone in AD. Finally, we observed a phenotypic shift of the peri-plaque microglia to a more reactive disease-associated microglia (DAM) phenotype, indicating that C4 could be an important factor in regulating microglial reactivity in AD. Altogether, our results demonstrate that C4 may have functions beyond the classical complement cascade and may serve as a key facilitator of AD-related glial function and pathology and a possible target for therapeutic modification.

Astrocytes are among the earliest cells to exhibit dysfunction in Alzheimers disease (AD), developing profound calcium signalling deficits before amyloid plaques have formed, yet the underlying mechanisms remain unknown. Lysosomal dysfunction is a hallmark of AD, but whether it initiates this early functional impairment or arises as a consequence of established pathology remains unresolved. Here, we find that astrocytic cytosolic calcium activity is suppressed prior to amyloid plaque deposition and is accompanied by reduced lysosomal acidification in vivo. Using a lysosome-targeted calcium indicator selectively expressed in astrocytes, we directly visualise lysosomal calcium dynamics in vivo and reveal a profound early loss of lysosomal calcium release, identifying lysosomal failure as an initiating event in astrocyte dysfunction in AD. Reduced expression of the lysosomal calcium channel TRPML1 provides the mechanistic basis for this deficit. Astrocyte-specific restoration of TRPML1 expression rescues lysosomal homeostasis and cytosolic calcium signalling and prevents astrocyte reactivity and morphological hypertrophy. Strikingly, early TRPML1 restoration prevents both the initial calcium hypoactivity observed before plaque formation and the later hyperactivity that characterises post-plaque disease, demonstrating that lysosomal calcium homeostasis stabilises astrocyte function across the disease trajectory. TRPML1 restoration also reduces amyloid plaque burden, indicating that astrocytic lysosomal competence directly shapes disease pathology. These findings identify lysosomal calcium failure as an early organelle-level mechanism linking amyloid stress to astrocyte dysfunction in AD, and position TRPML1-mediated lysosomal calcium signalling as a tractable target for limiting disease progression.

Neuroinflammation is a hallmark of several chronic neurodegenerative disorders, including Parkinson's disease (PD) and other synucleinopathies, and is closely associated with microglial activation. The inflammasome adaptor protein apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (ASC) undergoes oligomerization upon inflammasome activation, resulting in the formation of ASC specks. These structures are recognized by microglia as damage-associated molecular patterns (DAMPs), thereby promoting inflammatory signaling. Recent studies have demonstrated that extracellular ASC specks associate with amyloid-{beta} (A{beta}), and that uptake of ASC-A{beta} composites by microglia amplifies pro-inflammatory responses. Although ASC specks have also been shown to potentiate -synuclein (Syn) preformed fibril-induced pathology, their interaction with monomeric Syn and their effects on inflammasome activation remain poorly understood. Here, we co-stimulated murine SIM-A9 microglia with ASC-Syn assemblies and evaluated their effects on NLRP3 inflammasome activation. Electron microscopy revealed a close association between ASC fibrils and Syn monomers. Exposure of microglia to ASC-Syn enhanced NLRP3 inflammasome activation, as evidenced by increased ASC speck formation, caspase-1 activation, and secretion of IL-1{beta} and IL-18, when compared to ASC or Syn alone. In addition, immunohistochemical analyses of post mortem brain tissue from patients with dementia with Lewy bodies demonstrated ASC expression in regions exhibiting Syn pathology and showed ASC co-localization with Syn within Lewy bodies. Collectively, these findings identify ASC-Syn assemblies as potent amplifiers of NLRP3 inflammasome signaling and suggest a mechanism through which they may contribute to sustained neuroinflammation in synucleinopathies.

Genetic variation in APOE, which encodes a lipid transporter apolipoprotein E (apoE), is the strongest risk factor for late-onset Alzheimer's disease (AD). Although central nervous system (CNS) apoE is produced by various cell types, including astrocytes, microglia, and pericytes, it is unclear whether apoE lipoproteins are a homogeneous population or if their molecular composition varies depending on their cellular origin. Emerging evidence suggests that CNS apoE lipoproteins contribute to AD-related processes, including amyloid deposition, neuroinflammation, synaptic maintenance, and blood-brain barrier function in a cell type-specific manner. We hypothesized that the compositions of CNS apoE lipoproteins depend on their cellular origin and investigated the lipid and protein profiles of apoE particles secreted by induced pluripotent stem cell (iPSC)-derived brain cells and derived from human cerebrospinal fluid (CSF) using liquid chromatography-mass spectrometry (LC-MS/MS). Our results demonstrate that astrocytes, pericytes, and microglia secrete apoE lipoproteins with distinct, cell type-specific lipid and protein profiles. Astrocyte-secreted particles were enriched in sphingomyelins and proteins linked to lipid metabolism, whereas pericyte-secreted particles contained ether-linked phospholipids and proteins associated with antioxidant activity. The lipidation of microglial apoE was markedly lower, but these particles had higher levels of transferrin, apoC-II, and cathepsin D. Notably, one-third of identified features were cell type-specific, highlighting the substantial molecular specialization across cell types. Most lipids and proteins identified in cell-secreted apoE were also detected in CSF-derived particles. Our findings advance the understanding of apoE biology by shifting the focus from apoE as a single, homogeneous entity to a diverse population of complex particles, the composition of which might be linked to functions in health and neurodegenerative diseases.

INTRODUCTION: Understanding concordance across biofluids and platforms is critical for understanding neurodegenerative biomarkers results and translating them into clinical use; yet systematic comparisons remain limited. To address this gap, we performed large-scale proteomic profiling of patient-paired plasma and CSF to characterize cross-modal relationships. METHODS: We profiled paired plasma and CSF from 67 individuals using SomaScan 11K and NULISAseq CNS panels. Disease severity was assessed with the CDR+NACC FTLD-M Global Score. RESULTS: We identified 269 SomaScan and 18 NULISA proteins with significant cross-biofluid correlation. Cross-platform concordance within biofluids was strong. NEFL, NPTX2, TREM2, and CHIT1 demonstrated consistent cross-platform agreement. Associations with disease severity were compartment-specific, with decreased NPTX2 in CSF, increased NEFL and GFAP in plasma, and decreased TREM2 across biofluids. DISCUSSION: Cross-platform consistency supports biomarker robustness, while limited cross-biofluid concordance highlights compartmental biology. Given additional clinical correlations despite varying underlying pathology, these findings may point to shared neurodegenerative disorder pathways.

Signal peptide peptidase-like 2b (SPPL2b) is a brain-enriched intramembrane protease implicated in synaptic function, immune signaling, and neuronal development, but its physiological role in brain and neuronal homeostasis remains poorly understood. We investigated the impact of constitutive Sppl2b deletion on the brain proteome and neuronal function using quantitative shotgun proteomics in cortex and hippocampus from wild-type and SPPL2b-deficient mice at 3 and 12 months, combined with western blot, immunofluorescence, dendritic spine analysis, and behavioral testing. SPPL2b deficiency was associated with alterations in biological processes linked to axonal transport and synaptic vesicle trafficking, including consistent upregulation of the kinesin motor protein KIF1A and vesicle-associated membrane protein 2 (VAMP2). SPPL2b deletion also attenuated age-associated proteomic changes in synaptic pathways and was accompanied by increased dendritic spine density, morphological remodeling of pyramidal neurons, increased locomotor activity, and reduced anxiety-like behavior. These findings reveal a previously unrecognized association between SPPL2b and synaptic proteome remodeling during aging and nominate SPPL2b-dependent pathways as candidates for further mechanistic and functional investigation in neurodegenerative disease.

Importance Alzheimer disease (AD) is frequently accompanied by co-pathologies such as Lewy bodies, intracellular protein aggregates consisting of misfolded -synuclein, ubiquitin and several other proteins. These aggregated proteins contribute to the pathological and clinical heterogeneity of AD and are associated with a more rapid progression. Cerebrospinal fluid (CSF) measurement of aggregated -synuclein or skin biopsy histochemistry are the current biomarkers for Lewy body pathology in individuals with Parkinson's disease and related synucleinopathies but are invasive, not easily scalable for large studies or practical in clinical practice. Neuron-derived extracellular vesicles (nEVs) provide a feasible and tolerable alternative to detect Lewy body pathology. nEVs exit across the blood-brain barrier and deliver neuron-derived proteins into the systemic circulation, offering direct access to brain-level protein concentrations from peripheral blood, not afforded by conventional plasma biomarkers. Objective To use nEVs extracted from plasma to measure brain-derived -synuclein levels as a clinical biomarker of Lewy body pathology and synucleinopathy across clinically and pathologically characterized cohorts. Design, Setting, and Participants This multicohort observational study evaluated plasma nEV-derived -synuclein levels in 1,304 individuals, including 794 (61%) individuals without dementia, 469 (36%) individuals with AD, and 41 (3%) individuals with PD across four cohorts. Postmortem validation was performed from autopsy data in 127 individuals, including 96 (76%) individuals without, and 31 (24%) with, Lewy body pathology. Cerebrospinal fluid (CSF) -synuclein seed amplification assay data were available in a small subset of 54 (4.1%) of the group. Amyloid positron emission tomography (PET) data were available in 901(69.1%) of the total group. Exposure Clinical diagnosis, AD biomarker positivity, Lewy body pathology, CSF -synuclein seed assay status, and amyloid PET positivity. Main Outcomes and Measures Plasma nEV-derived -synuclein levels normalized to CD9 and assessed in relation to clinical diagnosis, AD biomarker status, neuropathologically confirmed Lewy body pathology, CSF seed assay results, and amyloid PET positivity. Results Compared with controls, plasma -synuclein levels from nEVs were significantly elevated among individuals with PD (controls mean 0.51, SD=0.24 vs PD mean=0.69, SD=0.23, P=8.66*10-). nEV-derived -synuclein levels were also significantly higher in P-tau181 and P-tau217 positive individuals with and without cognitive impairment compared to P-tau negative individuals. Elevated nEV-derived -synuclein levels were subsequently validated in individuals with postmortem Lewy body pathology (28.6% higher mean levels, P=0.02). Among 54 individuals with CSF -synuclein seed amplification assay, 8 (15%) were positive and showed a 18.2% increase in mean nEV -synuclein levels compared to individuals with negative -synuclein seed amplification. nEV-derived -synuclein levels were also significantly elevated in amyloid PET positive individuals with and without dementia (5.8% higher mean levels, P=8.50E-03) and clinical AD (9.3% higher mean levels, P=6.38E-12). Conclusions and Relevance Plasma -synuclein levels from nEVs likely reflect underlying synuclein pathology in the brain and have potential as a blood-based biomarker for detecting Lewy body pathology in PD and in AD and related dementias. nEVs cross the blood-brain barrier and carry neuron-derived cargo directly into the bloodstream, thus providing a unique window into brain -synuclein levels that is not accessible through conventional plasma biomarkers.

The human ABCA7 gene, which encodes ATP-binding cassette transporter A7 (ABCA7), is one of the strongest genetic risk factors for late-onset Alzheimers disease (AD), yet the molecular mechanisms linking ABCA7 deficiency to AD remain incompletely understood. Because impaired insulin signaling and neuroinflammation are increasingly recognized as key contributors to AD pathogenesis, and ABCA7 has been implicated in both metabolic and immune processes, we investigated whether ABCA7 deficiency is associated with alterations in these pathways using comparative brain proteomics. Whole-brain proteomes from wild-type, Abca7 knockout, AD model (APP), and APP- Abca7 knockout mice were analyzed at 50, 100, 150, and 200 days of age using label-free quantitative proteomics, followed by differential abundance analysis, gene ontology enrichment, subcellular localization analysis, protein-protein interaction network analysis, and comparison with human AD brain proteomic datasets. Comparative analyses identified age-dependent proteomic alterations associated with Abca7 deficiency, amyloid-beta pathology, and their interaction. Across all genotype comparisons, recurrently altered proteins and functional interaction networks consistently converged on insulin receptor and PI3K/AKT signaling, MAPK signaling, immune and complement pathways, vesicle trafficking and acidification, and the ubiquitin-proteasome system. Subcellular enrichment analysis further indicated preferential involvement of membrane-associated proteins, consistent with the established role of ABCA7 in membrane lipid transport and trafficking. Comparison with human AD proteomic data demonstrated substantial overlap while also identifying potentially novel proteins associated with Abca7deficiency in our mouse models. Together, these findings provide a systems-level characterization of the brain proteomic consequences of Abca7 deficiency and suggest that dysregulation of interconnected metabolic, immune, and vesicle-associated pathways may contribute to AD-related brain pathology.

Neurofibrillary tangles (NFTs) are a hallmark of Alzheimer's disease. However, the molecular basis underlying their spatial heterogeneity and biochemical complexity remain unclear. To address this, we performed mass spectrometry-based proteomic profiling of two neocortical regions with different susceptibilities to NFT pathology -- the inferior temporal (IT) and middle frontal (MF) cortices -- from 27 autopsy cases stratified by Braak stage (0-II, n=8; III-IV, n=11; V-VI, n=8). Brain homogenates were sequentially fractionated using buffers of increasing solubility (TBS, Na2CO, and Urea), followed by trypsin digestion and analysis by nanoLC-MS/MS with data-independent acquisition. Proteins were identified using PEAKS Studio 12 and linear mixed-effects models were applied to assess Braak stage-associated changes in protein abundance and solubility. A total of 5,573 protein groups were identified, including 452 differentially expressed proteins (DEPs), 183 bidirectional expression proteins (BEPs), and 693 differentially soluble proteins (DSPs) associated with NFT pathology. These proteins were enriched in pathways related to cytoskeletal organization, metabolism, vesicular trafficking, and proteostasis. Marked regional differences were observed, with limited overlap between IT and MF across DEPs, BEPs, and DSPs. Protein change in MF was dynamic with a higher number of BEPs and suggested active cytoskeletal remodeling, whereas IT showed fewer BEPs and evidence of structural disruption, including alterations in intermediate filament components, consistent with vulnerability of IT and possible compensatory/plasticity changes in MF cortex. MF cortex had the greatest downregulation of DEPs between Low and Mid Braak stages, while the transition from Mid to High Braak stage showed upregulation of most of DEPs in both regions. In addition, widespread changes in protein solubility were observed, particularly decreased solubility at later Braak stages, implicating disruption of proteostasis. Together, these findings highlight region- and stage-dependent proteomic alterations associated with tau pathology and underscore their relevance for understanding disease mechanisms and informing biomarker development.