Biology subjects

Zerr, I.

Publications and source records attributed to Zerr, I..

10 recordsLinked to original sources

bioRxiv2025

Tau oligomer heterogeneity and associated protein profile in slowly versus rapidly progressive Alzheimer's disease

Rapidly progressive Alzheimers disease (rpAD) is a rare but devastating clinical variant characterized by abrupt cognitive decline, yet the molecular features underlying this phenotype remain unknown. Tau oligomers (TauO) are key mediators of tau toxicity, but whether their biochemical properties differ across AD subtypes has not been examined in human brain. We isolated endogenous TauO from frontal cortex of well-characterized control, slowly progressive AD (spAD), and rpAD cases using T22 immunoprecipitation and performed ultrastructural, biochemical, and proteomic characterization. rpAD TauO displayed compact, densely aggregated morphology and exhibited the highest levels of disease-associated phosphorylation (pS396, pS422). Label-free proteomics revealed that control and spAD shared a robust TauO interactome enriched for translation, proteostasis, mitochondrial metabolism, and vesicle trafficking. Strikingly, these modules were absent in rpAD, which instead showed selective enrichment for aldehyde detoxification, amino-acid and carbon metabolism, and actin-regulatory pathways. rpAD TauO demonstrated increased association with SERPINA1, ALDH9A1, MAPRE3, DPYSL2/3, and NFASC, and reduced association with MRPL17 and C9. Functionally, rpAD TauO induced the strongest toxicity in SH-SY5Y cells. Together, these findings indicate that rpAD likely harbors a biochemically distinct TauO species, defining a molecular signature that may underpin its fulminant clinical progression and support the development of subtype-specific therapeutic strategies.

neuroscience↗

bioRxiv2025

Proteomic and Kinetic Characterization of Prion Seeding in Distinct Human CJD Strains Unveils Early Diagnostic Biomarkers

To enhance understanding of early diagnosis, differential disease progression rates, and the molecular profiles of human prion strains, we analyzed prion seeding activity over time in Creutzfeldt-Jakob disease (CJD)-infected mice using the real-time quaking-induced conversion (RT-QuIC) assay. Our previous work highlighted pre- clinical alterations in endocytic machinery and cytoskeleton-associated responses in CJD-affected brain regions. In this study, infectious prion strains derived from human CJD-MM1 and VV2 brain tissues were inoculated into tg340, tg361 (expressing approximately four times the human PrP-M129 and PrP-V129, respectively), and tg650 (expressing approximately six times the human PrP-M129) mice. A total of 188 brain samples (cortex) were analyzed from confirmed CJD-infected mice and control mice at both pre-clinical and clinical stages of the disease. Notably, we observed region- specific and PrP strain-specific differences in seeding activity at the pre-clinical stage of disease in CJD-MM1 and VV2 infected mice. The lag phase between the positive response ranged from 7.5 to 24.5 hours across all regions and disease stages. In the cortex, CJD-MM1-infected tg340 mice exhibited a prolonged lag phase ([~]24.5 hours), while CJD-VV2-infected tg341 mice showed minimal seeding response and relative fluorescence unit (RFU) signal rates. In contrast, the cerebellum of VV2 clinical stage mice exhibited a shorter lag phase, and VV2 preclinical stage mice showed significantly lower RFU signal rates. Proteomic profiling via SWATH-MS identified 500 and 682 differentially expressed proteins in the MM1 and VV2 models, respectively. Key proteins such as Gnl1, Stxbp1, Pllp, Gps1, Nefh, Ahsa1, Rala, Cacybp, Pdk1, Unc13a, Rab21, Rraga, Ppp1r9a, Eif4b, Atp2b2, Vps51, H2afx in CJD-MM1 and Gm10358, Tnc, Calb2, Ppm1h, Dnaja1, Gm45808, Hpcal1, Prkca, Dock3, Syn2, Agap2, Tmem126a, Fdps, Ndufa4 in CJD- VV2 showed significant alterations at the early pre-clinical stages, correlating with detectable prion replication. These molecular shifts highlight potential early-stage diagnostic biomarkers. Functional analyses revealed that both MM1 and VV2 subtypes engage early compensatory responses; however, MM1 primarily involves metabolic reprogramming and enhanced vesicle clearance, while VV2 is characterized by pronounced disturbances in calcium signaling and structural integrity at early stage of the disease. These findings emphasize the utility of RT-QuIC and proteomics in characterizing prion seeding and progression, providing valuable insights into the molecular mechanisms underlying prion diseases and potential early diagnostic markers.

neuroscience↗

bioRxiv2025

Molecular and structural remodeling of stress granules in slowly and rapidly progressive Alzheimer's disease

Stress granules (SGs) are dynamic ribonucleoprotein condensates that modulate RNA metabolism during cellular stress. Although SG dysfunction has been increasingly linked to neurodegenerative diseases, their structural and molecular remodeling in Alzheimers disease (AD), particularly rapidly progressive AD (rpAD), remains poorly understood. Here, we present a comprehensive multi-omics characterization of SGs from postmortem frontal cortex tissues of control, slowly progressive AD (spAD), and rpAD subjects. SGs were immunoprecipitated using Anti-TIAR antibodies and analyzed via transmission electron microscopy (TEM), LCMS/MS-based proteomics, and RNA sequencing. Key protein findings were validated in human cortical brain homogenates and a 3xTg mouse model of A{beta} and tau pathology. TEM revealed disease-specific SG morphologies: small spherical granules in controls; moderate clustering in spAD; and large, amorphous aggregates in rpAD. Proteomic profiling identified 1,667 high-confidence SG-associated proteins, including RNA-binding proteins and disease-linked proteins such as MAPT, APP, and SNCA. SGs in rpAD were significantly enriched for pathways involved in MAPK signaling, proteostasis, and neuroinflammation, while showing reduced abundance of key cytoskeletal and translational regulators, such as TUBA1B and EEF1A2. Transcriptome analysis revealed widespread depletion of long, GC-rich, protein coding RNAs in rpAD SGs. Notably dynamic dysregulation of TUBA1B was also observed in the 3xTg mouse model and human cortical tissues, highlighting cytoskeletal vulnerability during disease progression. Together, these findings uncover profound structural and molecular remodeling of SGs in AD, with rpAD exhibiting a distinctive shift towards pathological SG composition and function. Our results highlight a link between SG alterations and aggressive AD subtypes, providing new mechanistic insights and suggesting new potential targets for therapeutic intervention.

neuroscience↗

bioRxiv2025

Gpnmb Defines a Phagocytic State of Microglia Linked to Neuronal Loss in Prion Disease

Neurodegenerative conditions can induce the region-specific emergence of cell states relevant to their pathogenesis. To identify such phenomena, we generated a spatiotemporal transcriptomic atlas of mice infected with the RML prion strain. Thalamus and cerebellum experienced severe neuronal loss, developed intense microgliosis and, starting from 30 weeks post-inoculation, accumulated a novel microglial subpopulation characterized by strong expression of Glycoprotein non-metastatic melanoma protein B (Gpnmb). Elevated GPNMB levels were detected in the cerebrospinal fluid of sCJD patients, suggesting its possible usefulness as a biomarker of disease progression. The transcriptional profile of Gpnmb+ microglia reflected a state of enhanced phagocytic activity with upregulation of genes associated with lysosomal function, including vacuolar ATPase V0 domain subunit d2 (Atp6v0d2) and Galectin-3 (Lgals3). In microglia-like murine BV2 cells, Gpnmb upregulation was induced by soluble find-me signals released during apoptosis, but not by apoptotic bodies or prion accumulation. Likewise, human iPSC-derived microglia showed marked upregulation of GPNMB when co-cultured with apoptotic human neurons. Gpnmb ablation impaired the ability of BV2 cells to clear apoptotic cells, underscoring its role in maintaining microglial phagocytosis. Our findings define Gpnmb microglia as a distinct, apoptosis-driven phagocytic state, linking neuronal loss to microglial activation and positioning it as a key regulator of microglial responses to prion propagation.

neuroscience↗

bioRxiv2025

Detection of alpha synuclein seeding activity in tear fluid in patients with Parkinson's disease

Detection of alpha-synuclein seeding activity in tear fluid (TF) might provide a promising non-invasive biomarker for Parkinsons disease (PD) diagnosis. In this study, we applied the alpha-synuclein seeding amplification assay (aSynSAA) to detect misfolded alpha-synuclein (aSyn) aggregation in TF from PD patients. The discovery cohort included 11 PD patients and 13 controls, and the validation cohort consisted of 9 PD patients and 11 controls without synucleinopathies. The aSynSAA yielded positive results in over 55% of PD patients. These findings were confirmed in a second cohort, including patients with prion diseases as a negative control for synuclein pathology. Our results demonstrate for the first time the ability of aSynSAA to distinguish between PD and control groups in TF, with PD showing the highest seeding activity compared to prion disease and control groups. Further comparisons between cerebrospinal fluid (CSF) and TF samples from the same individuals revealed consistent seeding results across both biofluids. These findings highlight the potential of tear fluid as a novel, accessible medium for detecting Lewy body-specific misfolded synuclein aggregation in PD, which could aid in early diagnosis and disease progression monitoring.

neuroscience↗

bioRxiv2023

Cleavage site-directed antibodies reveal the prion protein in humans is shed by ADAM10 at Y226 and associates with misfolded protein deposits in neurodegenerative diseases

Proteolytic cell surface release ( shedding) of the prion protein (PrP), a broadly expressed GPI-anchored glycoprotein, by the metalloprotease ADAM10 impacts on neurodegenerative and other diseases in animal and in vitro models. Recent studies employing the latter also suggest shed PrP (sPrP) to be a ligand in intercellular communication and critically involved in PrP-associated physiological tasks. Although expectedly an evolutionary conserved event, and while soluble forms of PrP are present in human tissues and body fluids, neither proteolytic PrP shedding and its cleavage site nor involvement of ADAM10 or the biological relevance of this process have been demonstrated for the human body thus far. In this study, cleavage site prediction and generation (plus detailed characterization) of sPrP-specific antibodies enabled us to identify PrP cleaved at tyrosin 226 as the physiological and strictly ADAM10-dependent shed form in humans. Using cell lines, neural stem cells and brain organoids, we show that shedding of human PrP can be stimulated by PrP-binding ligands without targeting the protease, which may open novel therapeutic perspectives. Site-specific antibodies directed against human sPrP also detect the shed form in brains of cattle, sheep and deer, hence in all most relevant species naturally affected by fatal and transmissible prion diseases. In human and animal prion diseases, but also in patients with Alzheimers disease, sPrP relocalizes from a physiological diffuse tissue pattern to intimately associate with extracellular aggregates of misfolded proteins characteristic for the respective pathological condition. Findings and research tools presented here will accelerate novel insight into the roles of PrP shedding (as a process) and sPrP (as a released factor) in neurodegeneration and beyond.

neuroscience↗

bioRxiv2021

Ligands binding to the cellular prion protein induce its protective proteolytic release with therapeutic potential in neurodegenerative proteinopathies

The cellular prion protein (PrPC) is a central player in neurodegenerative diseases caused by protein misfolding, such as prion diseases or Alzheimers disease (AD). Expression levels of this GPI-anchored glycoprotein, especially at the neuronal cell surface, critically correlate with various pathomechanistic aspects underlying these diseases, such as templated misfolding (in prion diseases) and neurotoxicity and, hence, with disease progression and severity. In stark contrast to cell-associated PrPC, soluble extracellular forms or fragments of PrP are linked with neuroprotective effects, which is likely due to their ability to interfere with neurotoxic disease-associated protein conformers in the interstitial fluid. Fittingly, the endogenous proteolytic release of PrPC by the metalloprotease ADAM10 ( shedding) was characterized as a protective mechanism. Here, using a recently generated cleavage-site specific antibody, we shed new light on earlier studies by demonstrating that shed PrP (sPrP) negatively correlates with conformational conversion (in prion disease) and is markedly redistributed in murine brain in the presence of prion deposits or AD-associated amyloid plaques indicating a blocking and sequestrating activity. Importantly, we reveal that administration of certain PrP-directed antibodies and other ligands results in increased PrP shedding in cells and organotypic brain slice cultures. We also provide mechanistic and structural insight into this shedding-stimulating effect. In addition, we identified a striking exception to this, as one particular neuroprotective antibody, due to its special binding characteristics, did not cause increased shedding but rather strong surface clustering followed by fast endocytosis and degradation of PrPC. Both mechanisms may contribute to the beneficial action described for some PrP-directed antibodies/ligands and pave the way for new therapeutic strategies against devastating and currently incurable neurodegenerative diseases.

neuroscience↗

bioRxiv2019

Domain-specific quantification of prion protein in cerebrospinal fluid by targeted mass spectrometry

Therapies currently in preclinical development for prion disease seek to lower prion protein (PrP) expression in the brain. Trials of such therapies are likely to rely on quantification of PrP in cerebrospinal fluid (CSF) as a pharmacodynamic biomarker and possibly as a trial endpoint. Studies using PrP ELISA kits have reproducibly shown that CSF PrP is lowered in the symptomatic phase of disease, a potential confounder for reading out the effect of PrP-lowering drugs in symptomatic patients. To date it has been unclear whether the reduced abundance of PrP in CSF results from its incorporation into plaques, retention in intracellular compartments, downregulation as a function of the disease process, or other factors. Because misfolding or proteolytic cleavage could potentially render PrP invisible to ELISA even if its concentration were constant or increasing in disease, we sought to establish an orthogonal method for CSF PrP quantification. We developed a targeted mass spectrometry method based on multiple reaction monitoring (MRM) of nine PrP tryptic peptides quantified relative to known concentrations of isotopically labeled standards. Analytical validation experiments showed process replicate coefficients of variation below 15%, good dilution linearity and recovery, and suitable performance for both CSF and brain homogenate and across humans as well as preclinical species of interest. In N=55 CSF samples from individuals referred to prion surveillance centers with rapidly progressive dementia, all six human PrP peptides, spanning the N- and C-terminal domains of PrP, were uniformly reduced in prion disease cases compared to individuals with non-prion diagnoses. This confirms the findings from ELISA studies, demonstrating that lowered CSF PrP concentration in prion disease is a genuine result of the disease process and not merely an artifact of ELISA-based measurement. We provide a targeted mass spectrometry-based method suitable for preclinical and clinical quantification of CSF PrP as a tool for drug development.

neuroscience↗

bioRxiv2018

Age of onset in genetic prion disease and the design of preventive clinical trials

Regulatory agencies worldwide have adopted programs to facilitate drug development for diseases where the traditional approach of a randomized trial with a clinical endpoint is expected to be prohibitively lengthy or difficult. Here we provide quantitative evidence that this criterion is met for the prevention of genetic prion disease. We assemble age of onset or death data from N=1,094 individuals with high penetrance mutations in the prion protein gene (PRNP), generate survival and hazard curves, and estimate statistical power for clinical trials. We show that, due to dramatic and unexplained variability in age of onset, randomized preventive trials would require hundreds or thousands of at-risk individuals in order to be statistically powered for an endpoint of clinical onset, posing prohibitive cost and delay and likely exceeding the number of individuals available for such trials. Instead, the characterization of biomarkers suitable to serve as surrogate endpoints will be essential for the prevention of genetic prion disease. Biomarker-based trials may require post-marketing studies to confirm clinical benefit. Parameters such as longer trial duration, increased enrollment, and the use of historical controls in a post-marketing study could provide opportunities for subsequent determination of clinical benefit.

neuroscience↗

bioRxiv2018

Prion protein quantification in cerebrospinal fluid as a tool for prion disease drug development

Reduction of native prion protein (PrP) levels in the brain is an attractive and genetically validated strategy for the treatment or prevention of human prion diseases. However, clinical development of any PrP-reducing therapeutic will require an appropriate pharmacodynamic biomarker: a practical and robust method for quantifying PrP, and reliably demonstrating its reduction, in the central nervous system (CNS) of a living patient. Here we evaluate the potential of enzyme-linked immunosorbent assay (ELISA)-based quantification of human PrP in human cerebrospinal fluid (CSF) to serve as a biomarker for PrP-reducing therapeutics. We show that CSF PrP is highly sensitive to plastic adsorption during handling and storage, but its loss can be minimized by addition of detergent. We find that blood contamination does not affect CSF PrP levels, and that CSF PrP and hemoglobin are uncorrelated, together suggesting that CSF PrP is CNS-derived, supporting its relevance for monitoring the tissue of interest and in keeping with high PrP abundance in brain relative to blood. In a cohort with controlled sample handling, CSF PrP exhibits good within-subject test-retest reliability (mean coefficient of variation 13% in samples collected 8-11 weeks apart), a sufficiently stable baseline to allow therapeutically meaningful reductions in brain PrP to be readily detected in CSF. Together, these findings supply a method for monitoring the effect of a PrP-reducing drug in the CNS, enabling the development of prion disease therapeutics with this mechanism of action.

molecular biology↗