bims-proned Biomed News
on Proteostasis in neurodegeneration
Issue of 2026–01–04
thirteen papers selected by
Verena Kohler, Umeå University



  1. FEBS J. 2025 Dec 30.
      Protein aggregation and transmission are hallmarks of neurodegenerative diseases. Praja1 E3 ubiquitin ligase has been shown to suppress the aggregation of causative proteins in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, Parkinson's disease, Huntington's disease, and spinocerebellar degeneration, which include transactivation response DNA-binding protein of 43 kDa, fused in sarcoma, superoxide dismutase 1, α-synuclein, huntingtin, and ataxin-3. Aoki et al. demonstrated that Praja1 ubiquitinates and degrades tau, a key molecule in tauopathies such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy, and corticobasal syndrome, furthering our understanding of the role of Praja1 in neurodegenerative diseases and potential therapeutic approaches.
    Keywords:  Alzheimer's disease; Praja1 E3 ubiquitin ligase; neurodegeneration; tau; tauopathy
    DOI:  https://doi.org/10.1111/febs.70383
  2. Int J Mol Sci. 2025 Dec 17. pii: 12128. [Epub ahead of print]26(24):
      Alzheimer's disease (AD) is characterized by the accumulation and aggregation of tau and amyloid-β (Aβ). The pathophysiology and progression of AD are facilitated by the neurotoxic effects of these aggregated proteins, resulting in neurodegeneration and memory loss. In this context, the interaction between tau and Aβ42 is considered, but the mechanism underlying their pathogenic interplay remains unclear. Here, we addressed this question by studying the aggregation of full-length, unmodified tau and Aβ42 at physiologically low concentrations using atomic force microscopy (AFM). AFM imaging and data analyses demonstrate an increase in tau aggregation in the presence of Aβ42, characterized by increased sizes and number of aggregates. Importantly, tau aggregation occurs without the need for phosphorylation or any other post-translational changes. The analysis of the data demonstrates that tau and Aβ42 form co-aggregates, with no visible accumulation of Aβ42 aggregates alone. Given that the catalysis of tau aggregation by Aβ42 is observed at physiological low nanomolar concentrations of Aβ42, the finding suggests that such aggregation catalysis of tau by Aβ42 can be a molecular mechanism underlying the pathological tau aggregation process associated with the onset and development of Alzheimer's disease.
    Keywords:  AFM imaging; Alzheimer’s disease; aggregation; amyloid beta; tau
    DOI:  https://doi.org/10.3390/ijms262412128
  3. ACS Chem Biol. 2026 Jan 02.
      Aggregates of the protein α-synuclein may initially form in the gut before propagating to the brain in Parkinson's disease (PD). Indeed, our prior work supports that enteroendocrine cells, specialized intestinal epithelial cells, could play a key role in the development of this disease. Enteroendocrine cells natively express α-synuclein and form synapses with enteric neurons as well as the vagus nerve. Severing the vagus nerve reduces the load of α-synuclein aggregates in the brain, suggesting that this nerve is a conduit for gut-to-brain spread. Enteroendocrine cells line the gut lumen; as such, they are in constant contact with metabolites of the gut microbiota. We previously found that when enteroendocrine cells are exposed to nitrite─a potent oxidant produced by gut bacterial Enterobacteriaceae─a biochemical pathway is initiated that results in α-synuclein aggregation. Here, we detail the cellular and molecular mechanisms involved. First, we holistically profiled nitrite-exposed enteroendocrine cells through untargeted proteomics. Next, we performed targeted analyses that specifically probed the mechanistic role of dopamine, as our prior findings suggested that dopamine is critical for nitrite-induced α-synuclein aggregation. In dopamine-free HeLa cells treated with nitrite, α-synuclein aggregation was indeed suppressed. Proteomic signatures in dopamine-free cells treated with nitrite were distinct from those in nitrite-treated enteroendocrine cells, highlighting pathways relevant to intestinal development of PD. Intriguingly, we observed that enteroendocrine cells maintain viability upon exposure to nitrite and in the presence of α-synuclein aggregates. This cellular robustness suggests that these cells may be a reservoir of toxic α-synuclein aggregates. As a possible antidote, our findings show that benserazide and α-methyl tyrosine─chemical inhibitors of dopamine biosynthesis─limited aggregation. Curious about mechanisms of disease etiology outside of α-synuclein aggregation, we also profiled the enteroendocrine cell lipidome─an emerging area of interest in PD research─to motivate future targeted studies delineating the roles of dysregulated lipid metabolism in disease onset. Overall, these studies lay a foundation for mechanistically informed therapeutic targets to prevent the intestinal formation of α-synuclein aggregates before they spread to the brain.
    DOI:  https://doi.org/10.1021/acschembio.5c00686
  4. Neural Regen Res. 2025 Dec 30.
      Error-prone translation, resulting in inaccuracies in protein synthesis, is increasingly recognized as a critical contributor to proteostasis disruption and the pathogenesis of age-related neurological disorders. In recent years, numerous studies have elucidated that stochastic errors during mRNA translation may act as a molecular "tipping point" initiating pathogenic protein misfolding. A detailed analysis of how translation errors lead to protein misfolding, aggregation, and subsequent neurotoxicity will facilitate the identification of promising therapeutic targets for neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This article explores the contribution of mistranslation to proteostasis decline, focusing on the unique vulnerabilities of neuronal cells. We review the sources of translation errors, effects of ribosomal ambiguity and error-restrictive mutations, role of proteostatic mechanisms (such as molecular chaperones, ubiquitin-proteasome system, and unfolded protein response), and provide a unified perspective that links age-related translational infidelity to neurodegeneration. By synthesizing the most recent data obtained with genetically modified cellular and animal model studies, we highlight how age-associated decline in translational fidelity exacerbates proteostasis failure and propose potential therapeutic interventions targeting translation accuracy to mitigate neurodegeneration.
    Keywords:  aging; neurological disease; protein aggregation; protein misfolding; protein synthesis; proteostasis; ribosomal mistranslation; translation accuracy
    DOI:  https://doi.org/10.4103/NRR.NRR-D-25-00795
  5. STAR Protoc. 2025 Dec 27. pii: S2666-1667(25)00709-9. [Epub ahead of print]7(1): 104303
      The dynamics of the early steps of protein aggregation remain poorly understood, particularly in the case of α-synuclein (α-syn) aggregation, the hallmark of synucleinopathies. Here, we present a protocol that combines light-inducible protein aggregation (LIPA) with proximity biotinylation using an UltraID construct. We describe the workflow from protein expression to biochemical validation, including the purification of biotinylated proteins prior to liquid chromatography-mass spectrometry (LC-MS) analysis and subsequent validation. This platform provides a powerful strategy to identify proteins interacting with nascent α-syn aggregates. For complete details on the use and execution of this protocol, please refer to Teixeira et al.1.
    Keywords:  Cell biology; Cell culture; Molecular biology; Proteomics
    DOI:  https://doi.org/10.1016/j.xpro.2025.104303
  6. Ageing Res Rev. 2025 Dec 29. pii: S1568-1637(25)00352-6. [Epub ahead of print] 103006
      RNA G-quadruplexes (rG4s) are stable secondary structures formed by guanine-rich RNA sequences that have emerged as critical regulators of RNA metabolism. The rG4s are widespread in both coding and noncoding RNAs and have been implicated in regulation multiple post-transcriptional processes, including RNA stability, splicing, polyadenylation, nuclear export, localization, and translation. Recent findings real that rG4s play pathological roles in neurodegenerative diseases (NDs), including Alzheimer's disease (AD) and Parkinson's disease (PD). The rG4s function in stress granule dynamics, aberrant phase separation, and the nucleation of pathological protein assemblies, which is implicated in protein co-aggregation and pathological protein aggregation in NDs. Here, we provide an integrated synthesis of how rG4s influence protein aggregation through biophysical, cellular, and molecular mechanisms, with particular emphasis on rG4-driven perturbations of phase separation and aggregation pathways. The rG4s relevant disease pathogenesis, biomarker development, and therapeutic interventions in NDs are discussed. Furthermore, we highlight emerging translational opportunities, including the potential of rG4-targeting small molecules such as 5-aminolevulinic acid and other modulators, which may open new avenues for combating neurodegeneration.
    Keywords:  RNA G-quadruplexes; biomarkers; neurodegeneration; protein aggregation; therapeutics
    DOI:  https://doi.org/10.1016/j.arr.2025.103006
  7. Biochim Biophys Acta Proteins Proteom. 2025 Dec 27. pii: S1570-9639(25)00061-5. [Epub ahead of print] 141123
      Protein misfolding and aggregation into amyloid-like structures cause many pathological conditions and remain central to understanding protein homeostasis. Here, we report mechanistic insights into the aggregation of human serum albumin (HSA) under mild denaturing conditions. HSA adopts a partially unfolded intermediate state in mild denaturing conditions (1.8 M guanidine hydrochloride, pH 7.4) that is highly prone to aggregation. Kinetic analyses reveal a two-step pathway: an initial rapid formation of amorphous aggregates detected by light scattering, followed by their slower structural reorganization into β-sheet-rich spherical oligomers monitored by thioflavin T binding. Biophysical characterization using circular dichroism, dynamic light scattering (DLS), electron microscopy, tinctorial assays and mathematical modeling of the kinetics confirmed the role of amorphous aggregates as an intermediate state in oligomer formation. Both amorphous and spherical oligomeric species exhibited comparable cytotoxicity toward HEK 293 cells. These findings highlight a distinct aggregation route for HSA, expanding our understanding of how metastable intermediates facilitate toxic oligomer formation, and providing a model for dissecting early aggregation events in multidomain proteins.
    Keywords:  Aggregation kinetics; Amorphous aggregates; Amyloid-like oligomers; Cytotoxicity; Protein misfolding; Serum albumin
    DOI:  https://doi.org/10.1016/j.bbapap.2025.141123
  8. Biophys Rep. 2025 Dec 31. 11(6): 380-392
      α-Synuclein (α-Syn) is a presynaptic protein primarily associated with Parkinson's disease and other neurodegenerative diseases. The cholesterol content in SV membranes regulates α-Syn binding to synaptic vesicles, changing its function and modifying its aggregation. Using single-vesicle imaging, we show that low concentrations of cholesterol reduce vesicle clustering, and high concentrations enhance vesicle clustering mediated by α-Syn. Furthermore, using all-atom molecular dynamics simulation, we investigate the role of cholesterol in synaptic-like vesicle clustering mediated by α-Syn. In particular, we found cholesterol reduces hydrogen bonds and interaction energies in low concentrations, while high concentrations of cholesterol increase hydrogen bonds and interaction energies. Moreover, cholesterol also regulates lipid packing defects, and the condensation of cholesterol leads to the suppression of shallow packing defects, and enhancement of large defects with increasing cholesterol concentration. We revealed that cholesterol promoted vesicle clustering is due to the electrostatic interaction between cholesterol in the membrane and the N-terminal region of α-Syn. Moreover, this increased electrostatic interaction arises from a change in packing defect distribution of the protein-membrane interface induced by cholesterol condensation. This work highlights the complex interplay between α-Syn and cholesterol, emphasizing the importance of cholesterol levels in membranes and their impact on α-Syn function.
    Keywords:  Cholesterol; Lipids; Membranes; Proteins; Vesicles
    DOI:  https://doi.org/10.52601/bpr.2024.240047
  9. Biology (Basel). 2025 Dec 15. pii: 1787. [Epub ahead of print]14(12):
      Neurodegenerative diseases (NDDs), including Alzheimer's Disease (AD), Parkinson's Disease (PD), and Huntington's Disease (HD), share pathologic mechanisms including oxidative stress, mitochondrial dysfunction, and protein aggregation. However, they differ in age of onset and clinical progression. Emerging evidence highlights primary cilia (PC) as a key regulator of neuronal aging and the progression of these diseases. Dysfunctional PC may impair key signaling pathways, such as Sonic Hedgehog (Shh) and Wnt, promote oxidative stress, mitochondrial damage, and epigenetic instability. PC may also influence intercellular communication by regulating the biogenesis of exosomes and modulating tunneling nanotube (TNT) formation, both of which propagate toxic proteins between neurons. Mechanistically, the regulation of ciliary length is disrupted in AD, which leads to ciliary dysfunction that interferes with signaling pathways and promotes the aggregation of amyloid-beta. This amyloid-beta is then propagated through TNTs and exosomes, spreading neuronal damage. In PD, the accumulation of alpha-synuclein (α-syn) also impairs cilia function, thereby compromising the cell's response to oxidative stress. This results in the formation of abnormal TNTs and defective exosome-mediated clearance, ultimately contributing to neurodegeneration. Similarly, the mutant huntingtin protein aggregates within primary cilia in HD, morphologically disrupting them by obstructing intraflagellar transport. Damaged cilia are also associated with increased TNT formation and the exosomal release of toxic proteins, which leads to mitochondrial and epigenetic instability, ultimately promoting neuronal aging. Together, targeting ciliary function and its downstream regulation of TNTs and exosomes may provide a novel approach for slowing or halting disease progression across neurodegenerative diseases.
    Keywords:  amyloid-beta; extracellular vesicles; neurodegenerative disease; primary cilia; tunneling nanotubes
    DOI:  https://doi.org/10.3390/biology14121787
  10. Int J Mol Sci. 2025 Dec 08. pii: 11852. [Epub ahead of print]26(24):
      Mitochondrial dysfunction is a pivotal contributor to neurodegeneration. Neurons heavily rely on mitochondrial oxidative metabolism and therefore need highly efficient quality control mechanisms, including proteostasis, mitochondrial biogenesis, fusion-fission dynamics, and mitophagy, to sustain bioenergetics and synaptic function. With aging, deterioration of mitochondrial quality control pathways leads to impaired oxidative phosphorylation, excessive reactive oxygen species generation, calcium imbalance, and defective clearance of damaged organelles, ultimately compromising neuronal viability. Pathological protein aggregates, such as α-synuclein in Parkinson's disease, β-amyloid and tau in Alzheimer's disease, and misfolded superoxide dismutase 1 and transactive response DNA-binding protein 43 in amyotrophic lateral sclerosis, further aggravate mitochondrial stress, establishing self-perpetuating cycles of neurotoxicity. Such mitochondrial defects underscore mitochondria as a convergent pathogenic hub and a promising therapeutic target for neuroprotection. Intermediate filaments (IFs), traditionally viewed as passive structural elements, have recently gained attention for their roles in cytoplasmic organization, mitochondrial positioning, and energy regulation. Emerging evidence indicates that IF-mitochondria interactions critically influence organelle morphology and function in neurons. This review highlights the multifaceted involvement of mitochondrial dysfunction and IF dynamics in neurodegeneration, emphasizing their potential as targets for novel therapeutic strategies.
    Keywords:  axonal transport; cell architecture; cell quality; cytoskeleton; mitochondrial dynamics; mitochondrial quality; mitophagy; neurofilaments; neuron; reactive oxygen species
    DOI:  https://doi.org/10.3390/ijms262411852
  11. Genes (Basel). 2025 Dec 15. pii: 1496. [Epub ahead of print]16(12):
      Background/Objectives: Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB) are neurodegenerative disorders characterized by the accumulation of misfolded alpha-synuclein protein in the brain. Mutations in the glucocerebrosidase 1 (GBA1) gene have been identified as a significant genetic risk factor for both PD and DLB. GBA1 encodes for the lysosomal enzyme glucocerebrosidase, which is responsible for the breakdown of glucosylceramide (GC). Deficiencies in glucocerebrosidase activity lead to the accumulation of glucosylceramide within lysosomes, contributing to lysosomal dysfunction and impaired protein degradation. The aim of this narrative review is to update the underlying mechanisms by which GBA1 mutations contribute to the pathogenesis of PD and DLB. Methods: A comprehensive literature search was conducted across four major electronic databases (PubMed, Web of Science (Core Collection), Scopus, and Embase) from inception to 8 November 2025. The initial search identified approximately 1650 articles in total, with the number of hits from each database being as follows: PubMed (~450), Web of Science (~380), Scopus (~520), and Embase (~300). Results: The mechanism by which mutations in the GBA1 gene contribute to PD involves both loss-of- function and gain-of-function pathways, which are not mutually exclusive. Typically, GBA1 mutations lead to a loss of function by reducing the activity of the GCase enzyme, impairing the autophagy- lysosomal pathway and leading to α-synuclein accumulation. However, some mutant forms (GBA1L444P) of the GCase enzyme can also acquire a toxic gain of function, contributing to α-synuclein aggregation through mechanisms like endoplasmic reticulum stress and misfolding. While Venglustat effectively reduced GC levels, a key marker associated with GBA1-PD, the lack of clinical improvement led to the discontinuation of its development for this indication. Conclusions: GBA1-mediated lysosomal and lipid dysregulation represents a key pathogenic axis in PD and DLB. Understanding these mechanisms provides crucial insight into disease progression and highlights emerging therapeutic strategies-such as pharmacological chaperones, substrate reduction therapies, and gene-targeted approaches-aimed at restoring GCase function and lysosomal homeostasis to slow or prevent neurodegeneration.
    Keywords:  Dementia with Lewy Bodies (DLB); Parkinson’s disease (PD); glucocerebrosidase 1 (GBA1)
    DOI:  https://doi.org/10.3390/genes16121496
  12. Biomedicines. 2025 Dec 16. pii: 3104. [Epub ahead of print]13(12):
      Background/Objectives: The accumulation of specific amyloid proteins and peptides in the human brain is a hallmark of neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD). Beyond the central nervous system, circulating peripheral blood cells are also exposed to these pathological proteins, which may contribute to the systemic disease manifestation. Human platelets (PLTs) were used as an in vitro model to investigate the impacts of amyloid Aβ1-42 peptide oligomers (Aβ42) and on-pathway α-synuclein (α-syn), two key amyloids implicated in AD and PD, on platelet biophysical properties. Methods: Using atomic force microscopy, imaging and force-distance modes, we analyzed changes in surface nanostructure, morphometric and nanomechanical signatures of PLTs, derived from healthy donors, following exposure to increasing concentrations of Aβ42 and α-syn. Results: Our findings show that platelet activation progresses with increasing amyloid concentration, characterized by cytoskeletal remodeling (filopodia-to-pseudopodia and lamellipodia transformation). While Aβ42 causes progressive decrease in the platelet membrane roughness, α-syn exhibits a biphasic effect-initial smoothing followed by a pronounced increase in the roughness at high concentrations. Both amyloids induce substantial increase in membrane stiffness (Young's modulus). Conclusions: The changes in PLTs' biophysical properties closely resemble the previously observed modification in PLTs derived from AD and PD patients, suggesting that amyloid proteins' interactions with PLTs may contribute to their dysfunction. Our results underscore the potential of platelets as peripheral indicators of neurodegeneration and point to their role in the systemic pathology of amyloid-associated diseases.
    Keywords:  amyloid β peptide; neurodegenerative diseases; platelet morphometry; platelet nanomechanics; platelets; α-synuclein
    DOI:  https://doi.org/10.3390/biomedicines13123104
  13. Front Aging Neurosci. 2025 ;17 1664269
       Background: Parkinson's disease (PD) is traditionally defined by dopaminergic degeneration and α-synuclein aggregation. However, mounting evidence supports a multifactorial and systemic pathophysiology that extends beyond the central nervous system. This narrative review explores the interconnected mechanisms underlying sporadic PD, including environmental exposures, gut dysbiosis, α-synuclein pathology and propagation, systemic and neuroinflammation, metabolic dysfunctions (notably insulin and lipid metabolism), sleep disturbances, glymphatic impairment, and proteostatic failure.
    Results: The review highlights how α-synuclein pathology can originate peripherally, particularly in the enteric nervous system, and propagate to the brain via neuronal or hematogenous routes. It also examines the synergistic roles of systemic inflammation, immune dysregulation, mitochondrial dysfunction, and impaired protein clearance in promoting neurodegeneration.
    Conclusion: Collectively, these findings support a reconceptualization of PD as a systemic neurodegenerative disorder involving complex crosstalk between peripheral and central pathways. Understanding these multifaceted interactions opens new avenues for early diagnosis, biomarker discovery, and disease-modifying therapeutic strategies targeting the gut-brain axis, metabolic homeostasis, and proteostasis.
    Keywords:  dysbiosis; glymphatic system; lipid metabolism; neuroinflammation; oxidative stress; pathology
    DOI:  https://doi.org/10.3389/fnagi.2025.1664269