bims-proned Biomed News
on Proteostasis in neurodegeneration
Issue of 2025–06–29
fourteen papers selected by
Verena Kohler, Umeå University



  1. Proc Natl Acad Sci U S A. 2025 Jul;122(26): e2422427122
      The aggregation of α-synuclein into amyloid fibrils is a hallmark of Parkinson's disease. This process has been shown to directly involve interactions between proteins and lipid surfaces when the latter are present. Despite this importance, the molecular mechanisms of lipid-induced amyloid aggregation have remained largely elusive. Here, we present a global kinetic model to describe lipid-induced amyloid aggregation of α-synuclein. Using this framework, we find that α-synuclein fibrils form via a two-step primary nucleation mechanism and that lipid molecules are directly involved in both the nucleation and fibril elongation steps, giving rise to lipid-protein coaggregates. To illustrate the applicability of this kinetic approach to drug discovery, we identify the mechanism of action of squalamine, a known inhibitor of lipid-induced α-synuclein aggregation, revealing that this small molecule reduces the rate of lipid-dependent primary nucleation. Our work will likely guide the rational design of α-synuclein aggregation inhibitors.
    Keywords:  Parkinson’s disease; aggregation inhibitors; lipid-induced amyloid aggregation
    DOI:  https://doi.org/10.1073/pnas.2422427122
  2. Alzheimers Dement (N Y). 2025 Apr-Jun;11(2):11(2): e70117
       Introduction: Alzheimer's disease (AD) and Parkinson's disease (PD) are neurodegenerative disorders characterized by abnormal protein aggregation, with amyloid beta (Aβ) and α-synuclein (α-syn) as key pathological markers. Increasing evidence highlights a pathological interplay between Aβ and α-syn, exacerbating neurodegeneration in both AD and PD. In this study, we evaluated the effects of reducing amyloid precursor protein (APP) processing on α-syn pathology using a splice-switching oligonucleotide (SSO) targeting APP exon 15 in Thy1-α-syn transgenic (α-syn-tg) mice.
    Methods: α-syn-tg mice received systemic APP SSO treatment. Immunohistochemistry and immunoblotting assessed α-syn, phosphorylated α-syn (P-Syn), and APP C-terminal fragments (CTFs) in the cortex, hippocampus, and thalamus. Neuronal integrity in different brain regions were examined, and behavioral assessments evaluated cognitive and motor functions.
    Results: APP SSO treatment significantly reduced α-syn and P-Syn in the cortex, hippocampus, and thalamus while also reversing neuronal loss in the hippocampal CA3 region. Interestingly, α-syn-tg mice exhibited elevated levels of alternative APP CTFs, which were reduced by APP SSO treatment, implicating APP processing dysregulation in α-syn pathology. Although behavioral assessments revealed no significant impairments or improvements in female α-syn-tg mice.
    Discussion: Our findings demonstrate that targeting APP reduces α-syn pathology and rescues neuronal loss, supporting the therapeutic potential of APP modulation in synucleinopathies. While no behavioral changes were observed in transgenic mice, further research exploring different models and conditions may provide additional insights into the full range of therapeutic benefits. Future studies should optimize delivery methods and explore combination therapies to enhance outcomes in neurodegenerative diseases with overlapping proteinopathies.
    Highlights: APP-targeting SSO reduces α-syn and P-Syn in α-syn-tg mice.APP SSO lowers APP CTFs, linking APP processing to α-syn pathology.Neuronal loss in the hippocampal CA3 region is restored following APP SSO treatment.Behavioral assessments show no significant changes in female α-syn-tg mice.Findings support APP modulation as a potential strategy for synucleinopathies.
    Keywords:  APP processing; Alzheimer's disease (AD); Amyloid beta (Aβ); Parkinson's disease (PD); neurodegeneration; splice‐switching oligonucleotide (SSO); synucleinopathies; α‐Synuclein (α‐syn)
    DOI:  https://doi.org/10.1002/trc2.70117
  3. J Alzheimers Dis. 2025 Jun 22. 13872877251351305
      BackgroundAmyloid aggregation of α-Synuclein is a defining feature of several neurodegenerative disorders, including Parkinson's disease (PD), Lewy body dementia (LBD), and Alzheimer's disease (AD). While there have been many attempts to reduce the α-Synuclein burden of neuronal cells through direct targeting of the protein, the conformationally dynamic nature of α-Synuclein make it a particularly difficult target to drug. Given the correlation between α-Synuclein levels and both familial and environmentally induced synucleinopathies, targeting the α-Synuclein mRNA transcript offers an alternative therapeutic avenue.ObjectiveTo develop and evaluate protein-based RNA-binding therapeutics (PROTEIMERs) that selectively bind the 5' untranslated region (UTR) of α-Synuclein mRNA and inhibit its translation to reduce α-Synuclein levels.MethodsWe employed high-throughput phage display to identify novel RNA-binding PROTEIMER candidates targeting the 5'UTR of α-Synuclein mRNA. Binding affinities were assessed via surface plasmon resonance (SPR). Computational structural predictions were used to evaluate PROTEIMER-RNA interactions relative to known regulatory proteins IRP1 and IRP2. RNase domains were fused to the lead PROTEIMERs, and their RNA degradation activity was tested in vitro.ResultsThree PROTEIMERs were identified that bind the α-Synuclein 5'UTR with high affinity. Structural predictions supported specific interactions with the structured RNA region. RNase-fused PROTEIMERs demonstrated targeted RNA degradation and induced decay of α-Synuclein mRNA in vitro, indicating translational suppression capability.ConclusionsOur findings demonstrate the feasibility of using engineered protein therapeutics to target α-Synuclein mRNA via the 5'UTR. These PROTEIMERs represent a promising new strategy for reducing α-Synuclein levels and mitigating neurodegenerative progression in LBD, PD, and AD.
    Keywords:  Alzheimer's disease; PROTEIMER; Parkinson's disease; amyloid; mRNA; protein design; targeted degradation; α-Synuclein
    DOI:  https://doi.org/10.1177/13872877251351305
  4. Mol Cells. 2025 Jun 22. pii: S1016-8478(25)00071-8. [Epub ahead of print] 100247
      Neurodegenerative diseases involve toxic protein aggregation. Recent evidence suggests that biomolecular phase separation, a process in which proteins and nucleic acids form dynamic, liquid-like condensates, plays a key role in this aggregation. Optogenetics, originally developed to control neuronal activity with light, has emerged as a powerful tool to investigate phase separation in living systems. This is achieved by fusing disease-associated proteins to light-sensitive oligomerization domains, enabling researchers to induce or reverse condensate formation with precise spatial and temporal control. This review highlights how optogenetic systems such as OptoDroplet are being used to dissect the mechanisms of neurodegenerative disease. We examine how these tools have been applied in models of neurodegenerative diseases such as amyotrophic lateral sclerosis, Alzheimer's, Parkinson's, and Huntington's disease. These studies implicate small oligomeric aggregates as key drivers of toxicity and highlight new opportunities for therapeutic screening. Finally, we discuss advances in light-controlled dissolution of condensates and future directions for applying optogenetics to combat neurodegeneration. By enabling precise, dynamic control of protein phase behavior in living systems, optogenetic approaches provide a powerful framework for elucidating disease mechanisms and informing the development of targeted therapies.
    Keywords:  Biomolecular phase separation; Neurodegenerative diseases; OptoDroplet; Optogenetics; Protein aggregation; neurodegeneration
    DOI:  https://doi.org/10.1016/j.mocell.2025.100247
  5. Biomed Pharmacother. 2025 Jun 18. pii: S0753-3322(25)00456-1. [Epub ahead of print]189 118262
      Parkinson's disease (PD) affects 10 million individuals worldwide with no available disease modifying therapies. The pathological hallmark of PD, Lewy bodies, are characterized by aggregated α-synuclein (α-syn) inclusions in disease lesions. In preclinical models, aggregation of α-syn leads to neuronal dysfunction, cell death, and propagation of Lewy pathology. Six clinical stage α-syn targeting monoclonal antibodies that were developed to treat or slow the progression of PD have advanced into efficacy trials, but none to date have achieved their primary endpoints. Except cinpanemab, which binds the N-terminus of α-syn, all other clinical α-syn antibodies bind C-terminal epitopes. To evaluate the impact of binding characteristics on functional activity, we affinity matured cinpanemab and benchmarked it against the clinical antibodies that vary in their affinity and selectivity for aggregated forms of α-syn. Our evaluation shows the impact of epitope, affinity, selectivity, and assay format on PFF uptake, and PFF-seed induced aggregation and S129 phosphorylation of endogenous α-syn in cellular models of PD. The comparative assessment provides new insights into the properties of α-syn antibodies and should aid in the design of next generation therapeutics for the treatment of PD and other synucleinopathies.
    Keywords:  Alpha-synuclein; Parkinson’s disease; amlenetug; cinpanemab; immunotherapy; prasinezumab
    DOI:  https://doi.org/10.1016/j.biopha.2025.118262
  6. Mol Psychiatry. 2025 Jun 25.
      Alzheimer's disease (AD) and Alzheimer's disease-related dementias (ADRDs) are among the most prevalent neurodegenerative diseases, characterized by progressive cognitive decline driven by complex and overlapping pathological mechanisms. While amyloid plaques, neurofibrillary tangles, and Lewy bodies are well-established hallmarks, TAR DNA-binding protein 43 (TDP-43) pathology has emerged as a critical contributor to disease progression, particularly in cases exhibiting hippocampal sclerosis and severe brain atrophy. TDP-43 pathology is defined by its cytoplasmic mislocalization, aberrant aggregation, and nuclear depletion, leading to disruptions in RNA metabolism, stress granule dynamics, and mitochondrial function. Increasing evidence suggests that TDP-43 pathology not only exacerbates neuronal degeneration but also interacts with Aβ plaques, tau tangles, and α-synuclein aggregates, compounding neurodegenerative processes and accelerating cognitive decline. Despite its growing recognition, TDP-43 pathology remains underexplored compared to other proteinopathies in AD and ADRDs, highlighting the need for further mechanistic studies and targeted therapeutic development. In this review, we summarize the current understanding of TDP-43 pathology in AD and ADRDs, with a focus on its role in disease progression. We further discuss the molecular mechanisms underlying TDP-43-associated neurodegeneration in AD and ADRDs, emphasizing RNA dysregulation, mitochondrial dysfunction, disrupted protein homeostasis, stress response alternations, and nuclear-cytoplasmic transport impairments. Lastly, given the significant impact on disease pathology, we review ongoing efforts to treat TDP-43-associated neurodegeneration, including antisense oligonucleotides, small-molecule inhibitors, and peptide-based interventions aimed at restoring TDP-43 function or preventing its neurotoxicity and pathological aggregation.
    DOI:  https://doi.org/10.1038/s41380-025-03089-8
  7. Zhen Ci Yan Jiu. 2025 Jun 25. pii: 1000-0607(2025)06-0714-07. [Epub ahead of print]50(6): 714-720
      Parkinson's disease (PD) is a chronic progressive neurological degenerative disease caused by the degeneration of dopaminergic neurons in the substantia nigra. α-synuclein (α-Syn) misfolding and aggregation is the crucial pathogenesis of PD, and is closely related to the other pathogenesis, such as brain-gut axis dysfunction, mitochondrial dysfunction, oxidative stress, neuroinflammation, iron and lipid metabolic disorders, and autophagy lysosomal dysfunction. Acupuncture plays a neuroprotective role by attenuating neuroinflammation, regulating brain-gut axis, repairing ubiquitin-proteasome system and autophagy lysosomal system, and modulating signaling pathways, so as to inhibit α-Syn abnormal folding and aggregation. This article reviews the effect of α-Syn in the pathogenesis of PD and acupuncture treatment, so as to provide the valuable guidance for clinical treatment.
    Keywords:  Acupuncture; Parkinson’s disease; Research progress; α-synuclein
    DOI:  https://doi.org/10.13702/j.1000-0607.20240237
  8. ACS Chem Neurosci. 2025 Jun 25.
      The S100 family consists of calcium-binding proteins that are largely known for their contribution to neuroinflammatory processes. These proteins are associated with various cardiac and neurological functions as well as related diseases. A few S100 proteins can form unspecific or amyloid aggregates in neuropathologies and thus play a part in dementia pathogenesis. Among all S100 proteins, S100B and S100A9 aggregation properties are the most investigated; however, there is a lack of studies regarding other S100 members. In particular, S100A1 and S100A8 are also associated with neurological pathologies, but their interactions and aggregation are poorly understood. Therefore, in this study, we explored whether S100A1 and S100A8 proteins can form heterodimers, interact, or coaggregate. Our results revealed that S100A1 and S100A8 interactions and S100A8 amyloid aggregation are driven by calcium ions. We observed that while S100A1 remains mostly stable, S100A8 forms various types of spherical or unspecific aggregates. While they do not form stable heterodimers like calprotectin, their transient interactions facilitate the formation of worm-like amyloid fibrils, and the process is regulated by different calcium ion concentrations. At calcium ion saturation, both proteins are stabilized, leading to inhibition of aggregation. Overall, by employing a diverse range of techniques from amyloid and protein-specific fluorescence detection to electron-electron double resonance spectroscopy, we elucidated interactions between S100 proteins that might otherwise be overlooked, enhancing our understanding of their aggregation behavior.
    Keywords:  S100; aggregation; amyloid; inflammation; interaction; neurodegeneration
    DOI:  https://doi.org/10.1021/acschemneuro.5c00086
  9. Cells. 2025 Jun 16. pii: 907. [Epub ahead of print]14(12):
      Neurodegenerative diseases (NDDs) that are characterized by the accumulation of alpha-synuclein (α-syn) aggregates in both neurons and the non-neuronal cells of the brain are called synucleinopathies. The most common synucleinopathies includes Parkinson's disease (PD), Parkinson's disease dementia (PDD), multiple system atrophy (MSA), and dementia with Lewy bodies (DLB). Significant progress has been made in the development of positron emission tomography (PET) radiotracers for synucleinopathies, yielding several α-syn tracers that have entered clinical studies. However, selective α-syn imaging still faces inherent challenges. This review provides a comprehensive overview of the progress in α-syn PET radiotracers from three angles: Alzheimer's disease (AD)-derived scaffolds, representative compound scaffolds and analogs, and the identification of α-syn tracers through high-throughput screening (HTS). We discuss the characteristics, advantages, and limitations of the tracers for preclinical and clinical application. Finally, future directions in the development of radioligands for proteinopathies are discussed. There is no clinical available PET radiotracer for imaging α-syn aggregates, but these advances have laid a key foundation for non-invasive α-syn imaging and early diagnosis of synucleinopathies.
    Keywords:  Parkinson’s disease; high-throughput screening; synucleinopathy; tracer
    DOI:  https://doi.org/10.3390/cells14120907
  10. Int J Biol Macromol. 2025 Jun 24. pii: S0141-8130(25)06055-6. [Epub ahead of print] 145500
      The co-localization of phospho-tau proteins (p-tau) and amyloid beta (Aβ) or alpha-synuclein (α-Syn) aggregates and their combined pathological impacts have been recognized in the brains of both human and animal models of Alzheimer's disease (AD) and Parkinson's disease (PD). The fibrillation of amyloidogenic proteins is a dynamic process that can be affected by the presence of other proteins and therefore, it's essential to reveal how the cross-interaction between Aβ or α-Syn with p-tau affects their amyloidogenesis. Using simulation studies, we showed that cis and trans conformations of phosphorylated tau (phosphorylated at Thr231) show different affinities to Aβ and α-Syn. Trans p-tau showed more favorable and stronger interaction with Aβ and α-Syn and accelerated their aggregation. Consistently, the experimental approaches demonstrated that trans p-tau considerably enhances the fibrillation of both Aβ (from ~7 h to ~30 min) and α-Syn (from ~10 h to ~1 h) in a concentration-dependent manner, whereas cis p-tau, a neurotoxic isomer and early driver of tauopathy, exhibited a less pronounced acceleratory effect on amyloid aggregation (from 7 h to 5 h for Aβ and from 7 h to 5 h for α-Syn).
    Keywords:  Alzheimer's disease; Amyloidogenesis; Fibrillation; Parkinson's disease; Phosphorylated tau
    DOI:  https://doi.org/10.1016/j.ijbiomac.2025.145500
  11. Biomolecules. 2025 Jun 15. pii: 872. [Epub ahead of print]15(6):
      Tau pathology is one of the main pathological features of Alzheimer's disease (AD). Intracellular Tau may be released to the extracellular space upon neuron degeneration, where it has the potential to be toxic to other neurons. The propagation of Tau pathology, mediated by extracellular Tau aggregates, may underlie the pathogenesis of AD. Antibody therapies targeting Tau proteins are, therefore, considered highly promising. In this study, the cytotoxicity of extracellular Tau aggregates on SH-SY5Y cells was examined. The effect of extracellular Tau aggregates on intracellular Tau aggregation was also studied using a FRET-based assay. The extracellular Tau aggregates were found to cause intracellular Tau aggregation after entering the cells; meanwhile, ROS (reactive oxygen species) induced by Tau aggregates facilitated this process. A single-chain variable fragment antibody (scFv T1) inhibits Tau aggregation both extracellularly and intracellularly. ScFv T1 also inhibited the accumulation of ROS and alleviated the inflammation and apoptosis induced by Tau aggregates. These findings could provide experimental support for the study of neurotoxicity and related mechanisms of extracellular Tau aggregates, in addition to providing insights into the development of novel therapeutic agents to treat AD.
    Keywords:  Alzheimer’s disease; ROS; extracellular Tau aggregates; single-chain variable fragment antibody
    DOI:  https://doi.org/10.3390/biom15060872
  12. Mol Cell Proteomics. 2025 Jun 20. pii: S1535-9476(25)00116-1. [Epub ahead of print] 101017
      Human neurodegenerative conditions such as Parkinson's and Alzheimer's Disease are characterized by the formation and deposition of toxic protein species which exacerbate neuronal dysfunction, impacting the structure and function of the healthy brain. Deciphering the mechanisms underlying protein (mis)folding and aggregation is not only essential for a more coherent view of neurodegeneration, but also crucial for the development of novel therapeutics targeting this family of disorders. Key pathological drivers of neurodegeneration, such as alpha-synuclein and tau proteins, have traditionally proved extremely challenging to characterize structurally due to their intrinsic and widespread structural plasticity. Hydrogen-Deuterium eXchange Mass Spectrometry (HDX-MS) has emerged as a powerful tool to help circumvent this, owing to its ability to capture protein intrinsic disorder in solution, in addition to the transient structural conformations that typify protein aggregation pathways. This review brings together the most recent research where HDX-MS has shed light on mechanisms of neurodegeneration. We highlight how the technique has been successfully integrated into therapeutic development workflows targeting some of the most prevalent neurodegenerative diseases.
    Keywords:  Drug Discovery; HDX-MS; Neurodegeneration; Structural Proteomics; Therapeutics
    DOI:  https://doi.org/10.1016/j.mcpro.2025.101017
  13. FASEB J. 2025 Jun 30. 39(12): e70748
      Intracellular protein aggregation is a hallmark of aging and contributes to pathology in some age-associated diseases. In hereditary adult-onset neuromuscular diseases (NMDs), protein aggregates play a key role in disease onset and progression. The wild-type Poly(A) binding protein nuclear 1 (PABPN1) forms benign nuclear aggregates, whereas a short trinucleotide expansion leads to the formation of pathogenic aggregates, a hallmark of Oculopharyngeal Muscular Dystrophy (OPMD). In OPMD, the mutant PABPN1 causes skeletal muscle weakness. So far, the structural differences between benign and pathogenic protein aggregates and their effects on muscle cell biology remain poorly understood. We employed an array of advanced imaging modalities to explore the morphological differences between nuclear aggregates formed by non-pathogenic and pathogenic PABPN1 variants. Through analyses spanning micro- to nanoscale, we identified distinct structural features of aggregates formed by wild-type and expanded PABPN1. We demonstrate that these differences were more pronounced in differentiated muscle cells compared to proliferating cells. We further linked the structural features of PABPN1 aggregates to muscle cell biology, namely alterations in mitochondrial function and proteasomal activity. Our findings provide new insights into the structural distinctions between pathogenic and non-pathogenic aggregates and their implications for cellular dysfunction in NMDs.
    Keywords:  OPMD; aggregates structure; imaging; muscle; protein aggregates
    DOI:  https://doi.org/10.1096/fj.202501097R
  14. J Neurosci. 2025 Jun 24. pii: e1658242025. [Epub ahead of print]
      Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease characterized by death of lower and upper motor neurons. Although the mechanism behind the selective neuron loss is still unclear, several heterogenous genes have been causally linked to ALS. KIF5A encodes for a neuronally enriched kinesin involved in protein transport and mutations within this gene have been causally linked to different motor neuron diseases. The mutations identified in ALS patients are mostly predicted to alter its mRNA splicing, leading to a frameshift mutation and an aberrant 39 amino acid-long sequence in the C-terminal domain of KIF5A.Here we found that ALS-related KIF5A mutations induce the accumulation of the mutant form of the protein in human motoneurons, which are also characterized by the cytosolic mislocalization of TDP-43. This ALS hallmark was even exacerbated upon overexpression of the ALS-KIF5A protein in cells differentiated from healthy controls and primary neurons, suggesting a pathological connection between the cellular load of the mutant protein and TDP-43 pathology. While the terminal domain of the WT isoform is characterized by an acid isoelectric point (pI), the ALS variant presents a basic pI due to the altered aminoacidic composition of this sequence. We thus generated a KIF5A ALS isoform that retained part of the aberrant sequence but with lower pI. The overexpression of this mutated variant led to significantly lower protein aggregation and TDP-43 mislocalization than the ALS mutant. Our data show that re-establishing the correct pI rescues KIFA aggregation and significantly reduces the cytoplasmic mislocalization of TDP-43.Significance Statement Amyotrophic Lateral Sclerosis is a lethal neurodegenerative disease to which no cure is still known. Heterogenous genes have been causally linked to ALS, yet, the exact pathomechanism responsible for neuronal death remains unclear. One such gene is KIF5A which encodes for a neuronally enriched kinesin. Identified mutations cause incorrect mRNA splicing resulting in an aberrant C-terminal aminoacidic sequence. Here, we identified TDP-43 cytosolic enrichment, a hallmark common to many ALS models, in two distinct hiPSC-derived motoneuron lines harboring the ALS mutation KIF5Ac2993-1 G>A Moreover, we generated a KIF5A isoform that retained most of the aberrant sequence but did not promote protein aggregation nor TDP-43 mislocalization upon overexpression. These results shed further light on the pathobiochemistry of the ALS-KIF5A cases.
    DOI:  https://doi.org/10.1523/JNEUROSCI.1658-24.2025