bims-axbals Biomed News
on Axonal biology and ALS
Issue of 2025–08–03
35 papers selected by
TJ Krzystek
  1. Reconstructing Alzheimer's disease one cell type at a time using in vitro tricultures.
  2. Lysosomal glucocerebrosidase is needed for ciliary Hedgehog signaling: A convergent pathway contributing to Parkinson's disease.
  3. Repurposing FDA-approved drugs for treatment of amyotrophic lateral sclerosis using machine learning.
  4. Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.
  5. F-BAR proteins CIP4 and FBP17 function in cortical neuron radial migration and process outgrowth.
  6. Engineering fluorescent reporters in human pluripotent stem cells and strategies for live imaging human neurogenesis.
  7. AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact.
  8. In Vitro Evaluation of Exon Skipping in Disease-Specific iPSC-Derived Myocytes.
  9. Mitochondrial Damage and Autophagy Dysregulation in Alzheimer's Disease: Mechanisms and Therapeutic Opportunities.
  10. Glycerophospholipids in ALS: insights into disease mechanisms and clinical implication.
  11. The role of autophagy in the pathogenesis and treatment of multiple sclerosis.
  12. Synergic action of MicroRNAs and Wnts delivered by motor neuron EVs in promoting AChR clustering.
  13. Altered mRNA transport and local translation in i3Neurons with RNA-binding protein knockdown.
  14. When Does Amyotrophic Lateral Sclerosis Begin, and How Can We Tell?
  15. Mitochondrial dysfunction mediated by ER-calcium dysregulation in neurons derived from Alzheimer's disease patients.
  16. Rab14 promotes Parkin mediated mitophagy.
  17. CIN85 and CD2AP Are Novel Constituents of Dynamic Tubular Recycling Endosomes That Regulate Recycling Upon Recruitment by MICAL-L1.
  18. Remodelling of corticostriatal axonal boutons during motor learning.
  19. ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains.
  20. Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons.
  21. Huntingtin reduction results in altered nuclear structure and heterochromatic instability.
  22. Geometrical constraints dictate assembly and phenotype of human iPSC-derived motoneuronal spheroids.
  23. Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons.
  24. Tom40 functions as a channel for protein retrotranslocation in the mitochondria-associated degradation (MAD) pathway.
  25. Imp and Chinmo are required for embryonic motor neuron axon and dendrite targeting.
  26. The p97 ATPase and its adaptor UBXD8 maintain peroxisome pools by preventing pexophagy.
  27. The CCL2-CCR2 axis drives neuromuscular denervation in amyotrophic lateral sclerosis.
  28. Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing.
  29. Elevated ubiquitin phosphorylation by PINK1 contributes to proteasomal impairment and promotes neurodegeneration.
  30. CUMS stress facilitates hippocampal neural mitophagy through FIS1/MFF-mediated mitochondrial fragmentation.
  31. RNF13 mediates pH- and Ca2+-dependent regulation of lysosomal positioning.
  32. Membrane Contact Sites in Proteostasis and ER Stress Response.
  33. Protocol for direct reprogramming of canine fibroblasts to induced motor neurons.
  34. Perspectives on mitochondrial dysfunction in the regeneration of aging skeletal muscle.
  35. The Role of Prion Protein in Reelin/Dab1 Signaling: Implications for Neurodegeneration.
  1. Trends Neurosci. 2025 Jul 29. pii: S0166-2236(25)00152-3. [Epub ahead of print]
    Reconstructing Alzheimer's disease one cell type at a time using in vitro tricultures.
    Tatiana A Giovannucci, Charles Arber, Selina Wray.
      In a recent study, Lish and colleagues used a fully human-based, induced pluripotent stem cell (iPSC)-derived triculture model of neurons, astrocytes, and microglia to delineate non-cell autonomous contributions to familial Alzheimer's disease (AD). This approach offers a versatile platform to explore early disease mechanisms, dissect cell-cell interactions, and support the development of targeted therapeutic or biomarker strategies.
    Keywords:  astrocytes; glia; iPSC; microglia; neurodegeneration; neurons
    DOI:  https://doi.org/10.1016/j.tins.2025.07.010
  2. Proc Natl Acad Sci U S A. 2025 Aug 05. 122(31): e2504774122
    Lysosomal glucocerebrosidase is needed for ciliary Hedgehog signaling: A convergent pathway contributing to Parkinson's disease.
    Sreeja V Nair, Ebsy Jaimon, Ayan Adhikari, Jonas Nikoloff, Suzanne R Pfeffer.
      Parkinson's disease is characterized by loss of dopamine neurons that project to the dorsal striatum, and mutations in LRRK2 and GBA1 are the most common genetic causes of familial Parkinson's disease. Previously, we showed that pathogenic LRRK2 mutations inhibit primary cilia formation in rare interneurons and astrocytes of the mouse and human dorsal striatum. This blocks Hedgehog signaling and reduces synthesis of neuroprotective GDNF and NRTN, which normally support dopamine neurons vulnerable in PD. Here, we show that GBA1 mutations also impair Hedgehog signaling and Hedgehog-dependent neuroprotective factor production by a distinct mechanism. Loss of GBA1 activity increases lysosomal accessible cholesterol and thus decreases accessible cholesterol in primary cilia of cultured cells; this change in lipid composition blocks ciliary Hedgehog signaling that depends on accessible cholesterol. Consistent with defects in Hedgehog signaling in the mouse dorsal striatum, GBA1 mutant mice show reduced Hedgehog-induced Gdnf RNA expression in striatal cholinergic interneurons, with no detectable impact on cilia formation. Also, both LRRK2 and GBA1 mutations suppress Hedgehog-induced Bdnf expression in striatal astrocytes. These findings underscore the role of Hedgehog signaling in the nigrostriatal circuit and reveal a convergent mechanism by which distinct LRRK2 and GBA1 mutations may contribute to PD pathogenesis.
    Keywords:  Hedgehog signaling; LRRK2 kinase; Niemann–Pick type C disease; Parkinson’s disease; neuroprotection
    DOI:  https://doi.org/10.1073/pnas.2504774122
  3. Amyotroph Lateral Scler Frontotemporal Degener. 2025 Jul 31. 1-9
    Repurposing FDA-approved drugs for treatment of amyotrophic lateral sclerosis using machine learning.
    Saanvi Dogra, Valentina L Kouznetsova, Igor F Tsigelny.
       INTRODUCTION: Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by loss of motor neurons. Current medications are largely ineffective, associated with side effects, and hindered by a lack of agreement over treatment pathways. The time-intensive process and high costs further limit the development of therapeutics. Therefore, this research aimed to identify FDA-approved drugs that inhibit three proteins (Casein kinase 1, Protein tyrosine kinase 2, Ephrin type-A receptor 4) associated with ALS.
    METHODS: A machine learning (ML) model was trained for each protein to identify an inputted compound as an active inhibitor of that protein. The FDA-approved drugs were then screened through these models, and 18 drugs were identified as likely inhibitors for all three proteins. The results were validated through protein-ligand docking of each drug to its respective protein(s).
    RESULTS: Risperidone was the most active drug, with an average ML score of 1 and binding affinity of -8.9. The ML scores and binding affinities had a strong correlation, indicating reliability.
    CONCLUSION: This research predicted multiple drugs that can simultaneously target many proteins involved in ALS, creating more effective treatment options at a lower cost. This procedure can be applied to efficiently discover drugs for other diseases in the future.
    Keywords:  Amyotrophic lateral sclerosis; FDA-approved drugs; casein kinase 1; ephrin type-A receptor 4; machine learning; protein tyrosine kinase 2; protein–ligand docking
    DOI:  https://doi.org/10.1080/21678421.2025.2536027
  4. Acta Neuropathol. 2025 Jul 29. 150(1): 10
    Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.
    John F Tuddenham, Masashi Fujita, Emily Lee, Nivedita Nimmagadda, Anthony Khairallah, Claire Harbison, Xena E Flowers, Guillermo Coronas-Samano, Silas Maniatis, Aidan Daly, Julie A Schneider, Andrew F Teich, Jean Paul G Vonsattel, Peter A Sims, Wassim Elyaman, Elizabeth M Bradshaw, Lyle W Ostrow, Hemali Phatnani, Neil A Shneider, David A Bennett, Philip L De Jager, Serge Przedborski, Vilas Menon, Marta Olah.
      Development of therapeutic approaches that target specific microglia responses in amyotrophic lateral sclerosis (ALS) is crucial due to the involvement of microglia in ALS progression. Our study identifies the predominant microglia subset in human ALS primary motor cortex and spinal cord as an undifferentiated phenotype with dysregulated respiratory electron transport. Moreover, we find that the interferon response microglia subset is enriched in donors with aggressive disease progression, while a previously described potentially protective microglia phenotype is depleted in ALS. Additionally, we observe an enrichment of non-microglial immune cell, mainly NK/T cells, in the ALS central nervous system, primarily in the spinal cord. These findings pave the way for the development of microglia subset-specific therapeutic interventions to slow or even stop ALS progression.
    Keywords:  Amyotrophic lateral sclerosis; Microglia; Phenotypic heterogeneity; Single-cell RNA-sequencing
    DOI:  https://doi.org/10.1007/s00401-025-02913-3
  5. J Neurosci. 2025 Jul 28. pii: e1952242025. [Epub ahead of print]
    F-BAR proteins CIP4 and FBP17 function in cortical neuron radial migration and process outgrowth.
    Lauren A English, Russell J Taylor, Jillian Palmos, Connor J Cameron, Emily A Broker, Emma M TeVogt, Erik W Dent.
      Neurite initiation from newly born neurons is a critical step in neuronal differentiation and migration. Neuronal migration in the developing cortex is accompanied by dynamic extension and retraction of neurites as neurons progress through bipolar and multipolar states. However, there is a relative lack of understanding regarding how the dynamic extension and retraction of neurites is regulated during neuronal migration. In recent work we have shown that CIP4, a member of the F-BAR family of membrane bending proteins, inhibits cortical neurite formation in culture, while family member FBP17 induces premature neurite outgrowth. These results beg the question of how CIP4 and FBP17 function in radial neuron migration and differentiation in vivo, including the timing and manner of neurite extension and retraction. Indeed, the regulation of neurite outgrowth is essential for the transitions between bipolar and multipolar states during radial migration. To examine the effects of modulating expression of CIP4 and FBP17 in vivo, we used in utero electroporation, in combination with our published Double UP technique, to compare knockdown or overexpression cells with control cells within the same mouse tissue of either sex. We show that either knockdown or overexpression of CIP4 and FBP17 results in the marked disruption of radial neuron migration by modulating neuronal morphology and neurite outgrowth, consistent with our findings in culture. Our results demonstrate that the F-BAR proteins CIP4 and FBP17 are essential for proper radial migration in the developing cortex and thus play a key role in cortical development.Significance statement During embryonic development, radial migration of newly born cortical neurons is a complex process that underlies the proper formation of the neocortex, the outermost layers of neurons in the brain. Disruptions in radial migration results in profound effects on cognitive function and can lead to devastating developmental disabilities. To better understand this critical process in brain development, we examined two members of the F-BAR family of membrane-bending proteins, CIP4 and FBP17, which are present in the developing brain. We demonstrate that intracellular concentrations of these proteins must be tightly regulated. Increasing or decreasing protein levels has profound effects on neuronal morphology and proper radial migration, suggesting they are key players in cortical development.
    DOI:  https://doi.org/10.1523/JNEUROSCI.1952-24.2025
  6. Development. 2025 Aug 01. pii: dev.205082. [Epub ahead of print]
    Engineering fluorescent reporters in human pluripotent stem cells and strategies for live imaging human neurogenesis.
    Alwyn Dady, Lindsay Davidson, Nicolas Loyer, Sophie Rappich, Greg Findlay, Timothy Sanders, Jens Januschke, Kate G Storey.
      Investigation of cell behaviour and cell biological processes underlying human development is facilitated by creation of fluorescent reporters in human pluripotent stem cells, which can be differentiated into cell types of choice. Here we report use of a piggyBac transposon-mediated stable integration strategy to engineer human pluripotent stem cell reporter lines. These express a plasma membrane localised protein tagged with the fluorescent proteins eGFP or mKate2, the photoconvertible nuclear marker H2B-mEos3.2, or the cytoskeletal protein F-tractin tagged with mKate2. Focussing on neural development these lines were used to live image and quantify cell behaviours, including cell cycle progression and cell division orientation in spinal cord rosettes. Further, lipofection-mediated introduction of piggyBac constructs into human neural progenitors labelled single cells and small cell groups within rosettes, allowing individual cell behaviours including neuronal delamination to be monitored. Finally, using the F-tractin-mKate2 hiPSC line, novel actin dynamics were captured during proliferation in cortical neural rosettes. This study presents and validates new tools and techniques with which to interrogate human cell behaviour and cell biology using live imaging approaches.
    Keywords:  Human cortical development; Human pluripotent stem cells; Human spinal cord development; Live cell imaging; PiggyBac-mediated fluorescent reporters
    DOI:  https://doi.org/10.1242/dev.205082
  7. J Cell Biol. 2025 Oct 06. pii: e202411138. [Epub ahead of print]224(10):
    AI-directed voxel extraction and volume EM identify intrusions as sites of mitochondrial contact.
    Benjamin S Padman, Runa S J Lindblom, Michael Lazarou.
      Membrane contact sites (MCSs) establish organelle interactomes in cells to enable communication and exchange of materials. Volume EM (vEM) is ideally suited for MCS analyses, but semantic segmentation of large vEM datasets remains challenging. Recent adoption of artificial intelligence (AI) for segmentation has greatly enhanced our analysis capabilities. However, we show that organelle boundaries, which are important for defining MCS, are the least confident predictions made by AI. We outline a segmentation strategy termed AI-directed voxel extraction (AIVE), which refines segmentation results and boundary predictions derived from any AI-based method by combining those results with electron signal values. We demonstrate the precision conferred by AIVE by applying it to the quantitative analysis of organelle interactomes from multiple FIB-SEM datasets. Through AIVE, we discover a previously unknown category of mitochondrial contact that we term the mitochondrial intrusion. We hypothesize that intrusions serve as anchors that stabilize MCS and promote organelle communication.
    DOI:  https://doi.org/10.1083/jcb.202411138
  8. Methods Mol Biol. 2025 ;2964 163-178
    In Vitro Evaluation of Exon Skipping in Disease-Specific iPSC-Derived Myocytes.
    Hidetoshi Sakurai.
      Patient-derived disease-specific induced pluripotent stem cells (iPSCs) have opened the door to recreating pathological conditions in vitro using differentiation into diseased cells corresponding to each target tissue. To investigate muscular diseases, we have established a myogenic differentiation protocol mediated by inducible MYOD1 expression that drives human iPSCs into myocytes. This highly reproducible differentiation protocol yields a homogenous skeletal muscle cell population, reaching efficiencies as high as 90%. Such high efficiency enables us to evaluate the efficacy of exon skipping in disease-specific myocytes. These disease-specific iPSC-derived myocytes can be applied not only for the validation of the therapeutic efficacy of specific antisense oligonucleotide, but also for the screening of exon skipping chemicals combined with the multi-well differentiation system. Although we previously presented the protocol in 2018, we have updated the myogenic differentiation protocol to the current version.
    Keywords:  Disease-specific iPS cells; Doxycycline inducible differentiation; Exon skipping; MyoD; Myogenic differentiation
    DOI:  https://doi.org/10.1007/978-1-0716-4730-1_11
  9. Neurochem Res. 2025 Jul 28. 50(4): 251
    Mitochondrial Damage and Autophagy Dysregulation in Alzheimer's Disease: Mechanisms and Therapeutic Opportunities.
    Qian Yu, Li Li, Shuyi Yu, Jialin Han, Qian Cheng, Zhikang Cui, Hang Chen, Ming Li, Zhiming Lu.
      Alzheimer's disease (AD) is a neurodegenerative disorder that causes progressive neurodegeneration and a variety of cognitive deficits. Of note, mitochondrial malfunctions occur early in the disease's development. Mitophagy impairment leads to the build-up of damaged mitochondria inside the cells, causing malfunction and eventual death of the cells. This review summarizes the mechanisms linking mitochondrial damage and autophagy dysregulation to AD and highlights potential therapeutic opportunities. We summarize how mitochondrial dysfunction contributes to AD, including defects in mitochondrial biogenesis, impaired dynamics, the impact of AD-related protein aggregates on mitochondrial integrity, and defective axonal transport. We also explore the roles of mitophagy in AD, including its function in the removal of harmed proteins and organelles. Finally, we highlight the therapeutic strategies for the treatment of AD, targeting molecular components involved in mitochondrial damage and autophagy dysregulation in AD, i.e., antioxidants, mitochondrial modulators, and mitophagy enhancers.
    Keywords:  Alzheimer’s disease; Aβ; Mitochondrial dysfunction; Mitophagy; p-tau
    DOI:  https://doi.org/10.1007/s11064-025-04490-z
  10. Mol Neurodegener. 2025 Jul 26. 20(1): 85
    Glycerophospholipids in ALS: insights into disease mechanisms and clinical implication.
    Thibaut Burg, Ludo Van Den Bosch.
      Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting the adult motor system, with no effective treatments available. Despite extensive research efforts, the exact pathological cascade leading to progressive motor neuron degeneration remains elusive. Recent evidence highlights significant modifications in lipid metabolism during ALS progression, even before the onset of motor symptoms. Glycerophospholipids, the primary components of cellular membranes, are frequently altered in ALS patients and models. These lipids not only play a structural role in membranes, but also contribute to cellular metabolism, signaling pathways, and cell type-specific processes such as neuronal transmission and muscle contraction. In this review, we discuss glycerophospholipid physiological functions in the motor system and review recent studies demonstrating their alterations and the possible underlying pathological mechanisms in ALS. Furthermore, we discuss challenges emerging from studying lipid alterations in neurodegeneration and evaluate the therapeutic potential of glycerophospholipids.
    Keywords:  Amyotrophic lateral sclerosis; Glycerophospholipid; Lipid metabolism; Motor neuron; Neurodegeneration
    DOI:  https://doi.org/10.1186/s13024-025-00876-3
  11. Autophagy Rep. 2025 ;4(1): 2529196
    The role of autophagy in the pathogenesis and treatment of multiple sclerosis.
    Giulio Righes, Luana Semenzato, Konstantinos Koutsikos, Veronica Zanato, Paolo Pinton, Carlotta Giorgi, Simone Patergnani.
      Autophagy is a crucial cellular process responsible for the degradation and recycling of damaged or unnecessary components, maintaining cellular homeostasis and protecting against stress. Dysregulation of autophagy has been implicated in a variety of neurodegenerative diseases, including multiple sclerosis, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease. Various types of autophagy exist, each with distinct mechanisms, such as macroautophagy, mitophagy, lipophagy, and chaperone-mediated autophagy. These processes are essential for the removal of toxic substrates like protein aggregates and dysfunctional mitochondria, which are vital for neuronal health. In neurodegenerative diseases, the impairment of these clearance mechanisms leads to the accumulation of harmful substances, which accelerate disease progression. Modulating autophagy has emerged as a promising therapeutic strategy, with ongoing studies investigating molecules that can either stimulate or regulate this process. However, despite its potential, significant challenges remain in translating preclinical findings into clinically effective treatments. In this review, we will explore the different types of autophagy, their roles in neurodegenerative diseases, and the therapeutic potential associated with modulating these processes.
    Keywords:  Multiple sclerosis; autophagy; ferritinophagy; lipophagy; mielinophagy; mitophagy; therapy
    DOI:  https://doi.org/10.1080/27694127.2025.2529196
  12. Cell Commun Signal. 2025 Aug 01. 23(1): 360
    Synergic action of MicroRNAs and Wnts delivered by motor neuron EVs in promoting AChR clustering.
    Rachele Agostini, Paola Ceccaroli, Emanuela Polidori, Manuela Ferracin, Ilaria Pace, Serena Maggio, Andrea Cioccoloni, Michela Battistelli, Giulia Matacchione, Matilde Sbriscia, Fabiola Olivieri, Fabrizia Cesca, Vilberto Stocchi, Michele Guescini.
       BACKGROUND: The neuromuscular junction (NMJ) establishment occurs through complex communication events between motor neurons and muscle fibers; however, the molecular mechanisms leading to NMJ formation have yet to be fully elucidated. Little is known about the significance of extracellular vesicles (EVs) in mediating the interaction between motor neurons and muscle fiber in the NMJ establishment; this study investigates the role of motor neuron-derived EVs during the earliest stages of NMJ formation.
    METHODS: NSC-34 cells have been used as a model of motor neurons; EVs have been isolated during neurite development using a serial ultracentrifugation protocol specifically adjusted to isolate large and small EVs. Isolated EVs were quantified through Nanoparticles Tracking Assay and characterized by Western Blot and TEM analyses. The microRNA (miRNA) cargo of EV subpopulations was identified by small-RNA sequencing and the predicted miRNA downstream targets were investigated.
    RESULTS: NGS analysis of small RNAs carried by NSC-34-derived EVs identified a total of 245 EV specific miRNAs, most of which are up-regulated in NSC-34 cells and EVs during neurite stretching. Target prediction analysis evidenced how these miRNAs synergically target the Wnt signaling pathway. Moreover, we found that NSC-34-derived EVs carry Wnt proteins, including Wnt11, Wnt4 and Wnt3a. Since several studies suggested a role for the Wnt-associated signaling network in NMJ formation, we investigated the potential role of NSC-34 EVs in NMJ development and demonstrated that EV administration to myotubes increases acetylcholine receptor (AChR) cluster formation, as revealed by immunofluorescence staining with α-bungarotoxin. Moreover, myotube treatment with NSC-34-derived EVs led to GSK3β and JNK phosphorylation, followed by β-catenin nuclear translocation, suggesting that neuron-derived EVs can induce AChR clustering through Wnt pathway activation.
    CONCLUSION: These data demonstrate that EVs released from differentiated motor neurons carry multimodal signals, miRNAs, and Wnts, which can stimulate AChR clustering in myotubes, a fundamental preparatory stage for NMJ formation. These new data highlight that EVs may play a role in the NMJ establishment and function under physiological and pathological conditions, particularly neurodegenerative diseases.
    Keywords:  Acetylcholine receptor; Agrin; Extracellular vesicles; Neuromuscular junctions; Wnt signalling; β-catenin
    DOI:  https://doi.org/10.1186/s12964-025-02312-x
  13. Nucleic Acids Res. 2025 Jul 19. pii: gkaf709. [Epub ahead of print]53(14):
    Altered mRNA transport and local translation in i3Neurons with RNA-binding protein knockdown.
    Rachael Dargan, Alla Mikheenko, Nicholas L Johnson, Benjamin E Packer, Ziyi Li, Emma J Craig, Christina N Como, Stephanie L Sarbanes, Colleen Bereda, Ying Hao, Puja R Mehta, Matthew Keuss, Mike A Nalls, Yue A Qi, Cory A Weller, Pietro Fratta, Veronica H Ryan.
      Neurons rely on messenger RNA (mRNA) transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA-binding proteins (RBPs), including those associated with neurodegenerative diseases. Here, we use proteomics, transcriptomics, and microscopy to investigate the impact of RBP depletion on mRNA transport and local translation in induced pluripotent stem cell-derived neurons. We find thousands of transcripts enriched in neurites and that many of these transcripts are locally translated, possibly due to the shorter length of transcripts in neurites. Loss of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS)-associated RBPs TDP-43 and hnRNPA1 induce distinct alterations in the neuritic proteome and transcriptome. TDP-43 knockdown (KD) leads to slightly increased neuritic mRNA and translation, while hnRNPA1 loss has more moderate effects on local mRNA profiles, possibly due to compensation by hnRNPA3. These results highlight the crucial role of FTD/ALS-associated RBPs in mRNA transport and local translation in neurons and the importance of these processes in neuron health and disease.
    DOI:  https://doi.org/10.1093/nar/gkaf709
  14. Neurology. 2025 Aug 26. 105(4): e214058
    When Does Amyotrophic Lateral Sclerosis Begin, and How Can We Tell?
    Orla Hardiman.
      
    DOI:  https://doi.org/10.1212/WNL.0000000000214058
  15. Acta Neuropathol Commun. 2025 Jul 29. 13(1): 165
    Mitochondrial dysfunction mediated by ER-calcium dysregulation in neurons derived from Alzheimer's disease patients.
    Sarah Mustaly-Kalimi, Wacey Gallegos, Daniel Steinbrenner, Smriti Gupta, Aiden J Houcek, David A Bennett, Robert A Marr, Daniel A Peterson, Israel Sekler, Grace E Stutzmann.
      Tight regulation of mitochondrial Ca2+ is essential for neuronal bioenergetics and cellular metabolism. Ca2+ transfer from ER-localized ryanodine receptors (RyR) and inositol triphosphate receptors (IP3R) to the mitochondria maintains a steady Ca2+ source that fuels oxidative phosphorylation and ATP production. In Alzheimer's disease (AD), RyR-evoked Ca2+ release is markedly increased, contributing to synaptic deficits, protein mishandling, and memory impairment. Here, we demonstrate dysregulated RyR-Ca2+ release in neurons from familial and sporadic AD patients, and this directly compromises mitochondrial activity and contributes to AD cellular pathology. We measured an array of mitochondrial functions using fluorescent biosensors and optical imaging in RyR2-expressing HEK cells and neurons derived from AD and nonAD individuals. In neurons from AD patients, resting mitochondrial Ca2+ levels were elevated alongside increased free radical production and higher caspase-3 activity relative to nonAD neurons. RyR-evoked Ca2+ release further potentiated pathogenic mitochondrial responses in AD neurons, with increased Ca2+ uptake and exaggerated mitochondrial membrane depolarization. Additionally, clearance of damaged mitochondria was impaired in AD neurons, demonstrating consequences from dysfunctional lysosomes. Notably, impairments to mitochondria in AD neurons were largely prevented with the RyR negative allosteric modulator, Ryanodex. These findings highlight how excess RyR-Ca2+ release broadly contributes to early cellular pathology in AD which includes a cascade of ER, lysosomal, and mitochondrial deficits culminating in neuronal decline and degeneration. Additionally, pharmacological suppression of RyR-Ca2+ release preserves mitochondrial, ER and lysosomal function, thus providing a novel and effective therapeutic strategy.
    Keywords:  Alzheimer’s disease; Calcium dysregulation; Mitochondria; Ryanodine receptor; iPSC-derived neurons
    DOI:  https://doi.org/10.1186/s40478-025-02023-x
  16. Mol Biol Cell. 2025 Jul 30. mbcE25060271
    Rab14 promotes Parkin mediated mitophagy.
    Samina Momtaz, Marco Padilla-Rodriguez, Paola Cruz Flores, Natalia Rulli, Nam Yong Lee, Jean M Wilson.
      Mitochondrial degradation by mitophagy is essential to maintain cell metabolism; dysregulation can result in the accumulation of damaged mitochondria. While the Rab family of small GTPase proteins are involved with vesicular trafficking in the endocytic and biosynthetic pathways, Rab-GTPases also have a role in mitochondrial integrity. However, a role for Rab14, a trans-Golgi network (TGN)-endosomal Rab-GTPase in mitophagy has not been described. In cells knocked down for Rab14, mitochondria acquire an elongated morphology and increased levels of mitochondrial proteins, whereas overexpression of Rab14 decreased these proteins. Furthermore, mito-Keima assays show increased mitophagy upon Rab14 overexpression. Rab14-induced mitophagy is dependent on Parkin expression, as well as TBK1 and PI3K activity, placing it in the Parkin-dependent mitophagy pathway. 3D-reconstruction shows contact site formation between Rab14 and mitochondria, and inhibition of the TGN kinase PI(4)KIIIβ decreases Rab14-mitochondria contact sites and prevents Rab14-mediated mitophagy, suggesting that TGN-derived Rab14 vesicles mediate mitophagy. These results suggest that Rab14 promotes mitophagy and plays an essential role in modulating cellular metabolism. [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E25-06-0271
  17. Traffic. 2025 Jul-Sep;26(7-9):26(7-9): e70015
    CIN85 and CD2AP Are Novel Constituents of Dynamic Tubular Recycling Endosomes That Regulate Recycling Upon Recruitment by MICAL-L1.
    Gunjan Misri, Ajay B Murakonda, Naava Naslavsky, Steve Caplan.
      Recycling endosomes are essential for membrane trafficking, retrieving internalized cell surface receptors and lipids to the plasma membrane. In this study, we investigate the dynamics of tubular recycling endosomes (TREs) and their regulation. We demonstrate that TREs are highly dynamic structures that first undergo biogenesis and later fission upon internalization of CD98, a known clathrin-independent cargo. Our findings identify two new constituents and novel regulators of TRE function, CD2AP and CIN85, which are recruited to TRE through interactions with MICAL-L1 via their SH3 domains. Depletion of either CD2AP or CIN85 impairs recycling, demonstrating that these proteins play important roles in TRE function. Our study highlights the importance of coordinated protein interactions in maintaining endosomal function and identifies CD2AP and CIN85 as key regulators of the recycling pathway, potentially through their impact on the actin cytoskeleton. Understanding these mechanisms provides new insights into membrane trafficking and may have implications for diseases where endosomal recycling is disrupted.
    Keywords:  CD2AP; CIN85; MICAL‐L1; actin; capping protein; tubular recycling endosome
    DOI:  https://doi.org/10.1111/tra.70015
  18. Nature. 2025 Jul 30.
    Remodelling of corticostriatal axonal boutons during motor learning.
    Mengjun Sheng, Di Lu, Richard H Roth, Fuu-Jiun Hwang, Kaiwen Sheng, Jun B Ding.
      Motor skill learning induces long-lasting synaptic plasticity at dendritic spines1-4 and at the outputs of motor cortical neurons to the striatum5,6. However, little is known about corticostriatal axon activity and structural plasticity during learning in the adult brain. Here, using longitudinal in vivo two-photon imaging, we tracked thousands of corticostriatal axonal boutons in the dorsolateral striatum of awake mice. We found that learning a new motor skill dynamically regulated these boutons. The activities of motor corticostriatal axonal boutons exhibited selectivity for rewarded movements (RM) and unrewarded movements (UM). Notably, boutons on the same axonal branches showed diverse responses during behaviour. Motor learning significantly increased the proportion of RM boutons and reduced the heterogeneity of bouton activities. Moreover, motor learning induced profound structural dynamism in boutons. By combining structural and functional imaging, we saw that newly formed axonal boutons were more likely to exhibit selectivity for RM and were stabilized during motor learning, whereas UM boutons were selectively eliminated. These findings reveal a novel form of plasticity in corticostriatal axons and show that motor learning drives dynamic bouton reorganization to support motor skill acquisition and execution.
    DOI:  https://doi.org/10.1038/s41586-025-09336-w
  19. EMBO J. 2025 Jul 29.
    ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains.
    Maike Reinders, Bojana Kravic, Pinki Gahlot, Sandra Koska, Johannes van den Boom, Nina Schulze, Sophie Levantovsky, Stefan Kleine, Markus Kaiser, Yogesh Kulathu, Christian Behrends, Hemmo Meyer.
      The cellular response to lysosomal damage involves fine-tuned mechanisms of membrane repair, lysosome regeneration and lysophagy, but how these different processes are coordinated is unclear. Here we show in human cells that the deubiquitinating enzyme ATXN3 helps restore integrity of the lysosomal system after damage by targeting K48-K63-branched ubiquitin chains on regenerating lysosomes. We find that ATXN3 is required for lysophagic flux after lysosomal damage but is not involved in the initial phagophore formation on terminally damaged lysosomes. Instead, ATXN3 is recruited to a distinct subset of lysosomes that are decorated with phosphatidylinositol-(4,5)-bisphosphate and that are not yet fully reacidified. There, ATXN3, along with its partner VCP/p97, targets and turns over K48-K63-branched ubiquitin conjugates. ATXN3 thus facilitates degradation of a fraction of LAMP2 via microautophagy to regenerate the lysosomal membrane and to thereby reestablish degradative capacity needed also for completion of lysophagy. Our findings identify a key role of ATXN3 in restoring lysosomal function after lysosomal membrane damage and uncover K48-K63-branched ubiquitin chain-regulated regeneration as a critical element of the lysosomal damage stress response.
    Keywords:  Autophagy; Lysosome; Membrane; Stress Response; Ubiquitin
    DOI:  https://doi.org/10.1038/s44318-025-00517-x
  20. Nat Commun. 2025 Jul 25. 16(1): 6878
    Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons.
    Irika R Sinha, Parker S Sandal, Holly Spence, Grace D Burns, Aswathy Peethambaran Mallika, Fatemeh Abbasinejad, Katherine E Irwin, Anna Lourdes F Cruz, Vania Wang, Shaelyn R Marx, Josué Llamas Rodríguez, Ben Langmead, Jenna M Gregory, Philip C Wong, Jonathan P Ling.
      Nuclear clearance and cytoplasmic aggregation of TDP-43, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to transcriptome-wide inclusion of deleterious cryptic exons, a signature detected in presymptomatic biofluids and postmortem ALS-FTD brain tissue, but the upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion levels across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exons arises from heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores how public archives of sequencing data remain a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.
    DOI:  https://doi.org/10.1038/s41467-025-62004-5
  21. Hum Mol Genet. 2025 Aug 01. pii: ddaf126. [Epub ahead of print]
    Huntingtin reduction results in altered nuclear structure and heterochromatic instability.
    Jessica C Barron, Sean T Coady, Abigayle C Fleming, Samantha J Carew, Makenna C A Taylor, Emily P Hurley, Firoozeh Nafar, Matthew P Parsons.
      Huntington's disease (HD), a fatal neurodegenerative disease, arises due to a CAG repeat expansion in the huntingtin (HTT) gene. Non-pathogenic wild type HTT (wtHTT) is essential for neurodevelopment as well as many vital cellular functions within the adult brain; however, the consequences of wtHTT reduction in adulthood and particularly in extrastriatal regions of the brain have not been well characterized. Understanding the implications of wtHTT loss is essential as numerous genetic therapies for HD non-specifically reduce the expression levels of both mutant and wtHTT. The aim of the current study was to characterize the effect of wtHTT reduction from the whole cell to synaptic level in primary hippocampal neurons using conventional and super-resolution imaging methods. Our results identified the nucleus as an organelle that is particularly vulnerable to wtHTT reduction, with hippocampal neurons exhibiting increased nuclear size relative to the soma, DNA decompaction and a progressive loss of heterochromatin, and biphasic changes in nuclear pCREB signaling following siRNA-mediated wtHTT knockdown. Other structural assessments including dendritic complexity, spine density and synaptic morphology appeared to be largely unaffected in our wtHTT-lowered cells. These findings highlight the nucleus as an organelle that may be particularly sensitive to huntingtin-lowering in the mammalian brain.
    Keywords:  Chromatin; Epigenetics; Huntingtin; Huntington’s disease; Transcription
    DOI:  https://doi.org/10.1093/hmg/ddaf126
  22. Stem Cell Res Ther. 2025 Jul 31. 16(1): 417
    Geometrical constraints dictate assembly and phenotype of human iPSC-derived motoneuronal spheroids.
    Eleonora Mello, Stefano Sorrentino, Alessio Bucciarelli, Ermanno Cordelli, Elisa De Luca, Haakon Nygaard, Stefan Wendt, Alberto Rainer, Giuseppe Gigli, Lorenzo Moroni, Alessandro Polini, Pamela Mozetic.
       BACKGROUND: Neuronal spheroids represent an easy and versatile solution to model neuronal tissue in vitro. Conventional approaches to generate spheroids lack accurate size control, scalability, and customizability. This is even more exacerbated in case of pluripotent stem cell (PSC) derived spheroids, which remain challenging to standardize. Microwell devices address these limitations, providing an optimal balance between accessibility and scalability. With the aim of optimizing culture conditions, we parametrically investigated the role of microwell geometry on the formation and maturation of iPSC-derived motor neuron precursor (MNP) spheroids.
    METHODS: We developed a customizable mold device using Digital Light Processing (DLP) 3D printing to fabricate agarose microwell arrays with distinct aspect ratios for culturing hiPSC-derived MNP spheroids with high reproducibility. We generated nine different pyramidal microwell array geometries for culturing size-controlled spheroids in the 40-140 μm diameter range. We then evaluated the differential expression of genes related to cell proliferation and motor-neuron differentiation as function of microwell geometry and spheroid size.
    RESULTS: Our results indicate that spheroid size is significantly influenced by the microwell geometry, reliably due to cell partitioning at the seeding stage. Expression of proliferation and differentiation markers, such as motor neuron and pancreas homeobox 1 (MNX1) and Islet-1 (ISL1) transcription factors, is also dependent on microwell geometry and spheroid morphological descriptors.
    CONCLUSION: Our approach enables the scalable production of size-controlled MNP spheroids and underscores the effect of geometrical confinement on regulating motor neuron differentiation.
    Keywords:  HiPSCs; ISL1; MNX1; Microwell; Motor neurons; Neuronal spheroids
    DOI:  https://doi.org/10.1186/s13287-025-04547-4
  23. Open Biol. 2025 Jul;15(7): 250200
    Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons.
    Jishu Xu, Michaela Hörner, Elena Buena Atienza, Kalaivani Manibarathi, Maike Nagel, Stefan Hauser, Jakob Admard, Nicolas Casadei, Stephan Ossowski, Rebecca Schuele.
      Long-read RNA sequencing has transformed transcriptome analysis by enabling comprehensive mapping of full-length transcripts, providing an unprecedented resolution of transcript diversity, alternative splicing and transcript-specific regulation. In this study, we employed nanopore long-read RNA sequencing to profile the transcriptomes of three cell types commonly used to model brain disorders, human fibroblasts, induced pluripotent stem cells and stem cell-derived cortical neurons, identifying extensive transcript diversity with 15 072 transcripts in stem cell-derived cortical neurons, 13 048 in fibroblasts and 12 759 in induced pluripotent stem cells. Our analyses uncovered 35 519 differential transcript expression events and 5135 differential transcript usage events, underscoring the complexity of transcriptomic regulation across these cell types. Importantly, by integrating differential transcript expression and usage analyses, we gained deeper insights into transcript dynamics that are not captured by gene-level expression analysis alone. Differential transcript usage analysis highlighted transcript-specific changes in disease-relevant genes such as APP, KIF2A and BSCL2, associated with Alzheimer's disease, neuronal migration disorders and degenerative axonopathies, respectively. This added resolution emphasizes the significance of transcript-level variations that often remain hidden in traditional differential gene expression analyses. Overall, our work provides a framework for understanding transcript diversity in both pluripotent and specialized cell types, which can be used to investigate transcriptomic changes in disease states in future work. Additionally, this study underscores the utility of differential transcript usage analysis in advancing our understanding of neurodevelopmental and neurodegenerative diseases, paving the way for identifying transcript-specific therapeutic targets.
    Keywords:  alternative splicing; human-derived cortical neurons; induced pluripotent stem cells; long-read RNA-sequencing; transcript usage; transcriptomics
    DOI:  https://doi.org/10.1098/rsob.250200
  24. Commun Biol. 2025 Jul 29. 8(1): 1122
    Tom40 functions as a channel for protein retrotranslocation in the mitochondria-associated degradation (MAD) pathway.
    Pin-Chao Liao, Tzu-Ying Lin, Catherine A Tsang, Chen-Jing Huang, Katherine Filpo, Istvan Boldogh, Liza A Pon.
      The mitochondria-associated degradation pathway (MAD) mediates removal and elimination of damaged, unfolded mitochondrial proteins by the ubiquitin-proteasome system (UPS). Previous studies revealed that MAD is critical for mitochondrial protein quality control and that MAD function extends beyond mitochondrial outer membrane (MOM) to proteins within the organelle. Here, we reconstitute retrotranslocation of MAD substrates from the mitochondrial matrix across mitochondrial inner and outer membranes in cell-free systems. This retrotranslocation is ATP-dependent but membrane potential-independent. We also identify a role for the TOM complex, the protein import channel in the MOM, in this process. Inhibition of protein translocation across the Tom40p channel reduces the retrotranslocation of MAD substrates. Our studies support the model that the TOM complex is a bidirectional protein channel in the MOM: it mediates retrotranslocation of damaged mitochondrial proteins across the MOM in the MAD pathway for mitochondrial protein quality control in addition to its function in import of proteins into the organelle.
    DOI:  https://doi.org/10.1038/s42003-025-08549-z
  25. Biol Open. 2025 Jul 15. pii: bio062105. [Epub ahead of print]14(7):
    Imp and Chinmo are required for embryonic motor neuron axon and dendrite targeting.
    Katherine H Fisher, Sen-Lin Lai, Chris Q Doe.
      Neural progenitors generate distinct neuronal populations over time. Drosophila larval neural progenitors, neuroblasts (NBs), generate neuronal diversity by expressing temporal gradients of transcription factors and RNA-binding proteins, including early factors Imp and Chinmo and late factors Syp, Mamo, and Broad. These factors have been well characterized in the larval central nervous system (CNS), yet nothing is known about their expression or function in the embryonic CNS. We show that embryonic Imp is expressed in a low-to-high temporal gradient, the opposite of the larval Imp gradient. Embryonic Chinmo is expressed in all post-mitotic neurons, but not in a gradient, while the late larval factors Mamo, E93, Syp, and Broad show little embryonic expression. We show that Imp is required for Chinmo expression in postmitotic neurons, and loss of Chinmo - but not Imp - derepresses Syp. Finally, we tested whether Imp and Chinmo are required for motor neuron molecular identity or morphology. Although neither is required to specify temporal or molecular neuronal identity, both are required for axon targeting to the correct body wall muscle, and downregulating dendrite outgrowth. We conclude that temporal factors are regulated differently in embryos and larvae, and that Imp and Chinmo are required for proper neuronal axon and dendrite projections.
    Keywords:  Axon; Chinmo; Dendrite; Imp; Motor neuron; Neuroblast; RNA-binding protein; Syncrip
    DOI:  https://doi.org/10.1242/bio.062105
  26. J Cell Biol. 2025 Sep 01. pii: e202409024. [Epub ahead of print]224(9):
    The p97 ATPase and its adaptor UBXD8 maintain peroxisome pools by preventing pexophagy.
    Iris D Montes, Suganthan Amirthagunanathan, Rakesh Ganji, Joao A Paulo, Brittany A Ahlstedt, Ly Nguyen, Amit S Joshi, Malavika Raman.
      Peroxisomes perform key metabolic functions in eukaryotic cells. Loss of peroxisome function causes peroxisome biogenesis disorders and severe childhood diseases with disrupted lipid metabolism. One mechanism regulating peroxisome abundance is degradation via selective autophagy (pexophagy). However, the mechanisms regulating pexophagy remain poorly understood in mammalian cells. Here, we find that the evolutionarily conserved AAA-ATPase p97/VCP and its adaptor UBXD8/FAF2 are essential for maintaining peroxisome abundance. From quantitative proteomics studies, we show that loss of UBXD8 affects the abundance of many peroxisomal proteins and that the depletion of UBXD8 results in a loss of peroxisomes. Loss of p97-UBXD8 and inhibition of p97 catalytic activity increase peroxisomal turnover through autophagy and can be rescued by depleting key autophagy proteins and E3 ligases or overexpressing the deubiquitylase USP30. We find increased ubiquitylation of PMP70 and PEX5 in cells lacking UBXD8 or p97. Our findings identify a new role of the p97-UBXD8 in regulating peroxisome abundance by removing ubiquitylated peroxisome membrane proteins to prevent pexophagy.
    DOI:  https://doi.org/10.1083/jcb.202409024
  27. Nat Commun. 2025 Aug 01. 16(1): 7053
    The CCL2-CCR2 axis drives neuromuscular denervation in amyotrophic lateral sclerosis.
    Bernát Nógrádi, Kinga Molnár, Rebeka Kristóf, Orsolya Horváth, Yu-Ting Huang, Zara Ridgway, Amaia Elicegui, Sandra Fuertes-Alvarez, Sonia Alonso-Martin, Gábor J Szebeni, Nikolett Gémes, Abdullah Ramadan, Hannah L Smith, István A Krizbai, Roland Patai, László Siklós, Péter Klivényi, Helena Chaytow, Thomas H Gillingwater.
      Systemic immune changes have been implicated in amyotrophic lateral sclerosis (ALS), but precise mechanisms and cellular targets remain unknown. Neuromuscular junction (NMJ) denervation is another major pathophysiological event in ALS, but it remains unclear whether immune system dysregulation contributes to this process. Here, we report leukocyte and macrophage infiltration in ALS patient-derived skeletal muscle biopsies. Immune cell infiltration was replicated across the hTDP-43, TDP-43A315T (male only) and TDP-43M337V mouse models, occurring from pre-symptomatic stages and targeted to NMJ-enriched muscle regions. Proteomic analysis implicated the CCL2-CCR2 axis as a driving factor. CCL2+ cells were enriched around NMJs in hTDP-43 mice, and in ALS patient skeletal muscle. Local treatment with CCL2-neutralising antibodies or normal IgG antibodies in hTDP-43 mice reduced leukocyte infiltration and ameliorated NMJ denervation. These results demonstrate that the CCL2-CCR2 axis drives immune cell infiltration targeting NMJs in ALS, identifying a potential avenue for therapeutic intervention to prevent NMJ denervation.
    DOI:  https://doi.org/10.1038/s41467-025-62351-3
  28. Exp Biol Med (Maywood). 2025 ;250 10593
    Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing.
    Eleonora Sabetta, Karin Rallmann, Jonas Bergquist, Pille Taba, Abigail L Pfaff, Bal Hari Poudel, Davide Ferrari, Massimo Locatelli, Sulev Kõks.
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder presenting progressive weakness of the bulbar and extremity muscles, leading to a wide-ranging clinical phenotype. More than 30 genes have been associated to genetically inherited ALS yet, approximately 85%-90% of ALS cases are sporadic. Short tandem repeats expansions, have recently been found in clinically diagnosed ALS patients and are currently investigated as potential genetic biomarkers. In this paper we compare the investigation of pathological tandem repeat expansions on a group of ALS patients by comparing the standard short-read sequencing (SRS) technique with a long-read-sequencing (LRS) method which has recently become more accessible. Blood samples from 47 sporadic ALS cases were subjected to SRS by Illumina Whole Genome Sequencing. The genome-wide tandem repeat expansions were genotyped using GangSTR, while wANNOVAR was used for variant annotation. Uncertain cases were further explored using LRS. SRS identified pathological expansions in HTT, ATXN2, and CACNA1A genes in one patient, which were not confirmed with LRS. The latter identified large tandem repeat expansions in the C9orf72 gene of one patient that were missed by SRS. Our findings suggest that LRS should be preferred to SRS for accurate identification of pathological tandem repeat expansions.
    Keywords:  genetic architecture; long-read sequencing; neurodegenerative disorders; short-read sequencing; sporadic amyotrophic lateral sclerosis (ALS); tandem repeats
    DOI:  https://doi.org/10.3389/ebm.2025.10593
  29. Elife. 2025 Jul 31. pii: RP103945. [Epub ahead of print]14
    Elevated ubiquitin phosphorylation by PINK1 contributes to proteasomal impairment and promotes neurodegeneration.
    Cong Chen, Tong-Yao Gao, Hua-Wei Yi, Yi Zhang, Tong Wang, Zhi-Ling Lou, Tao-Feng Wei, Yun-Bi Lu, Tingting Li, Chun Tang, Wei-Ping Zhang.
      Ubiquitin (Ub), a central regulator of protein turnover, can be phosphorylated by PINK1 (PTEN-induced putative kinase 1) to generate S65-phosphorylated ubiquitin (pUb). Elevated pUb levels have been observed in aged human brains and in Parkinson's disease, but the mechanistic link between pUb elevation and neurodegeneration remains unclear. Here, we demonstrate that pUb elevation is a common feature under neurodegenerative conditions, including Alzheimer's disease, aging, and ischemic injury. We show that impaired proteasomal activity leads to the accumulation of sPINK1, the cytosolic form of PINK1 that is normally proteasome-degraded rapidly. This accumulation increases ubiquitin phosphorylation, which then inhibits ubiquitin-dependent proteasomal activity by interfering with both ubiquitin chain elongation and proteasome-substrate interactions. Specific expression of sPINK1 in mouse hippocampal neurons induced progressive pUb accumulation, accompanied by protein aggregation, proteostasis disruption, neuronal injury, neuroinflammation, and cognitive decline. Conversely, Pink1 knockout mitigated protein aggregation in both mouse brains and HEK293 cells. Furthermore, the detrimental effects of sPINK1 could be counteracted by co-expressing Ub/S65A phospho-null mutant but exacerbated by over-expressing Ub/S65E phospho-mimic mutant. Together, these findings reveal that pUb elevation, triggered by reduced proteasomal activity, inhibits proteasomal activity and forms a feedforward loop that drives progressive neurodegeneration.
    Keywords:  PINK1; biochemistry; chemical biology; mouse; neurodegeneration; phosphorylation; proteasome; ubiquitin
    DOI:  https://doi.org/10.7554/eLife.103945
  30. J Neurophysiol. 2025 Aug 01.
    CUMS stress facilitates hippocampal neural mitophagy through FIS1/MFF-mediated mitochondrial fragmentation.
    Xiaoke Qiu, Shaoda Lai, Yingyi Zhang, Shengtao Huang, Han Li, Junsheng Liu, Yong Huang, Zhinan Zhang.
      The chronic unpredictable mild stress (CUMS) paradigm influences the neuronal count in the dentate gyrus (DG) region of the hippocampus, potentially linking to mitophagy induced by mitochondrial fragmentation. Fission mitochondrial 1 (FIS1)/mitochondrial fission factor (MFF) represents one of the mechanisms regulating mitochondrial fission and autophagy. Herein, we investigated the effects of CUMS on mitophagy and mitochondrial fragmentation in hippocampal DG neurons, along with their modulation of the mitochondrial fission pathway governed by FIS1/MFF. Our results demonstrated that CUMS stress augmented mitophagy in hippocampal DG neurons. Concurrently, it exacerbated the tendency towards mitochondrial fragmentation. The impact on the upstream regulatory pathway of mitochondrial fragmentation manifested as upregulation of FIS1 and downregulation of MFF, resulting in a net loss of mitochondrial content and a subsequent energy deficit. These findings suggest that CUMS stress, by modulating the FIS1/MFF balance, increase mitophagy stemming from mitochondrial fragmentation in hippocampal DG neurons.
    Keywords:  Depression; FIS1; MFF; mitochondria fragmentation; mitophagy
    DOI:  https://doi.org/10.1152/jn.00523.2024
  31. Cell Rep. 2025 Jul 24. pii: S2211-1247(25)00824-1. [Epub ahead of print]44(8): 116053
    RNF13 mediates pH- and Ca2+-dependent regulation of lysosomal positioning.
    Lan Thi Trinh, Anh Van Vu, Seunghye Shin, Chanhaeng Lee, Sang-Hee Park, Eun-Bee Cho, Yunseok Heo, Hyun Jin Kim, Sungjoo Kim, Jong-Bok Yoon.
      Environmental factors such as extracellular pH (pHe) and nutrition status affect lysosomal localization and autophagy, but how pHe, intracellular pH (pHi), and Ca2+ regulate lysosome transport is not well understood. Here, we identify RNF13 as a key regulator of lysosomal positioning via pHi- and Ca2+-dependent degradation of ARL8B. Ca2+-activated apoptosis-linked gene 2 (ALG-2) promotes retrograde lysosomal transport while increasing pHi and decreasing lysosomal pH (pHlys). Elevated pHi deprotonates RNF13 at His332, enabling its interaction with Ca2+-bound ALG-2 and inhibition of ARL8B-mediated anterograde transport. Alkaline pHe elevates pHlys and activates the lysosomal Ca2+ channel TRPML3, enhancing RNF13 activity and driving lysosomes toward a perinuclear position. Thus, starvation or alkaline pHe induces ALG-2 activation and pHi elevation, facilitating RNF13-mediated ARL8B degradation. In contrast, acidic pHi suppresses RNF13, keeping ARL8B levels high even when ALG-2 is active. These findings reveal a coordinated mechanism involving Ca2+ signaling and pH dynamics in regulating lysosomal positioning.
    Keywords:  ARL8B; CP: Cell biology; RNF13; TRPML1; TRPML3; autophagy; intracellular Ca(2+); intracellular pH; lysosomal positioning; lysosome; protein degradation
    DOI:  https://doi.org/10.1016/j.celrep.2025.116053
  32. Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251363050
    Membrane Contact Sites in Proteostasis and ER Stress Response.
    Febe Vermue, Aysegul Sapmaz, Ilana Berlin.
      Execution of all cellular functions depends on a healthy proteome, whose maintenance requires multimodal oversight. Roughly a third of human proteins reside in membranes and thus present unique topological challenges with respect to biogenesis and degradation. To meet these challenges, eukaryotes have evolved organellar pathways of protein folding and quality control. Most transmembrane proteins originate in the endoplasmic reticulum (ER), where they are subject to surveillance and, if necessary, removal through either ER-associated proteasomal degradation (cytosolic pathway) or selective autophagy (ER-phagy; organellar pathway). In the latter case, ER cargoes are shuttled to (endo)lysosomes - the same organelles that degrade cell surface molecules via endocytosis. Here, we provide an overview of dynamic coordination between the ER and endolysosomes, with a focus on their engagement in specialized physical interfaces termed membrane contact sites (MCSs). We cover how cross-compartmental integration through MCSs allows biosynthetic and proteolytic organelles to fine-tune each other's membrane composition, organization, and dynamics and facilitates recovery from proteotoxic stress. Along the way, we highlight recent developments and open questions at the crossroads between organelle biology and protein quality control and cast them against the backdrop of factor-specific diseases associated with perturbed membrane homeostasis.
    Keywords:  endolysosome; endoplasmic reticulum; membrane contact sites; proteostasis; proteotoxic stress
    DOI:  https://doi.org/10.1177/25152564251363050
  33. STAR Protoc. 2025 Jul 24. pii: S2666-1667(25)00381-8. [Epub ahead of print]6(3): 103975
    Protocol for direct reprogramming of canine fibroblasts to induced motor neurons.
    Ryan S Anderson, Amelia C Corona, Masatoshi Suzuki, Susannah J Sample.
      Direct reprogramming of canine fibroblasts to induced motor neurons in vitro opens the door to molecular characterization, functional analysis, and therapeutic screening of canine age-related neurodegenerative diseases. Here, we present a protocol for generating canine induced motor neurons directly from primary dermal fibroblasts. We provide a step-by-step guide for isolating and maintaining primary dermal fibroblasts from dogs, obtaining a stock of reprogrammable cells, and performing the direct reprogramming process. We then detail procedures for validating the motor neuron identity.
    Keywords:  Cell Differentiation; Cell culture; Health Sciences; Model Organisms; Neuroscience
    DOI:  https://doi.org/10.1016/j.xpro.2025.103975
  34. Cell Mol Biol Lett. 2025 Jul 28. 30(1): 94
    Perspectives on mitochondrial dysfunction in the regeneration of aging skeletal muscle.
    Kai Wang, Mailin Gan, Yuhang Lei, Tianci Liao, Jiaxin Li, Lili Niu, Ye Zhao, Lei Chen, Yan Wang, Li Zhu, Linyuan Shen.
      As the global population trends toward aging, the number of individuals suffering from age-related debilitating diseases is increasing. With advancing age, skeletal muscle undergoes progressive oxidative stress infiltration, coupled with detrimental factors such as impaired protein synthesis and mitochondrial DNA (mtDNA) mutations, culminating in mitochondrial dysfunction. Muscle stem cells (MuSCs), essential for skeletal muscle regeneration, also experience functional decline during this process, leading to irreversible damage to muscle integrity in older adults. A critical contributing factor is the loss of mitochondrial metabolism and function in MuSCs within skeletal muscle. The mitochondrial quality control system plays a pivotal role as a modulator, counteracting aging-associated abnormalities in energy metabolism and redox imbalance. Mitochondria meet functional demands through processes such as fission, fusion, and mitophagy. The significance of mitochondrial morphology and dynamics in the mechanisms of muscle regeneration has been consistently emphasized. In this review, we provide a comprehensive summary of recent advances in understanding the mechanisms of aging-related mitochondrial dysfunction and its role in hindering skeletal muscle regeneration. Additionally, we present novel insights into therapeutic approaches for treating aging-related myopathies.
    Keywords:  Aging; Mitochondrial dynamics; Mitophagy; Oxidative stress; Skeletal muscle regeneration
    DOI:  https://doi.org/10.1186/s11658-025-00771-1
  35. Viruses. 2025 Jun 29. pii: 928. [Epub ahead of print]17(7):
    The Role of Prion Protein in Reelin/Dab1 Signaling: Implications for Neurodegeneration.
    Irene Giulia Rolle, Anna Burato, Merve Begüm Bacınoğlu, Fabio Moda, Giuseppe Legname.
      The cellular prion protein (PrPC) is studied in prion diseases, where its misfolded isoform (PrPSc) leads to neurodegeneration. PrPC has also been implicated in several physiological functions. The protein is abundant in the nervous system, and it is critical for cell signaling in cellular communication, where it acts as a scaffold for various signaling molecules. The Reelin signaling pathway, implicated both in Alzheimer's and prion diseases, engages Dab1, an adaptor protein influencing APP processing and amyloid beta deposition. Here, we show, using Prnp knockout models (Prnp0/0), that PrPC modulates Reelin signaling, affecting Dab1 activation and downstream phosphorylation in both neuronal cultures and mouse brains. Notably, Prnp0/0 mice showed reduced responsiveness to Reelin, associated with altered Dab1 phosphorylation and Fyn kinase activity. Even though no direct interaction between PrPC and Reelin/ApoER2 was found, Prnp0/0 neurons showed lower NCAM levels, a well-established PrPC interactor. Prion infection further disrupted the Reelin signaling pathway, thus downregulating Dab1 and Reelin receptors and altering Reelin processing, like Alzheimer's disease pathology. These findings emphasize PrPC indirect role in Dab1 signaling via the NCAM and Fyn pathways, which influence synaptic function and neurodegeneration in prion diseases.
    Keywords:  Dab1; Reelin; cleavage; neurodegeneration; prion protein
    DOI:  https://doi.org/10.3390/v17070928
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