bims-axbals 2025-11-30 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2025–11–30
thirty-one papers selected by
TJ Krzystek

TDP-43 Regulates Rab4 Levels to Support Synaptic Vesicle Recycling and Neuromuscular Connectivity in Drosophila and Human ALS Models.
A human forebrain organoid model phenocopies dysregulated RNA and protein homeostasis in ALS/FTD-associated TDP-43 proteinopathies.
KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS.
SLP2/PHB Aggregates in ALS Mouse Models and Patients: Implications Beyond CHCHD10-Associated Motor Neuron Disease.
Neurodegenerative Disease and Autophagy in iPSC models.
Upregulation of sphingomyelin and ABCA8 in response to TDP-43 pathology in amyotrophic lateral sclerosis brain.
Elevation of the mechanically-sensitive protein emerin links nuclear mechanotransduction to tau-induced cytoskeletal remodeling in neurons.
Amyloidogenic oligomers derived from TDP-43 LCD promote the condensation and phosphorylation of TDP-43.
Structural basis for binding of RILPL1 to TMEM55B reveals a lysosomal platform for adaptor assembly through a conserved peptide motif.
Disruption of the PIKfyve complex unveils an adaptive mechanism to promote lysosomal repair and mitochondrial homeostasis.
Cutting-edge treatments in amyotrophic lateral sclerosis: the role of molecular pathogenesis in targeted therapies.
Impaired AIS plasticity in ankyrin-G mutant mice alters cortical excitability and behavior.
Loss of ARF5 impairs recovery after lysosomal damage.
Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia.
Protein misfolding and its dual role in neurodegeneration and cancer progression.
Homocysteine disrupts lysosomal function by V-ATPase inhibition.
Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics.
Brain Organoids in Neurodegenerative Disease Modeling: Advances, Applications and Future Perspectives.
Lentiviral Vector-Mediated Gene Delivery for iPSC-Related Neuroscience Research.
Dynamics of Excitability in Axonal Trees.
Development of a Human Preclinical Platform for the Identification of Neuroprotective Compounds.
Exploring TANK-Binding Kinase 1 in Amyotrophic Lateral Sclerosis: From Structural Mechanisms to Machine Learning-Guided Therapeutics.
Autophagy and mitophagy at the synapse and beyond: implications for learning, memory and neurological disorders.
Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration.
An induced pluripotent stem cell-based chemical genetic approach for studying spinal muscular atrophy.
A distal promoter and aberrant splicing enable canonical translation of out-of-frame proteins in Huntington's disease.
Portioning organelles for autophagic clearance.
The neuropathy-linked protein TECPR2 is a Rab5 effector that regulates cargo recycling from early endosomes.
CYFIP1 governs the development of cortical axons by modulating calcium availability.
Axon guidance deficits in a human sensory-like neuron model of Fabry disease.
Molecular Mechanism of Hydroxyl Safflower Yellow A in Knee Osteoarthritis through Modulation of Autophagy via Inhibition of the HIF-1α/BNIP3 Pathway.

Int J Mol Sci. 2025 Nov 14. pii: 11030. [Epub ahead of print]26(22):

TDP-43 Regulates Rab4 Levels to Support Synaptic Vesicle Recycling and Neuromuscular Connectivity in Drosophila and Human ALS Models.

Monsurat Gbadamosi, Giulia Romano, Michela Simbula, Giulia Canarutto, Linda Ottoboni, Stefania Corti, Fabian Feiguin.

  The pathological loss of nuclear TDP-43 is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leading to extensive alterations in RNA metabolism and a broad number of neuronal transcripts. However, the key effectors linking TDP-43 dysfunction to synaptic defects remain unclear. In this study, using Drosophila and human iPSC-derived motoneurons, we identify Rab4 as a direct and conserved target of TDP-43, whose expression is necessary and sufficient to recover synaptic vesicle recycling, neuromuscular junction growth, and locomotor function in TDP-43-deficient motoneurons. Moreover, Rab4 activity promotes the presynaptic recruitment of futsch/MAP1B, a microtubule-associated protein also regulated by TDP-43, which autonomously supports synaptic growth and vesicle turnover. Together, these findings define a TDP-43/Rab4/futsch/MAP1B regulatory axis that couples endosomal dynamics to cytoskeletal assembly. Furthermore, this functionally coherent module provides a mechanistic basis for understanding how synaptic vulnerability is amplified in disease and offers a framework to identify key compensatory targets capable of sustaining neuronal function in the absence of TDP-43.

Keywords:  ALS; Drosophila; FTD; MAP1B; NMJs; Rab4; TDP-43; endosomal trafficking; synaptic vesicle

DOI:  https://doi.org/10.3390/ijms262211030
bioRxiv. 2025 Nov 10. pii: 2025.11.09.687455. [Epub ahead of print]

A human forebrain organoid model phenocopies dysregulated RNA and protein homeostasis in ALS/FTD-associated TDP-43 proteinopathies.

Qi Zhang, Meng Liu, Xiaojuan Fan, Natalie Chin, Yue Xu, Jessica Suh, Soukaina Amniouel, Kaari Linask, Jizhong Zou, Markus Hafner, Lichun Ma, Wei Zheng, Yihong Ye.

Background: TAR DNA-binding protein 43 ( TDP-43) proteinopathy is a central hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet current experimental models fail to reproduce the full pathological spectrum without external stress or TDP-43 overexpression. This study aims to establish a human induced pluripotent stem cells (iPSC)-derived system that spontaneously manifests TDP-43 pathology driven by an ALS-associated TDP-43 mutation.
Methods: We generated forebrain 3-D organoid cultures from iPSC carrying the TDP-43 K181E patient mutation. Single-cell RNA sequencing was used to define transcriptional alterations across cell types, and enhanced crosslinking immunoprecipitation (eCLIP) was applied to examine the global RNA binding and splicing defects in mutant organoids. We further used immunostaining, RT-PCR and biochemical assays to confirm TDP-43 proteinopathy and validate findings from the multi-omics analyses.
Results: The TDP-43 K181E organoids recapitulated key disease features, including cytoplasmic p-TDP-43 accumulation, RNA dysregulation, and cryptic exon inclusion. Single-cell analysis revealed a population of immature neurons with enhanced neuroinflammation and altered translation capacity. Comparative transcriptomics showed that the ALS mutation-induced transcriptional changes strongly overlap with those in ALS patient-derived brains. eCLIP analysis showed that mutant TDP-43 exhibited altered RNA-binding specificity, resulting in widespread RNA mis-splicing and cryptic exon inclusion. RT-PCR confirmed PRDM2 , a gene regulating cell senescence, is mis-spliced in mutant cells. These defects collectively disrupt neuronal homeostasis and cell-cell communications.
Conclusions: Our iPSC-derived forebrain organoid model displays spontaneous TDP-43 proteinopathies and associated molecular dysfunctions without artificial manipulation. The model offers a robust platform for dissecting the mechanisms of TDP-43-mediated neurodegeneration and advancing therapeutic discovery in ALS and FTD.

DOI: https://doi.org/10.1101/2025.11.09.687455
bioRxiv. 2025 Nov 02. pii: 2025.10.31.685813. [Epub ahead of print]

KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS.

Phuong Le, Neeraj K Lal, Shuhao Xu, Sara Mumford, Megan Huang, Dong Yang, Orel Mizrahi, Benjamin Hoover, Brian Yee, Yuan Mei, Katherine Rothamel, Hsuan-Lin Her, Steven M Blue, Neil A Shneider, Gene W Yeo.

Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as RNA-binding proteins (RBPs) remain unclear. Here, we demonstrate that KIF5A, a neuron-specific kinesin implicated in amyotrophic lateral sclerosis (ALS), functions as an RBP. We show that KIF5A directly binds mRNAs encoding synaptic ribosomal proteins and is required for their synaptic localization and for maintaining normal synaptic composition and function. Additionally, we show ALS-linked KIF5A mutations confer gain-of-function properties, enhancing mRNA binding, increasing synaptic ribosomal protein accumulation, inducing neuronal hyperexcitability, and impairing stress responses. These findings reveal a previously unrecognized mechanism by which mutant KIF5A disrupts synaptic homeostasis. Our work positions a kinesin motor protein as an RBP with critical roles in mRNA transport, local translation, and stress response.
Highlights: KIF5A interacts with mRNA encoding synaptic ribosomal proteinsKIF5A is required for normal synaptic composition and functionKIF5A binds to G3BP1 and G3BP1 stress granule associated proteinsKIF5A mutant ALS patient-derived motor neurons have abnormal synaptic function and stress response.

DOI: https://doi.org/10.1101/2025.10.31.685813
Int J Mol Sci. 2025 Nov 08. pii: 10852. [Epub ahead of print]26(22):

SLP2/PHB Aggregates in ALS Mouse Models and Patients: Implications Beyond CHCHD10-Associated Motor Neuron Disease.

Emmanuelle C Genin, Françoise Lespinasse, Alessandra Mauri-Crouzet, Luc Dupuis, Véronique Paquis-Flucklinger.

  Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterized by motor neuron (MN) degeneration, frequently overlapping with frontotemporal dementia (FTD). Protein aggregation is a hallmark of these disorders, yet the role of aggregates in ALS pathogenesis remains unclear. Previously, stomatin-like protein 2 (SLP2) and prohibitin (PHB) aggregates were identified in a model of CHCHD10-related ALS (Chchd10S59L/+ mice). This study raises the question of the presence and possible involvement of these aggregates in ALS beyond CHCHD10-associated motor neuron disease (MND). Using immunohistofluorescence, we analyzed SLP2/PHB expression in the spinal MNs and hippocampus of two ALS mouse models: FusΔNLS and Sod1G86R. Additionally, post-mortem spinal cord tissues from 27 ALS and ALS-FTD patients were analyzed. SLP2/PHB aggregates were identified in spinal MNs and the hippocampus of FusΔNLS mice but not in Sod1G86R mice. In ALS patients, SLP2/PHB aggregation was observed in four cases, including two with C9ORF72 mutations. Interestingly, aggregates were absent in SOD1-associated ALS patients. These findings suggest that SLP2/PHB aggregation is not specific to CHCHD10 variants but may contribute to the pathogenesis of ALS from different origins. The age-related accumulation of these aggregates highlights their potential role in disease progression and as therapeutic targets. Future studies should investigate their mechanistic contributions across different ALS subtypes.

Keywords:  Amyotrophic Lateral Sclerosis; CHCHD10; SLP2/PHB aggregates; motor neuron disease

DOI:  https://doi.org/10.3390/ijms262210852
Neurosci Res. 2025 Nov 26. pii: S0168-0102(25)00174-9. [Epub ahead of print] 104991

Neurodegenerative Disease and Autophagy in iPSC models.

Sodbileg Odonchimed, Keiko Imamura, Haruhisa Inoue.

  Neurodegenerative diseases are characterized by the gradual deterioration of specific neuronal populations, ultimately resulting in motor, cognitive, or behavioral impairments. Despite the worldwide increase in disease incidence, effective therapies remain unavailable. A common pathological hallmark of neurodegenerative diseases is the accumulation of misfolded protein aggregates, which impair normal cellular function. Accordingly, numerous studies and therapeutic strategies have focused on targeting these toxic aggregates and protein quality control via autophagy, a vital cellular recycling mechanism. Autophagy dysregulation has been implicated in the pathogenesis of several neurodegenerative diseases. Induced pluripotent stem cell (iPSC) technology has emerged as a powerful platform for modeling neurodegenerative diseases, and iPSC-derived models provide human-relevant systems for studying autophagic dysfunction in vitro. In this review, we discuss the key findings of recent studies investigating autophagy in iPSC-based models of neurodegenerative diseases, including Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and other diseases.

Keywords:  autophagy; disease model; iPSCs; neurodegenerative disease

DOI:  https://doi.org/10.1016/j.neures.2025.104991
Brain Pathol. 2025 Nov 23. e70053

Upregulation of sphingomyelin and ABCA8 in response to TDP-43 pathology in amyotrophic lateral sclerosis brain.

Finula I Isik, Russell Pickford, Nicolas Dzamko, Kerry-Anne Rye, Woojin Scott Kim.

  Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease characterized by the degeneration of motor neurons and the presence of TAR DNA-binding protein 43 (TDP-43) aggregation in the brain. Dyslipidemia is a common feature of ALS, and increasing evidence indicates that lipid dysregulation in the central nervous system underlies ALS pathology. Sphingomyelin is a sphingolipid that is highly enriched in the human brain. However, very little is known about changes in sphingomyelin in the context of ALS brain. We therefore undertook a comprehensive analysis of sphingomyelin in the disease-affected motor cortex and disease-unaffected cerebellum in sporadic ALS with TDP-43 pathology using liquid chromatography-mass spectrometry. We found that sphingomyelin was significantly increased in the ALS motor cortex compared to controls and was strongly associated with disease duration. In contrast, sphingomyelin was unaltered in the cerebellum. The increase in sphingomyelin was associated with an upregulation of ATP-binding cassette subfamily A member 8 (ABCA8), a sphingomyelin transporter, only in the motor cortex of ALS. Importantly, both sphingomyelin and ABCA8 were associated with TDP-43 only in the motor cortex. These results suggest that increases in sphingomyelin and ABCA8 could be a protective response against TDP-43 pathology.

Keywords:  ABCA8; TDP‐43; amyotrophic lateral sclerosis; motor cortex; sphingomyelin

DOI:  https://doi.org/10.1111/bpa.70053
bioRxiv. 2025 Oct 15. pii: 2025.10.15.682650. [Epub ahead of print]

Elevation of the mechanically-sensitive protein emerin links nuclear mechanotransduction to tau-induced cytoskeletal remodeling in neurons.

Claira Sohn, Sammy Pardo, Dana Molleur, Satvik R Paduri, Morgan Lambert, Morgan G Thomas, Erich J Sohn, Susan T Weintraub, Bess Frost.

Tauopathies are a group of neurodegenerative disorders, including Alzheimer's disease, that are neuropathologically defined by deposition of pathological forms of tau in the brain. While tau is reported to drive neurotoxicity by negatively affecting cytoskeletal, nucleoskeletal, and genomic architecture, the mechanisms mediating tau-induced dysfunction of the cytoskeleton and nucleoskeleton are incompletely understood. Based on proteomic profiling, we identify a suite of cytoskeletal and nucleoskeletal proteins with differing abundance in a cellular model of tauopathy, iTau. Building upon previous findings that pathogenic forms of tau reduce nuclear tension, we find that protein levels of emerin, a central regulator of nuclear mechanotransduction, are significantly elevated in iTau cells and in induced pluripotent stem cell (iPSC)-derived neurons carrying a mutation in the microtubule-associated protein tau ( MAPT ) gene that causes autosomal dominant frontotemporal dementia. We find that neuronal emerin overexpression is sufficient to drive neurotoxicity, increase overall levels of filamentous actin (F-actin), and induce nuclear invagination, cellular phenotypes that also occur in settings of tauopathy. Mass spectrometry-based identification of emerin-interacting proteins in iTau-derived neurons reveals increased interactions with cytoskeletal proteins and reduced interactions with nuclear proteins. Indeed, we find that emerin relocalizes from the nucleus to the cytosol in the setting of tauopathy, suggesting that pathogenic tau impacts nuclear mechanotransduction pathways. Overall, we identify emerin as a mediator of cytoskeletal remodeling in tauopathy and provide a foundation for future studies into the mechanosensitive function of emerin in neurons.
SIGNIFICANCE STATEMENT: Cells experience and respond to diverse mechanical forces that shape their morphology, function, and survival through a process termed "mechanotransduction." While well studied in non-neuronal cells, neuronal mechanotransduction remains poorly understood despite exposure of the brain to vascular flow, movement, injury, and disease. We identify the mechanosensitive protein emerin as a key regulator of nuclear mechanotransduction in neurons. Emerin overexpression is sufficient to increase filamentous actin, induce nuclear invagination, and drive neurotoxicity, revealing a novel function for emerin in neurons. In cellular models of tauopathy, emerin is elevated and relocalizes from the nucleus to the cytoplasm, where it alters cytoskeletal structure. These findings establish emerin as a mechanosensitive regulator in neurons and link disrupted nuclear neuronal mechanotransduction to neurodegeneration.

DOI: https://doi.org/10.1101/2025.10.15.682650
Chem Sci. 2025 Nov 14.

Amyloidogenic oligomers derived from TDP-43 LCD promote the condensation and phosphorylation of TDP-43.

Bryan Po-Wen Chen, Chi-Chang Lee, Ruei-Yu He, An-Chi Huang, Jie-Rong Huang, Jerry Chun Chung Chan, Joseph Jen-Tse Huang.

The aberrant aggregation of TAR DNA-binding protein 43 (TDP-43) is a hallmark of amyotrophic lateral sclerosis (ALS). While TDP-43 aggregation can occur via both classical amyloidogenesis and phase separation-mediated mechanisms, the role of amyloidogenic oligomers in modulating TDP-43 condensation remains unclear. Herein, we employ a reverse micelle method to prepare uniform oligomers derived from the low-complexity domain of TDP-43, termed D1core oligomers. These amyloidogenic oligomers are toxic, potently induce phase separation of recombinant TDP-43 C-terminal domains, and promote phosphorylation of cytosolic TDP-43 condensates in cells. Compared to monomeric or fibrillar forms, D1core oligomers uniquely enhance the condensation propensity of wild-type TDP-43 and further potentiate aggregation of the ALS-associated A315T mutant. Live-cell studies using fluorescence recovery after photobleaching reveal that oligomer-induced condensates are modulated by HSP70, which preserves their liquid-like properties. These findings provide new insights into the interplay between TDP-43 oligomers, phase separation, and aggregation, advancing our understanding of ALS-related proteinopathy.

DOI: https://doi.org/10.1039/d5sc05433h
Structure. 2025 Nov 27. pii: S0969-2126(25)00436-8. [Epub ahead of print]

Structural basis for binding of RILPL1 to TMEM55B reveals a lysosomal platform for adaptor assembly through a conserved peptide motif.

Dieter Waschbüsch, Prosenjit Pal, Raja S Nirujogi, Melanie Cavin, Jaijeet Singh, Dario R Alessi, Amir R Khan.

  Inherited mutations in VPS35 and LRRK2 kinase lead to hyperphosphorylation of Rab GTPases. RH2 domain-containing proteins from the RILP homology family, such as RILPL1, are Rab effectors that recognize the LRRK2-phosphorylated switch 2 threonine of phospho-Rab8A and phospho-Rab10. Phospho-Rabs are also seen on lysosomal membranes in complex with RILPL1 and TMEM55B, a 284-residue lysosomal membrane protein lacking homology to known proteins. Here, we report crystal structures of the cytosolic region 80-166 of TMEM55B alone and in complex with a C-terminal RILPL1 peptide, which we define as the TMEM55B-binding motif (TBM). The RILPL1 TBM sits in a shallow groove across two tandem RING-like domains of TMEM55B, each forming a Zn2+-stabilized 40-residue β-sandwich. Co-immunoprecipitation and mass spectrometry studies indicate that TMEM55B forms complexes independently of phospho-Rabs with conserved TBMs found in JIP3, JIP4, OCRL, WDR81, and TBC1D9B. These studies suggest that TMEM55B acts as a central hub for adaptor recruitment on lysosomes.

Keywords:  LRRK2 kinase; RILPL1; TMEM55B; X-ray crystallography; cytosolic adaptor proteins; lysozome; membrane trafficking; phosphorylated Rab GTPases

DOI:  https://doi.org/10.1016/j.str.2025.11.003
Nat Commun. 2025 Nov 28. 16(1): 10761

Disruption of the PIKfyve complex unveils an adaptive mechanism to promote lysosomal repair and mitochondrial homeostasis.

Candice Kutchukian, Maria Casas, Rose E Dixon, Eamonn J Dickson.

Lysosomes are essential organelles that regulate cellular homeostasis through complex membrane interactions. Phosphoinositide lipids play critical roles in orchestrating these functions by recruiting specific proteins to organelle membranes. The PIKfyve/Fig4/Vac14 complex regulates PI(3,5)P₂ metabolism, and intriguingly, while loss-of-function mutations cause neurodegeneration, acute PIKfyve inhibition shows therapeutic potential in neurodegenerative disorders. We demonstrate that PIKfyve/Fig4/Vac14 dysfunction triggers a compensatory response where reduced mTORC1 activity leads to ULK1-dependent trafficking of ATG9A and PI4KIIα from the TGN to lysosomes. This increases lysosomal PI(4)P, facilitating cholesterol and phosphatidylserine transport at ER-lysosome contacts to promote membrane repair. Concurrently, elevated lysosomal PI(4)P recruits ORP1L to ER-lysosome-mitochondria three-way contacts, enabling PI(4)P transfer to mitochondria that drives ULK1-dependent fragmentation and increased respiration. These findings reveal a role for PIKfyve/Fig4/Vac14 in coordinating lysosomal repair and mitochondrial homeostasis, offering insights into cellular stress responses.

DOI: https://doi.org/10.1038/s41467-025-65798-6
Stem Cell Res Ther. 2025 Nov 23.

Cutting-edge treatments in amyotrophic lateral sclerosis: the role of molecular pathogenesis in targeted therapies.

Ramin Raoufinia, Ghazal Alyari, Amin Tadayoni Nia, Mohammad Reza Abbaszadegan, Ali Mahmoudi, Sajjad Shafaeibajestan, Ehsan Saburi, Jalil Tavakol-Afshari, Mehdi Hassani, Faezeh Jamali, Shahram Salari, Amir Reza Boroumand, Hamid Reza Rahimi.

  Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterized by the selective loss of motor neurons (MNs), leading to progressive muscle weakness, atrophy, and ultimately paralysis. This review provides a comprehensive overview of the molecular mechanisms underlying ALS pathogenesis, the genetic mutations associated with both familial and sporadic forms of the disease, and the latest therapeutic strategies aimed at mitigating disease progression. mutations in genes such as C9orf72, SOD1, TARDBP, and FUS have been implicated in ALS, with an intricate interplay of protein misfolding, oxidative stress, mitochondrial dysfunction, excitotoxicity, and neuroinflammation contributing to motor neuron degeneration. While current FDA-approved treatments such as Riluzole and Edaravone offer only modest benefits and do not significantly halt disease progression. Emerging therapies, including gene therapies (e.g., antisense oligonucleotides (ASOs) and CRISPR/Cas9, stem cell-based approaches, and neurotrophic factor supplementation, are demonstrating promising results in preclinical and early-phase clinical trials. novel approaches aim to target, modulate, and promote regeneration, renewed hope for future ALS treatments. However, several challenges remain, including effective delivery methods, safety concerns, and the inherent complexity of ALS pathology, ongoing research continues to explore these innovative interventions with the goal of improving clinical outcomes for patients. This review highlights the importance of personalized therapeutic approaches and underscores the necessity of continued innovation in ALS research, with the ultimate goal of developing disease-modifying therapies and, potentially, a cure for this fatal condition.

Keywords:   C9orf72 mutation; SOD1 mutation; Amyotrophic lateral sclerosis; CRISPR/Cas9; Gene therapy; Neurodegenerative diseases; Neurotrophic factors; RNA interference; Riluzole; Stem cell therapy

DOI:  https://doi.org/10.1186/s13287-025-04781-w
Proc Natl Acad Sci U S A. 2025 Dec 02. 122(48): e2513363122

Impaired AIS plasticity in ankyrin-G mutant mice alters cortical excitability and behavior.

Min Li, Bingqing Zhao, Zhimin Lu, Liu Zhe, Yue Han, Yating Chen, Huichao Wang, Yu Wang, Chunsheng Wu, Mingjie Zhang, Keyu Chen, Rui Yang.

  The developing brain undergoes neuroplasticity driven by learning, experience, and memory formation. The axon initial segment (AIS) is a specialized membrane domain within the proximal axon that initiates action potential. Studies have demonstrated that the AIS exhibits plasticity by altering its length and/or localization to adjust the excitability in response to neural stimuli. However, how AIS plasticity may affect brain function is unclear. The 480-kDa giant ankyrin-G protein (gAnkG) is the master organizer of AISs and nodes of Ranvier. Previously, we reported that a neurodevelopmental disorder-linked variant (Thr1861Met) in the neuron-specific domain of gAnkG causes the formation of diffused AISs in cultured ankyrin-G null neurons. Here, we generated a knock-in mouse harboring this mutation. The knock-in mice displayed impairments in motor coordination and social interaction. Neurons from these knock-in mice formed elongated AISs with no significant reduction in the accumulation of key AIS components-including ankyrin-G, β4-spectrin, voltage-gated sodium channels, and neurofascin. Crucially, unlike wild-type AISs, which shorten in response to stimulation by high K+ or chemogenetics (designer receptors exclusively activated by designer drugs), the elongated AISs in mutant neurons failed to undergo such shortening, indicating a deficit in AIS plasticity. Neurons in the primary motor cortex and anterior cingulate cortex of knock-in mice exhibited AISs of normal length at early stage but failed to undergo the developmental shortening observed in wild-type neurons; by postnatal day 60, this resulted in elongated AISs and increased neuronal excitability in these regions. Thus, the gAnkG protein mutation impairs activity-dependent AIS plasticity, leading to abnormal neuronal excitability and behavioral deficits.

Keywords:  ankyrin-G; axon initial segment; intrinsically disordered protein; neurodevelopmental disorders; neuron plasticity

DOI:  https://doi.org/10.1073/pnas.2513363122
Front Mol Biosci. 2025 ;12 1699266

Loss of ARF5 impairs recovery after lysosomal damage.

Martyna O Iwaniec, Christopher J Bott, James E Casanova.

  Lysosomal dysfunction is a defining feature of aging and neurodegenerative diseases, where lysosomal membrane permeabilization and release of its contents can trigger cellular death pathways. To counteract this, cells rely on lysosomal quality control mechanisms, many of which depend on lipid delivery to repair damaged membranes. However, the regulatory pathways governing this process remain unclear. In this study, we investigated whether canonical ARF GTPases, best known for their roles in Golgi and endosomal vesicular trafficking, are recruited to damaged lysosomes and contribute to their repair. Using LysoIP-based lysosome isolation, super-resolution immunofluorescence imaging, and functional assays in HeLa and HEK293 cells, we found that ARF1, ARF5, and ARF6 localize to lysosomal membranes following L-leucyl-L-leucine methyl ester (LLOME)-induced permeabilization. While loss of ARF6 did not impair recovery, ARF5 depletion resulted in a nearly complete block of lysosomal repair. These findings identify ARF proteins as early responders to lysosomal damage and suggest isoform-specific roles in coordinating the pathways of lysosomal quality control.

Keywords:  ARF; ORP; OSBP; lysosome; repair

DOI:  https://doi.org/10.3389/fmolb.2025.1699266
bioRxiv. 2025 Oct 15. pii: 2025.10.15.682441. [Epub ahead of print]

Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia.

Sang Hwa Kim, Claire E Boos, Mark Scalf, Akasha K Wilkemeyer, Lloyd M Smith, Randal S Tibbetts.

Ubiquilin-2 (UBQLN2) is a ubiquitin (Ub)-binding shuttle protein that is mutated in X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS/FTD-linked mutations in UBQLN2 disrupt its conformation, increasing its tendency to form cytoplasmic aggregates that may disrupt cellular regulation through loss-of-function (LOF) and gain-of-function (GOF) effects. To explore how ALS-associated mutations impact UBQLN2 function, we performed quantitative mass spectrometry (MS)-based interactome analysis using affinity-purified UBQLN2 from inducible pluripotent stem cells (iPSCs) and induced motor neurons (iMNs) expressing wild-type UBQLN2 (UBQLN2WT), a UBQLN2P497H clinical mutant, or a UBQLN24XALS allele harboring four disease mutations. Proteins showing enhanced association with ALS-mutant UBQLN2 proteins included PEG10, a known degradation target of UBQLN2, and BAG6, a chaperone involved in the triage of mislocalized proteins (MLPs). BAG6 knockdown inhibited the solubility recovery of both wild-type and ALS-mutant UBQLN2 proteins following heat stress (HS), suggesting it functions as a UBQLN2 holdase. In addition, knockdown of BAG6 or knockout of UBQLN2 led to PEG10 accumulation, implicating both in PEG10 turnover; however, neither BAG6 nor UBQLN2 was required for PEG10 degradation in response to HS. The aggregation prone UBQLN24XALS mutant showed increased PEG10 binding and modestly delayed PEG10 turnover while PEG10 degradation was not significantly different between UBQLN2WT and UBQLN2P497H iPSCs. The combined findings implicate BAG6 a UBQLN2 holdase and identify a suite of proteins whose altered binding may contribute to pathologic changes in UBQLN2-associated ALS/FTD.

DOI: https://doi.org/10.1101/2025.10.15.682441
Adv Protein Chem Struct Biol. 2025 ;pii: S1876-1623(25)00088-4. [Epub ahead of print]148 355-377

Protein misfolding and its dual role in neurodegeneration and cancer progression.

Rajeshwer Singh Jamwal, Bhawani Sharma, Minerva, Agamya Gupta, Swati Misri, Raju Shankaryan, Ruchi Shah, Rakesh Kumar.

  Protein misfolding is a fundamental biological process with profound implications for human health and disease. Typically, proteins assume precise three-dimensional structures to perform their functions, a process safeguarded by the proteostasis network, which comprises molecular chaperones, the ubiquitin-proteasome system (UPS), and autophagy. However, genetic mutations, oxidative stress, and environmental insults can disrupt folding, leading to the accumulation of non-functional or toxic conformations. In neurodegenerative diseases such as Huntington's disease (HD), Parkinson's disease (PD), Alzheimer's disease (AD), Amyotrophic lateral Sclerosis (ALS), chronic misfolding results in toxic protein aggregates like amyloid-β, tau, and α-synuclein. These disrupt synaptic function, induce oxidative and nitrosative stress, and trigger apoptosis, ultimately leading to progressive neuronal loss. Dysregulation of the unfolded protein response (UPR) and weakened proteostasis with aging exacerbate disease pathology. In contrast, cancer cells utilize protein misfolding to enhance their survival and progression. Misfolded oncoproteins, such as mutant p53, not only evade degradation but also acquire oncogenic properties. Tumor cells hijack the UPR and chaperone networks, upregulate heat shock proteins, and manipulate oxidative stress responses to withstand hypoxia, nutrient deprivation, and rapid proliferation. Cancer stem cells (CSCs) further adapt to proteotoxic stress, contributing to tumor heterogeneity, therapy resistance, and immune evasion. The dual role of protein misfolding, driving degeneration in neurons while supporting proliferation in tumors, underscores its centrality in disease biology. Future research should focus on identifying early biomarkers of proteostasis imbalance and exploiting shared molecular pathways for the development of novel therapeutic interventions.

Keywords:  Cancer progression; Molecular chaperones; Neurodegeneration; Protein misfolding; Proteostasis; Ubiquitin–proteasome system (UPS); Unfolded protein response (UPR)

DOI:  https://doi.org/10.1016/bs.apcsb.2025.10.001
J Cell Biol. 2026 Jan 05. pii: e202503081. [Epub ahead of print]225(1):

Homocysteine disrupts lysosomal function by V-ATPase inhibition.

Yang Yang, Qianjin Kong, Chaolian Liu, Fengyang Wang, Meijiao Li, Shalan Li, Yuehui Shi, Leonard Krall, Xin Wang, Shan He, Kai Jiang, Xuna Wu, Mei Yang, Chonglin Yang.

Lysosomes are degradation and signaling organelles central to metabolic homeostasis. It remains unclear whether and how harmful metabolites compromise lysosome function in the etiopathology of metabolic disorders. Combining Caenorhabditiselegans and mouse models, we demonstrate that homocysteine, an intermediate in methionine-cysteine metabolism and the cause of the life-threatening disease homocystinuria, disrupts lysosomal functions. In C. elegans, mutations in cystathionine β-synthase cause strong buildup of homocysteine and developmental arrest. We reveal that homocysteine binds to and homocysteinylates V-ATPase, causing its inhibition and consequently impairment of lysosomal degradative capacity. This leads to enormous enlargement of lysosomes with extensive cargo accumulation and lysosomal membrane damage in severe cases. Cbs-deficient mice similarly accumulate homocysteine, displaying abnormal or damaged lysosomes reminiscent of lysosomal storage diseases in multiple tissues. These findings not only uncover how a metabolite can damage lysosomes but also establish lysosomal impairment as a critical contributing factor to homocystinuria and homocysteine-related diseases.

DOI: https://doi.org/10.1083/jcb.202503081
bioRxiv. 2025 Nov 09. pii: 2025.11.07.687201. [Epub ahead of print]

Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics.

Hailey Q Wang, Demetria G Fortson, Eavan D Burton, Hunter S Whitbeck, Briana M Robles, Letitia Bortey, Avi J Adler, Jordan I Kalai, Giovanna Napoleone, Erin L Barnhart.

Mitochondrial transport, fusion, and fission are necessary for neuronal development, but the role of mitochondrial dynamics in neuronal maintenance remains unclear. In this work, we employed functional in vivo imaging of neurons in the Drosophila visual system, HS ("horizontal system") cells, to determine how adult-onset deficits in mitochondrial dynamics affect mitochondrial localization, local regulation of ATP, and dendrite maintenance. In mature HS neurons, inhibition of mitochondrial transport or fusion depleted mitochondria from the dendrite over time but, surprisingly, had no effect on dendrite morphology. Moreover, adult-restricted mitochondrial mis- localization affected neither visual stimulus-driven dendritic calcium responses nor local, dynamic regulation of ATP levels. In contrast, when induced during development, the same perturbations caused mitochondrial mis-localization, loss of dendrite complexity, abrogation of stimulus-locked calcium responses and ATP fluctuations, and age-dependent dendrite degeneration. Thus, although mitochondrial dynamics are necessary during neuronal development, mature dendrites are capable of maintaining form and function in vivo in the absence of properly-positioned mitochondria.

DOI: https://doi.org/10.1101/2025.11.07.687201
Mol Neurobiol. 2025 Nov 22. 63(1): 142

Brain Organoids in Neurodegenerative Disease Modeling: Advances, Applications and Future Perspectives.

Wei Wang, Shiyi Tan, Xulei Zuo, Xingxing Gao, Li Ma, Rongli Sun, Geyu Liang, Lihong Yin, Yuepu Pu, Juan Zhang.

  Neurodegenerative diseases (NDDs) represent incurable and debilitating conditions characterized by progressive deterioration of neurological function. Investigating neurodegeneration remains a critical global challenge in aging societies. Brain organoids-self-organizing three-dimensional structures derived from human pluripotent stem cells-recapitulate cell types and cytoarchitectures of the developing human brain. This in vitro model system has advanced our bridge between conventional two-dimensional cultures and in vivo models. Brain organoids emulate early neural tube formation, neuroepithelial differentiation, and whole-brain regionalization. Furthermore, region-specific organoid models now facilitate mechanistic investigation into acquired and inherited NDDs' pathogenesis, alongside drug discovery and toxicity screening. In this review, we (i) delineate the epidemiology and pathobiology of major NDDs, (ii) analyze limitations of current animal models, (iii) critically evaluate brain organoid generation methodologies, and (iv) focus on organoid applications in modeling Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS).

Keywords:  Brain organoids; Disease modeling; Human-induced pluripotent stem cells (hiPSCs); Neurodegenerative diseases

DOI:  https://doi.org/10.1007/s12035-025-05293-7
Methods Mol Biol. 2026 ;2974 227-237

Lentiviral Vector-Mediated Gene Delivery for iPSC-Related Neuroscience Research.

Taro Okunomiya, Keiko Imamura, Taku Kashiyama, Takashi Sakurai, Hiroyuki Hioki, Haruhisa Inoue.

  The induced pluripotent stem cell (iPSC) technology provides human neural cells unprecedented material for neuroscience research. Lentiviral vectors have the advantage of being able to transfer genes into nondividing cells, which is useful for the identification and purification of specific neurons generated from human iPSCs, as well as for analysis of their function. Furthermore, the lentiviral vector has long-term expression and large gene capacity. This chapter describes protocols for lentiviral generation, labeling of iPSC-derived motor neurons with fluorescent proteins, and imaging of synaptic function.

Keywords:  Gene delivery; Induced pluripotent stem cells; Lentiviral vector; Nondividing cells; Purification; Synapse imaging

DOI:  https://doi.org/10.1007/978-1-0716-4807-0_19
Biophys J. 2025 Nov 27. pii: S0006-3495(25)03448-4. [Epub ahead of print]

Dynamics of Excitability in Axonal Trees.

Laurie D Cohen, Tamar Galateanu, Shimon Marom.

  We report that axons of cortical neurons, structurally intricate excitable media, maintain remarkably high fidelity in transmitting somatic spike timing, even during complex spontaneous network activity that includes extremely short (2-3 msec) inter-spike intervals. This robustness underscores their function as reliable conducting devices under physiological conditions. It is nevertheless well established that under artificially imposed, high-rate pulsing stimuli, axonal conduction can fail, with vulnerability depending on distance and branching. In line with this, we demonstrate that conduction failures can also occur at frequencies as low as 10 Hz, provided that stimulation is sustained for several seconds. Under these conditions, propagation delays increase and failures accumulate, particularly in distal branches, whereas effects are negligible at 1-4 Hz. Simulations incorporating cumulative sodium channel inactivation at vulnerable sites reproduce these dynamics. Our findings refine the view of axons as active, heterogeneous structures: they are exceptionally reliable across most physiological regimes, yet exhibit limits under prolonged or extreme stimulation, a regime that is critical for understanding axonal excitability, especially during sustained drive or in pathological conditions.

Keywords:  axon physiology; excitability; high-density microelectrode arrays (HD-MEA); inactivation; neuroscience

DOI:  https://doi.org/10.1016/j.bpj.2025.11.2682
Eur J Neurosci. 2025 Nov;62(10): e70328

Development of a Human Preclinical Platform for the Identification of Neuroprotective Compounds.

Raquel Guerrero González, Elif Nur Yilmaz, Stefanie Albrecht, Maurine Fucito, Damiana Pieragostino, Alina Schmidt, Simone König, Una FitzGerald, Tanja Kuhlmann.

  Multiple sclerosis (MS) is the most common inflammatory and demyelinating disease affecting the central nervous system (CNS). While immune-modulating drugs can prevent new lesions by targeting lymphocyte activity, treating relapse-independent disease progression remains challenging. Persisting CNS inflammation, leading to axonal and neuronal injury along with failure of compensatory mechanisms, such as brain plasticity and remyelination, drives disease progression. Thus, identifying neuroprotective and/or remyelination-promoting compounds is urgently needed. We developed an in vitro platform utilizing human-induced pluripotent stem cell (iPSC)-derived neurons and oligodendrocytes to assess neuroprotective and potentially promyelinating effects of selected compounds. We established assays mimicking MS pathophysiologies, such as neuronal loss and axonal injury. Proteomic analysis revealed modulation of molecular mechanisms. Findings were validated in an acute cuprizone (CPZ) mouse model. We demonstrated that pioglitazone and minocycline protected against glutamate-induced axonal injury, rotenone-induced neuronal death and promoted oligodendrocyte differentiation. Proteomic analyses suggest that pioglitazone's neuroprotective effect may involve reducing mitochondrial reactive oxygen species (ROS) production via PGC-1α and stabilizing axonal transport through GSK3β phosphorylation. Minocycline mainly impacted glutathione metabolism. In the cuprizone model, both compounds displayed neuroprotective effects but did not reduce demyelination or oligodendroglial loss. In summary, our findings demonstrate that human preclinical IPSC platforms can be used to characterize the neuroprotective properties of compounds and thus may aid the selection of drugs for clinical trials. Moreover, the platform's flexibility allows for the easy incorporation of additional disease-specific phenotypic assays.

Keywords:  axonal damage; demyelination; glutamate excitotoxicity; human iPSC; minocycline; multiple sclerosis; neuroprotection; oligodendrocyte differentiation; oxidative stress; pioglitazone

DOI:  https://doi.org/10.1111/ejn.70328
Life (Basel). 2025 Oct 24. pii: 1665. [Epub ahead of print]15(11):

Exploring TANK-Binding Kinase 1 in Amyotrophic Lateral Sclerosis: From Structural Mechanisms to Machine Learning-Guided Therapeutics.

Farah Anjum, Maram Jameel Hulbah, Anas Shamsi, Taj Mohammad.

  TANK-binding kinase 1 (TBK1) has emerged as one of the most compelling genetic contributors to amyotrophic lateral sclerosis (ALS), with heterozygous loss-of-function and pathogenic missense variants identified in patients across the ALS-frontotemporal dementia (FTD) spectrum. TBK1 participates in various core cellular processes associated with motor neuron vulnerability, including autophagy, mitophagy, and innate immune regulation, indicating that TBK1 is likely a key determinant of ALS pathogenesis. Structurally, TBK1 exhibits a trimodular organization comprising a kinase domain, a ubiquitin-like domain, and a scaffold/dimerization domain. Multiple experimentally resolved conformations and inhibitor-bound complexes provide a foundation for structure-guided therapeutic design. Here, we synthesize current genetic and mechanistic evidence linking TBK1 dysfunction to ALS, emphasizing its dual roles in autophagy and neuroinflammation. We also summarize advances in structure-based and AI-assisted drug discovery approaches targeting TBK1. Finally, we outline key translational challenges, including isoform selectivity, biomarker validation, and central nervous system (CNS) delivery, highlighting TBK1 as a promising yet complex therapeutic target in ALS. By integrating computational modeling, machine learning frameworks, and experimental pharmacology, future research may accelerate the translation of TBK1 modulators into clinically effective therapies.

Keywords:  TANK-binding kinase 1; amyotrophic lateral sclerosis; deep learning; drug screening; machine learning; structure-function relationship

DOI:  https://doi.org/10.3390/life15111665
Autophagy. 2025 Nov 23. 1-43

Autophagy and mitophagy at the synapse and beyond: implications for learning, memory and neurological disorders.

Jiayi Lu, Damian N Di Florio, Patricia Boya, Sandra Maday, Wolfdieter Springer, Charleen T Chu.

  The human brain is one of the most metabolically active tissues in the body, due in large part to the activity of trillions of synaptic connections. Under normal conditions, macroautophagy/autophagy at the synapse plays a crucial role in synaptic pruning and plasticity, which occurs physiologically in the absence of disease- or aging-related stressors. Disruption of autophagy has profound effects on neuron development, structure, function, and survival. Neurons are dependent upon maintaining high-quality mitochondria, and alterations in selective mitochondrial autophagy (mitophagy) are heavily implicated in both genetic and environmental etiologies of neurodegenerative diseases. The unique spatial and functional demands of neurons result in differences in the regulation of metabolic, autophagic, mitophagic and biosynthetic processes compared to other cell types. Here, we review recent advances in autophagy and mitophagy research with an emphasis on studies involving primary neurons in vitro and in vivo, glial cells, and iPSC-differentiated neurons. The synaptic functions of genes whose mutations implicate autophagic or mitophagic dysfunction in hereditary neurodegenerative and neurodevelopmental diseases are summarized. Finally, we discuss the diagnostic and therapeutic potentials of autophagy-related pathways.Abbreviations: AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; APP: amyloid beta precursor protein; ASD: autism-spectrum disorder; BDNF: brain-derived neurotrophic factor; BPAN: β-propeller protein associated neurodegeneration; CR: caloric restriction; ΔN111: deleted N-terminal region 111 residues; DLG4/PSD95: discs large MAGUK scaffold protein 4; ER: endoplasmic reticulum; FTD: frontotemporal dementia; HD: Huntington disease; LIR: LC3-interacting region; LRRK2: leucine rich repeat kinase 2; LTD: long-term depression; LTP: long-term potentiation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; OMM: outer mitochondrial membrane; PD: Parkinson spectrum diseases; PGRN: progranulin; PINK1: PTEN induced kinase 1; PRKA/PKA: protein kinase cAMP-activated; PtdIns3P: phosphatidylinositol-3-phosphate; p-S65-Ub: ubiquitin phosphorylated at serine 65; PTM: post-translational modification; TREM2: triggering receptor expressed on myeloid cells 2.

Keywords:  Biomarkers; Parkinson disease; dementia; dendritic spines; mitochondria; neurodegenerative diseases; neurodevelopmental disorders; synaptic plasticity

DOI:  https://doi.org/10.1080/15548627.2025.2581217
bioRxiv. 2025 Oct 30. pii: 2025.10.28.685144. [Epub ahead of print]

Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration.

Irene Dalla Costa, Emily Michenfelder, Sophia Siciliano, Anika Tapita, Courtney N Buchanan, Lauren S Vaughn, Jinyoung Lee, Juan Oses-Prieto, Chunlong Ma, Elizabeth Thames, Nitzan Samra, Shifra Ben-Dor, Rebecca Haffner-Krausz, Mary McElveen, Terika P Smith, Nabanita Nawar, Pimyupa Manaswiyoungkul, Patrick T Gunning, Mike Fainzilber, Alma L Burlingame, Haining Zhu, Eran Perlson, Pabitra K Sahoo, Jeffery L Twiss.

Nerve injury triggers localized translation of axonal mRNAs to respond to injury and nerve regeneration. The core stress granule protein G3BP1 sequesters axonal mRNAs in granules before and after axotomy. G3BP1 granule disassembly can be regulated by post-translational modifications, including phosphorylation of S149 phosphorylation and acetylation of human K376 (mouse K374). Axonal G3BP1 undergoes phosphorylation after axotomy, but acetylation of G3BP1 in axons was unknown. Here we show that rodent G3BP1 undergoes K374 acetylation after axotomy is ELP3-dependent, which enhances axonal protein synthesis, accelerates nerve regeneration, and supports functional recovery. ELP3-depleted neurons exhibit reduced axon growth and increased axonal G3BP1 granules. The proximal axons degenerate rapidly despite maintaining soma connectivity, an effect prevented by expression of acetylmimetic G3BP1.Together, these findings identify G3BP1 acetylation via ELP3 as a critical regulator of both axonal regeneration and neuronal resilience, revealing a post-translational mechanism that links stress granule regulation to neuronal repair and protection.

DOI: https://doi.org/10.1101/2025.10.28.685144
bioRxiv. 2025 Nov 05. pii: 2025.11.04.686319. [Epub ahead of print]

An induced pluripotent stem cell-based chemical genetic approach for studying spinal muscular atrophy.

Richard M Giadone, Kristina M Holton, Xiaoyu Hu, Ted Natoli, Sabrina Ghosh, Stanley P Gill, Aravind Subramanian, Lee L Rubin.

Spinal muscular atrophy (SMA) is a genetic disease characterized by degeneration of spinal cord motor neurons and neuromuscular junctions. Despite recent development in therapies for SMA, treatment efficacy largely relies on administration of drugs early in disease progression and is impacted by underlying patient genetics. Drug discovery for other diseases of the central nervous system (CNS) has also been hindered by heterogeneity in patient genetics and clinical presentations, as well as the need for early intervention. To address these hurdles, we utilized a chemical genetic-based screening approach to adapt the Connectivity Map (CMAP)/L1000 platform to study SMA. To do this, we differentiated moderate and severe SMA patient-specific induced pluripotent stem cells into neuronal cells utilizing a forward programming differentiation protocol, exposed each to 360 neuroactive or CNS disease-related compounds, and interrogated resulting changes in expression of >400 neural genes in a platform we term CMAP neuro . In doing so, we generated 4,559 transcriptional profiles identifying stimuli that modulate gene expression differences across SMA neurons. Finally, we make these data queryable, allowing the research community to 1.) identify CNS disease-related perturbagens that mimic or reverse differentially expressed genes, or 2.) explore the transcriptional response of a given perturbation in diverse SMA neuronal cells.

DOI: https://doi.org/10.1101/2025.11.04.686319
bioRxiv. 2025 Oct 20. pii: 2025.10.20.683480. [Epub ahead of print]

A distal promoter and aberrant splicing enable canonical translation of out-of-frame proteins in Huntington's disease.

Rachel Anderson, Tanishk Soni, Ankur Jain.

Expanded CAG trinucleotide repeats cause more than a dozen neurodegenerative diseases, including Huntington's disease (HD). In several disorders, these repeats are translated in multiple reading frames without identifiable AUG start codons. This process, called repeat-associated non-AUG (RAN) translation, generates aggregation-prone proteins, but its molecular basis remains unclear. Here, using affinity capture of CAG-repeat-containing RNAs, we identify a previously unannotated promoter ~33 kb upstream of the HTT gene. Transcripts initiating from this promoter undergo repeat-length-dependent aberrant splicing into exon 1 of the canonical HTT, embedding the CAG repeat in AUG-initiated frames encoding polyalanine and polyserine proteins. Comparative genomics indicates that this upstream promoter is primate-specific, helping explain inconsistencies across rodent models. Our findings establish a direct, AUG-dependent, splicing-mediated mechanism for out-of-frame repeat proteins in HD, expose critical gaps in current animal models, and identify novel splice junctions as potential therapeutic targets.

DOI: https://doi.org/10.1101/2025.10.20.683480
Autophagy. 2025 Nov 28.

Portioning organelles for autophagic clearance.

Mikhail Rudinskiy, Maurizio Molinari.

  The lysosomal/vacuolar clearance of portions of organelles including the endoplasmic reticulum (ER), mitochondria, the Golgi apparatus and the nucleus, organellophagy, is mediated by autophagy receptors anchored at the surface of their respective organelles. Organellophagy receptors are activated, induced or derepressed in response to stimuli such as nutrient or oxygen deprivation, accumulation of toxic or aged macromolecules, membrane depolarization, pathogen invasion, cell differentiation and many others. Their activation drives the portioning of the homing organelle, and the engagement of Atg8/LC3/GABARAP (LC3) proteins via LC3-interacting regions (LIRs) that results in autophagic clearance. In our latest work, we elaborate on the fact that all known mammalian and yeast organellophagy receptors expose their LIR embedded within intrinsically disordered regions (IDRs), i.e. cytoplasmic stretches of amino acids lacking a fixed three-dimensional structure. Our experiments reveal that the IDR modules of organellophagy receptors are interchangeable, required and sufficient to induce the fragmentation of the organelle that displays them at the limiting membrane, independent of LC3 engagement. LC3 engagement drives lysosomal delivery. Building on these findings, we propose harnessing practical and therapeutic potential of controlled organelle fragmentation and organellophagy through ORGAnelle TArgeting Chimeras (ORGATACs).

Keywords:  Endoplasmic reticulum (Er)phagy; ORGAnelle TArgeted chimeras (ORGATACs); intrinsically disordered regions (IDRs); mitophagy; organellophagy receptors; targeted organelle degradation

DOI:  https://doi.org/10.1080/15548627.2025.2597458
Nat Commun. 2025 Nov 26. 16(1): 10537

The neuropathy-linked protein TECPR2 is a Rab5 effector that regulates cargo recycling from early endosomes.

Sankalita Paul, Rajat Pant, Poonam Sharma, Kshitiz Walia, Suhasi Gupta, Adhil Aseem, Kamlesh Kumari Bajwa, Ruben George, Yudish Varma, Tripta Bhatia, Rajesh Ramachandran, Amit Tuli, Mahak Sharma.

Small GTP-binding proteins of the Rab, Arf, and Arf-like family mediate the recruitment of their effectors to subcellular membrane-bound compartments, which in turn mediate vesicle budding, motility, and tethering. Here, we report that Tectonin-β-propeller repeat containing protein 2 (TECPR2), a protein mutated in a form of hereditary sensory and autonomic neuropathy (HSAN), is an effector of early endosomal Rab protein, Rab5. We demonstrate that the HSAN-associated missense variants of TECPR2 are defective in Rab5 binding and, consequently, in membrane recruitment. Furthermore, our findings reveal that depletion of TECPR2 impairs recycling of a subset of cargo receptors, including α5β1 integrins, leading to their lysosomal degradation. TECPR2 interacts with SNX17 and subunits of the WASH complex, molecular players that regulate the formation of actin-dependent cargo retrieval subdomain on the early endosomes. Finally, we show that TECPR2 depletion in zebrafish embryos results in decreased survival, impaired movement and altered neuromuscular synaptic morphology. Our study suggests that TECPR2 functions as a linker between Rab5 and the actin-dependent cargo retrieval machinery, providing insights into how mutations in TECPR2 may result in a neurodegenerative disorder.

DOI: https://doi.org/10.1038/s41467-025-65568-4
Nat Commun. 2025 Nov 28. 16(1): 10764

CYFIP1 governs the development of cortical axons by modulating calcium availability.

Carlotta Ricci, Maëllie Julie Midroit, Federico Caicci, Tilmann Achsel, Nuria Domínguez-Iturza, Claudia Bagni.

The human CYFIP1 gene is linked to Autism Spectrum Disorder (ASD) and Schizophrenia (SCZ), both associated with brain connectivity defects and corpus callosum abnormalities. Previous studies demonstrated that Cyfip1-heterozygous mice exhibit diminished bilateral functional connectivity and callosal defects-resembling observations in ASD and SCZ patients. Here, we demonstrate that CYFIP1 is crucial for cortical axonal development and identify insufficient calcium uptake as the pivotal mechanism. In vivo, Cyfip1 heterozygosity delays callosal axon growth and arborization. Additionally, Cyfip1-deficient cortical neurons and axons have reduced intracellular calcium, along with impaired mitochondria morphology, activity, and motility. Mechanistically, CYFIP1 binds and stabilises the mRNA of specific voltage-gated calcium channel subunits, explaining the decreased calcium concentration in Cyfip1+/- cells. Notably, elevating intracellular calcium rescues delayed axonal growth and mitochondrial defects in Cyfip1-deficient neurons. These findings highlight that, by regulating mRNA metabolism, CYFIP1 ensures proper callosal development, offering insights into brain connectivity disruptions underlaying neurodevelopmental disorders.

DOI: https://doi.org/10.1038/s41467-025-65801-0
Exp Neurol. 2025 Nov 20. pii: S0014-4886(25)00429-7. [Epub ahead of print]397 115564

Axon guidance deficits in a human sensory-like neuron model of Fabry disease.

Christoph Erbacher, Aneeta Andrews, Till Sauerwein, Maximilian Breyer, Panagiota Arampatzi, Maximilian Koch, Stephanie Lamer, Tom Gräfenhan, Andreas Schlosser, Nurcan Üçeyler.

  Fabry disease (FD) is a rare genetic galactosidase alpha (GLA) gene associated lysosomal disorder caused by alpha-galactosidase A (AGAL) deficiency, leading to sphingolipid (globotriaosylceramide, Gb3) accumulation in multiple tissues. Burning pain due to small fiber neuropathy is an early symptom with great impact on health-related quality of life. The pathophysiological role of Gb3 accumulations in sensory neurons of the dorsal root ganglia is incompletely understood. We have differentiated induced pluripotent stem cells of an isogenic GLA knockout line (p.S364del, hemizygous) and its healthy control into sensory-like neurons to model FD in vitro. We have compared both lines on transcriptional and proteomic level and investigated the effects of AGAL enzyme supplementation. FD sensory neurons showed dysregulation of disease-related pathways, including axon guidance at both RNA and protein level and microfluidic assays revealed shorter neurite length. While AGAL did not restore the transcriptomic state, it reduced Gb3 accumulation and lowered protein ephrin 5 A and glycoprotein M6A level. These findings highlight axon guidance alterations in an isogenic human FD sensory neuron model, with potential implications for early central and peripheral innervation in small fiber neuropathy.

Keywords:  Axon guidance; Disease model; Fabry disease; Induced pluripotent stem cells; Sensory-like neuron

DOI:  https://doi.org/10.1016/j.expneurol.2025.115564
J Vis Exp. 2025 Nov 04.

Molecular Mechanism of Hydroxyl Safflower Yellow A in Knee Osteoarthritis through Modulation of Autophagy via Inhibition of the HIF-1α/BNIP3 Pathway.

Dao Ke, Yanni Ma, Jin Chen, Jianwen Chen, Haofan Chen.

The reduction of autophagy in cartilage tissue is closely linked to the development of knee osteoarthritis (KOA), yet the mechanisms by which Hydroxyl safflower yellow A (HSYA) exerts protective effects remain incompletely understood. In this study, human KOA chondrocytes were isolated and assigned to different treatment groups, including normal control, blank model, HSYA, hypoxia-inducible factor-1α (HIF-1α) inhibitor, autophagy inducer, HSYA combined with HIF-1α inhibitor, and HSYA combined with autophagy inducer. Proinflammatory cytokines (IL-1β, TNF-α, IL-6) were quantified by ELISA, protein expression of HIF-1α, BNIP3, and autophagy-related markers was examined by Western blotting, and autophagic vesicles in mitochondria were evaluated using monodansylcadaverine staining and transmission electron microscopy. Compared with the normal control, the blank model group showed significantly increased levels of IL-1β, TNF-α, IL-6, and HIF-1α, accompanied by higher apoptosis rates, reduced proliferation, and downregulation of autophagy-related proteins (P < 0.05). Treatment with HSYA, HIF-1α inhibitor, or autophagy inducer significantly upregulated autophagy-related protein expression and reduced inflammatory cytokine levels. Moreover, HSYA combined with HIF-1α inhibitor or autophagy inducer produced the most pronounced effects, with marked reductions in cytokine release and apoptosis, along with enhanced chondrocyte proliferation and mitochondrial autophagic vesicle formation (P < 0.05). These findings demonstrate that HSYA exerts chondroprotective effects in KOA, at least in part, through inhibition of the HIF-1α/BNIP3 pathway, thereby promoting autophagy and attenuating inflammatory injury in chondrocytes.

DOI: https://doi.org/10.3791/69491