bims-axbals 2025-07-27 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2025–07–27
33 papers selected by
TJ Krzystek

Rapid and inducible mislocalization of endogenous TDP43 in a novel human model of amyotrophic lateral sclerosis.
PPM1M, an LRRK2-counteracting, phosphoRab12-preferring phosphatase with a potential link to Parkinson's disease.
Dysregulation of huntingtin interacting protein networks in human juvenile Huntington's disease brain.
Using circular RNAs to target toxic RNA-binding proteins in amyotrophic lateral sclerosis.
Secretory autophagy mediates lysosomal and autophagic degradation for α-synuclein proteostasis.
Leucine-Rich Repeat Kinase 2 Regulates Mitochondria for Zygotic Genome Activation in Mouse Early Embryos.
Targeting oxidized phosphatidylcholines in SOD1-associated ALS: therapeutic potential of PC-OxPL-VecTab®.
ALS-associated RNA-binding proteins promote UNC13A transcription through REST downregulation.
RNA helicase maheshvara interacts with TDP-43 and exacerbates neurodegeneration in Drosophila model of amyotrophic lateral sclerosis.
Investigation of ABCA4 Missense Variants and Potential Small Molecule Rescue in Retinal Organoids.
Trimeric superoxide dismutase 1 antibody as a universal biomarker for ALS.
Tissue-engineered neuromuscular organoids.
M6A-dependent RNA condensation underlies FUS autoregulation and can be harnessed for ALS therapy development.
Dicer Is Involved in Cytotoxicity and Motor Impairment Induced by TBPH Deficiency.
CircRNA_26782 Regulates Axonal Growth via Inhibiting the Autophagy Pathway in a Rat Model of Spinal Cord Injury.
Xenotransplantation of Human Umbilical Mesenchymal Stromal Cells Derived from Wharton's Jelly Mitigates Mouse Amyotrophic Lateral Sclerosis.
Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids.
Neurodegenerative disease in C9orf72 repeat expansion carriers: population risk and effect of UNC13A.
Effects of SLC6A8 mutation-induced creatine deficiency on cellular function in fibroblasts.
Role of Mitochondria-Associated ER in Apoptosis.
CRISPR/Cas9-mediated generation of two isogenic CEP290-mutated iPSC lines.
Protein Misfolding and Aggregation as a Mechanistic Link Between Chronic Pain and Neurodegenerative Diseases.
Dysregulation of the endosomal sorting complex III is linked to neurodegeneration in progressive multiple sclerosis.
Protocol for CRISPR-based manipulation and visualization of endogenous α-synuclein in cultured mouse hippocampal neurons.
Early and non-destructive prediction of the differentiation efficiency of human induced pluripotent stem cells using imaging and machine learning.
Synovial organoids: From fundamental construction to groundbreaking applications in arthritic disorders.
TFEB overexpression alleviates autophagy-lysosomal deficits caused by progranulin insufficiency.
The emerging role of eIF5A hypusination as a unique and underexplored mechanism in proteinopathies and neurological diseases.
Unraveling the mystery: How autophagy deficiency in dopaminergic neurons drives human Parkinson's disease.
Hypergravity and ERK Inhibition Combined Synergistically Reduce Pathological Tau Phosphorylation in a Neurodegenerative Cell Model.
A Model-Based Approach to Neuronal Electrical Activity and Spatial Organization Through the Neuronal Actin Cytoskeleton.
A High-Throughput ImmunoHistoFluorescence (IHF) Method for Sub-Nuclear Protein Analysis in Tissue.
3D-Printed Scaffolds Promote Enhanced Spinal Organoid Formation for Use in Spinal Cord Injury.

Elife. 2025 Jul 24. pii: RP95062. [Epub ahead of print]13

Rapid and inducible mislocalization of endogenous TDP43 in a novel human model of amyotrophic lateral sclerosis.

Johanna Ganssauge, Sophie Hawkins, Seema Chandramohan Namboori, Szi Kay Leung, Jonathan Mill, Akshay Bhinge.

  Transactive response DNA binding protein 43 kDa (TDP43) proteinopathy, characterized by the mislocalization and aggregation of TDP43, is a hallmark of several neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS). In this study, we describe the development of a new model of TDP43 proteinopathy using human induced pluripotent stem cell (iPSC)-derived neurons. Utilizing a genome engineering approach, we induced the mislocalization of endogenous TDP43 from the nucleus to the cytoplasm without mutating the TDP43 gene or using chemical stressors. Our model successfully recapitulates key early and late pathological features of TDP43 proteinopathy, including neuronal loss, reduced neurite complexity, and cytoplasmic accumulation and aggregation of TDP43. Concurrently, the loss of nuclear TDP43 leads to splicing defects, while its cytoplasmic gain adversely affects microRNA expression. Strikingly, our observations suggest that TDP43 is capable of sustaining its own mislocalization, thereby perpetuating and further aggravating the proteinopathy. This innovative model provides a valuable tool for the in-depth investigation of the consequences of TDP43 proteinopathy. It offers a clinically relevant platform that will accelerate the identification of potential therapeutic targets for the treatment of TDP43-associated neurodegenerative diseases, including sporadic ALS.

Keywords:  ALS; TDP43; genetics; genomics; human; iPSC; microRNA; neuroscience; proteinopathy; splicing

DOI:  https://doi.org/10.7554/eLife.95062
Cell Rep. 2025 Jul 20. pii: S2211-1247(25)00802-2. [Epub ahead of print]44(8): 116031

PPM1M, an LRRK2-counteracting, phosphoRab12-preferring phosphatase with a potential link to Parkinson's disease.

Global Parkinson’s Genetics Program (GP2)

  Leucine-rich repeat kinase 2 (LRRK2) phosphorylates a subset of Rab GTPases that regulate receptor trafficking, and LRRK2-activating mutations are linked to Parkinson's disease. Rab phosphorylation is a transient event that can be reversed by phosphatases, including protein phosphatase, Mg2+/Mn2+ dependent 1H (PPM1H), which acts on phosphorylated Rab 8A (phosphoRab8A) and phosphoRab10. Here, we report a phosphatome-wide small interfering RNA (siRNA) screen that identified PPM1M as a phosphoRab12-preferring phosphatase that also acts on phosphoRab8A and phosphoRab10. Upon knockout from cultured cells or mice, PPM1M displays selectivity for phosphoRab12. As shown previously for mice harboring LRRK2 pathway mutations, knockout of Ppm1m leads to primary cilia loss in striatal cholinergic and parvalbumin interneurons. We also identified a rare PPM1M mutation in patients with Parkinson's disease that is catalytically inactive when tested in vitro and in cells. These findings identify PPM1M as a key player in the LRRK2 signaling pathway and provide a new therapeutic target for the possible benefit of patients with Parkinson's disease.

Keywords:  CP: Cell biology; CP: Neuroscience; LRRK2 kinase; Parkinson’s disease; Rab GTPase; phosphatase; primary cilia

DOI:  https://doi.org/10.1016/j.celrep.2025.116031
J Huntingtons Dis. 2025 Jul 23. 18796397251358348

Dysregulation of huntingtin interacting protein networks in human juvenile Huntington's disease brain.

Sonia Podvin, Brin Rosenthal, Charles Mosier, Enlin Wei, Kathleen M Fisch, Vivian Hook.

  BackgroundHuman Huntington's disease (HD) is a genetic neurodegenerative disorder caused by the mutant HTT gene containing CAG repeat expansions, resulting in motor dysfunction and behavioral deficits. CAG repeats of 40-53 occur in adult HD and 60-120 repeats occur in early onset juvenile HD, differing from the normal range of 5-35 repeats.ObjectiveThe HTT gene is translated to the huntingtin (HTT) protein that interacts with proteins in the development of HD. There have been few studies of HTT protein interactors in human HD brain. Therefore, this study evaluated the hypothesis that dysregulation of HTT protein interactors occurs in human juvenile HD brains.MethodsThe strategy of this study was to analyze proteomic data of human juvenile HD brain putamen and cortex regions for dysregulation of HTT interacting proteins, using a database that we compiled of HTT interactors identified in HD model systems from yeast to HD mice.ResultsResults showed significant dysregulation of HTT protein interactors of mitochondria, signal transduction, RNA splicing, chromatin organization, translation, membrane trafficking, endocytosis, vesicle, protein modification, granule membrane, and macroautophagy pathways. The majority of downregulated and upregulated HTT interactors occurred in the putamen region compared to cortex. Dysregulation displayed downregulation of mitochondria and signal transduction interactors, combined with upregulation of RNA splicing, chromatin organization, and translational interactors. Network analysis revealed interactions among clusters of HTT interactors.ConclusionsThese findings demonstrate prevalent dysregulation of HTT protein interactors in human juvenile HD brain, especially in the putamen region that controls movement deficits in HD.

Keywords:  HTT gene; HTT interacting proteins; Huntington's disease; bioinformatics; brain; cortex; huntingtin (HTT) protein; juvenile Huntington's disease; mass spectrometry; proteomics; putamen

DOI:  https://doi.org/10.1177/18796397251358348
Mol Ther Methods Clin Dev. 2025 Sep 11. 33(3): 101525

Using circular RNAs to target toxic RNA-binding proteins in amyotrophic lateral sclerosis.

Anne Kruse Hollensen, Matilde Helbo Sørensen, Sofie Vesterbæk Thomsen, Henriette Sylvain Thomsen, Christian Kroun Damgaard.

  Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron degeneration and is in many cases associated with mutations in genes encoding RNA-binding proteins (RBPs), including fused in sarcoma (FUS) and heterogeneous nuclear ribonuclearprotein A1 (hnRNPA1). These mutations often cause cytoplasmic mislocalization and aggregation of these typically nuclear proteins. Current treatment options for ALS are limited, highlighting the need for new therapeutic strategies. Here, we demonstrate an approach using circular RNAs (circRNAs) to target disease-associated RBPs for degradation. We designed circRNAs containing binding sites for both the target RBPs (FUS or hnRNPA1) and ring finger and CCCH-type domains 2 (RC3H2), an RNA-binding E3 ubiquitin ligase. Through RNA immunoprecipitations and protein analyses, we show that these circRNAs can form ternary complexes with their target RBPs and RC3H2. Importantly, we observed significant reductions in steady-state protein levels of ALS-associated FUS-P525L (20%) and hnRNPA1-P288S (30%) mutants when treated with their respective targeting circRNAs. These findings provide proof of concept for using circRNAs as scaffolds to promote the degradation of disease-associated RBPs, establishing a foundation for developing advanced RNA-based therapeutic strategies for ALS and potentially other RBP-related diseases.

Keywords:  ALS; E3 ubiquitin ligase RC3H2; FUS; circRNA PROTAC; disease-causing RBPs; hnRNPA1

DOI:  https://doi.org/10.1016/j.omtm.2025.101525
J Biol Chem. 2025 Jul 17. pii: S0021-9258(25)02324-5. [Epub ahead of print] 110474

Secretory autophagy mediates lysosomal and autophagic degradation for α-synuclein proteostasis.

Taiki Sawai, Yoshitsugu Nakamura, Shigeki Arawaka.

  Autophagy has two distinct pathways, degradation and secretion. Autophagic degradation plays a pivotal role in proteostasis. However, the role of autophagic secretion in proteostasis maintenance is not fully understood. Here, we investigate how the blockade of autophagic secretion impairs proteostasis in SH-SY5Y cells. siRNA-mediated knockdown of a modulator for autophagosome formation, ATG5, BECN1 or FIP200 inhibited autophagic flux and secretion, causing accumulation of Triton X-100-insoluble α-synuclein, which is an aggregate-prone protein responsible for neuronal loss in Parkinson's disease. The blockade of autophagic secretion by knockdown of t-SNARE SNAP23 or STX4 increased autophagic flux for p62 degradation, but these knockdowns induced enlargement and membrane damage of lysosomes as well as lysosomal dysfunction. SNAP23 or STX4 knockdown caused accumulation of Triton X-100-insoluble α-synuclein against induction of lysophagy. GBA knockdown showed lysosomal damage with the increase in autophagic secretion. RAB8A, a small GTPase regulator of polarized sorting to the plasma membrane, knockdown blocked autophagic secretion and produced lysosomal damage. SNAP23, STX4 or RAB8A knockdown further accelerated accumulation of Triton X-100-insoluble α-synuclein caused by a lysosomal protease inhibitor cocktail. Collectively, these findings suggest that SNAP23, STX4 or RAB8A knockdown blocks autophagic secretion and upregulates autophagic flux as a compensatory response to help maintain degradation. However, these knockdowns impair α-synuclein proteostasis because of lysosomal damage that they induce, counteracting compensatory effects of autophagic degradation, including lysophagy. Autophagic secretion and degradation may collaboratively form the clearance pathway required for maintaining lysosomal function by reducing the burden of aggregate-prone protein cargo.

Keywords:  Parkinson disease; autophagy; lysosome; protein secretion; proteostasis; synuclein

DOI:  https://doi.org/10.1016/j.jbc.2025.110474
Microsc Microanal. 2025 Jul 15. pii: ozaf037. [Epub ahead of print]31(4):

Leucine-Rich Repeat Kinase 2 Regulates Mitochondria for Zygotic Genome Activation in Mouse Early Embryos.

Yu-Lan Lu, Zi-Yu Wei, Xiao-Ting Yu, Li-Zhou Qin, Lin-Lin Hu, Shao-Chen Sun, Shang-Lin Yang.

  Leucine-rich repeat kinase 2 (LRRK2) is a multidomain protein known for its involvement in neurodegenerative disorders, particularly Parkinson's disease, where it is considered one of the most common genetic contributors. LRRK2 plays multiple roles in cellular signaling, protein trafficking, and cytoskeletal dynamics. In present study, using mouse as the mammalian model, we reported its important roles in early embryo development. We showed that LRRK2 accumulated around nucleus before two-cell stage but distributed in the cytoplasm of blastomeres after four-cell stage. Loss of LRRK2 activity induced two-cell to four-cell transition defects, indicating the failure of zygotic genome activation during embryo development. We showed the mitochondria dysfunction after LRRK2 inhibition, since the mitochondria distribution, intensity, ATP production, and mitochondria number were all altered. This might further induce the evaluated ROS level for the occurrence of oxidative stress. Besides, we also observed that the cortex and cytoplasmic actin in the blastomere of embryos were decreased, which further linked with mitochondria. In summary, we showed that LRRK2 activity is essential for actin-based mitochondria distribution and function, which further controls the occurrence of oxidative stress for mouse early embryo development.

Keywords:  Parkinson’s disease; actin; mitochondria; oocyte; oxidative stress

DOI:  https://doi.org/10.1093/mam/ozaf037
Front Neurosci. 2025 ;19 1620181

Targeting oxidized phosphatidylcholines in SOD1-associated ALS: therapeutic potential of PC-OxPL-VecTab®.

Andreia Gomes-Duarte, Sofia Pascoal, Rob Haselberg, Marina Sogorb-Gonzalez, Sander van Deventer.

  Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by progressive motor neuron degeneration. Mutations in the superoxide dismutase 1 (SOD1) gene account for a significant fraction of familial ALS (fALS) cases. Oxidative stress and oxidized phosphatidylcholines (PC-OxPL) contribute to neuroinflammation and neuronal damage, and to motor neuron degeneration in ALS. We previously demonstrated the therapeutic efficacy of an AAV-delivered anti-PC-OxPL single-chain variable fragment (PC-OxPL-VecTab®) in neutralizing PC-OxPL toxicity in the periphery and central nervous system (CNS), but the therapeutic potential of PC-OxPL-VecTab® has not been investigated in the context of fALS and SOD1-associated ALS. We report that PC-OxPL accumulation contributes to the pathological phenotypes associated with SOD1G93A iPSC-derived motor neurons and the corresponding mouse model. The current findings further demonstrate that PC-OxPL-VecTab® is efficacious in neutralizing the downstream effects of SOD1-associated PC-OxPL accumulation, such as altered gene expression and axonal health in SOD1 motor neurons, as well as a pathological lipid profile in the SOD1G93A mouse model. Collectively, the present study underscores the significance of PC-OxPL dysfunction in the context of SOD1 genotypes and sheds light on the potential of PC-OxPL-VecTab® for therapeutically targeting ALS.

Keywords:  adeno-associated viruses; amyotrophic lateral sclerosis; gene therapy; oxidized phosphatidylcholines; superoxide dismutase 1

DOI:  https://doi.org/10.3389/fnins.2025.1620181
EMBO J. 2025 Jul 24.

ALS-associated RNA-binding proteins promote UNC13A transcription through REST downregulation.

Yasuaki Watanabe, Naoki Suzuki, Tadashi Nakagawa, Masaki Hosogane, Tetsuya Akiyama, Naotoshi Kageyama, Yukino Funayama, Hitoshi Warita, Satoru Morimoto, Hideyuki Okano, Masashi Aoki, Keiko Nakayama.

  Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by selective loss of motor neurons. Although multiple pathophysiological mechanisms have been identified, no comprehensive understanding of these heterogeneous processes has been achieved. The ALS-associated RNA-binding protein (RBP) TDP-43 has previously been shown to stabilize UNC13A mRNA by preventing cryptic exon inclusion. Here, we show that the ALS-associated RBPs MATR3, FUS, and hnRNPA1 regulate UNC13A expression by targeting the transcriptional repressor REST. These RBPs bind to and downregulate REST mRNA to promote UNC13A transcription. Loss of any of these RBPs in cultured cells or in iPSC-derived motor neurons carrying the ALS-causing FUS P525L mutation leads to REST overexpression, and the same is observed in motor neurons of individuals with familial or sporadic ALS. The functional convergence of four RBPs on the regulation of UNC13A expression underscores the important role of this process for synaptic integrity, and its association with ALS pathogenesis could be relevant for the development of new therapeutic agents.

Keywords:  ALS; Cryptic Exon; FUS; REST; UNC13A

DOI:  https://doi.org/10.1038/s44318-025-00506-0
Neurobiol Dis. 2025 Jul 19. pii: S0969-9961(25)00252-9. [Epub ahead of print] 107036

RNA helicase maheshvara interacts with TDP-43 and exacerbates neurodegeneration in Drosophila model of amyotrophic lateral sclerosis.

Pranjali Pandey, Rituparna Das, Harshita Yadav, Ashim Mukherjee, Mousumi Mutsuddi.

  Drosophila maheshvara (mahe) encodes a conserved DEAD box RNA helicase that regulates various important signaling pathways like Notch and JAK/STAT, pathways that have been functionally implicated in neuronal development. In order to identify novel modulators of mahe as well as to unravel its role in neurodegenerative disorders, a genetic modifier screen using Drosophila models of neurodegenerative disorders was carried out. From this screen, we identified mahe to be a potent modifier of TDP-43 mediated proteinopathy in Drosophila model of Amyotrophic Lateral Sclerosis (ALS). We demonstrate that Mahe genetically interacts and associates with cytosolic hyperphosphorylated toxic aggregates of TDP-43 leading to enhanced TDP-43 mediated neurodegenerative phenotype. Increased autophagy, cytoskeletal disruption, and FMRP-mediated translational repression of neuronal target Futsch were observed, potentially contributing to neuronal dysfunction. The current study indicates a strong interaction of mahe and TDP-43 (TARDBP) resulting in augmentation of TDP-43 mediated neurodegenerative phenotypes which parallels ALS clinical pathology.

Keywords:  Amyotrophic lateral sclerosis; Autophagy; Dead box RNA helicase; FMRP; Futsch; TDP-43

DOI:  https://doi.org/10.1016/j.nbd.2025.107036
Invest Ophthalmol Vis Sci. 2025 Jul 01. 66(9): 58

Investigation of ABCA4 Missense Variants and Potential Small Molecule Rescue in Retinal Organoids.

Davide Piccolo, Paul Sladen, Rosellina Guarascio, Kalliopi Ziaka, Michael E Cheetham.

Purpose: ABCA4-related retinopathy is the most common monogenic eye disorder in the world and is currently untreatable. Missense variants in ABCA4 constitute ∼60% of causal ABCA4-related retinopathy variants, often resulting in misfolded or dysfunctional protein products. Despite their prevalence, the molecular mechanisms by which these missense mutations impair ABCA4 function are not fully understood, primarily due to limitations in suitable cellular models. In this study, we investigated the cellular and molecular consequences of ABCA4 missense variants using a human photoreceptor-like model system.
Methods: We used CRISPR/Cas9 technology to introduce two ABCA4 missense misfolding variants, T983A and R2077W, which are associated with ABCA4-associated retinopathy, into control induced pluripotent stem cells (iPSCs). The iPSCs were differentiated into retinal organoids, characterized and treated with small molecules.
Results: The expression level of ABCA4 missense proteins was reduced compared to WT ABCA4 suggesting the variants were degraded in a photoreceptor-like environment. The localization of the missense variants was also altered with negligible ABCA4 detectable in the retinal organoid outer segments compared to the isogenic control. Two small molecule compounds, AICAR and 4-PBA, previously identified as potential ABCA4 folding correctors in vitro, were tested for their ability to enhance ABCA4 traffic to the outer segment. The compounds did not appear to promote ABCA4 folding and traffic in photoreceptors and instead led to a decrease in ABCA4 transcript levels and protein.
Conclusions: These data highlight that retinal organoids are an exquisite model to investigate pathogenic variants in ABCA4 and test small compounds for translation to the human retina.

DOI: https://doi.org/10.1167/iovs.66.9.58
Res Sq. 2025 Jul 15. pii: rs.3.rs-6941118. [Epub ahead of print]

Trimeric superoxide dismutase 1 antibody as a universal biomarker for ALS.

Nikolay Dokholyan, Brianna Hnath, Rachel Dokholyan, Zachary Simmons.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to the loss of motor neurons, resulting in paralysis and death. Currently, there are no specific biomarkers available for diagnosing ALS. As a result, diagnosis currently relies on excluding other conditions, which forces patients to endure months or even years of uncertainty. The absence of a specific, reliable diagnostic tool has hindered both early intervention and therapeutic progress. Here we develop a novel synthetic antibody that can detect a toxic form of a known protein linked to ALS. This trimeric assembly of superoxide dismutase 1 (SOD1) is a soluble, structurally distinct oligomer that is highly toxic in cell models. The antibody selectively binds this trimer and differentiates individuals with the disease from healthy people and from those with other neurodegenerative diseases (Alzheimer's and Parkinson's disease). This breakthrough provides the first disease-specific diagnostic tool for this condition and reveals a shared pathological signature across patients, even in cases without genetic mutations. After decades without a specific diagnostic tool, this antibody signifies a long-awaited breakthrough, finally offering clinicians and researchers a reliable window into ALS pathology.

DOI: https://doi.org/10.21203/rs.3.rs-6941118/v1
Commun Biol. 2025 Jul 19. 8(1): 1074

Tissue-engineered neuromuscular organoids.

Beatrice Auletta, Pietro Chiolerio, Giada Cecconi, Lucia Rossi, Luigi Sartore, Francesca Cecchinato, Gilda Barbato, Agnese Lauroja, Edoardo Maghin, Maria Easler, Paolo Raffa, Silvia Angiolillo, Wei Qin, Roberta Frison, Sonia Calabrò, Chiara Villa, Onelia Gagliano, Cecilia Laterza, Davide Cacchiarelli, Matilde Cescon, Monica Giomo, Yvan Torrente, Camilla Luni, Martina Piccoli, Nicola Elvassore, Anna Urciuolo.

Skeletal muscle development, homeostasis, and function rely on complex interactions among multiple cell types and the extracellular matrix (ECM). Developing in vitro models that recapitulate both intrinsic cellular and extrinsic ECM elements of innervated skeletal muscle is crucial for advancing basic biology and disease modeling studies. Here, we combine tissue engineering approaches with human induced pluripotent stem cell (hiPSC) technology to create tissue-engineered neuromuscular organoids (t-NMOs). Using decellularized muscles as scaffolds, hiPSCs differentiate to form organoids that establish a continuum with the provided biomaterial. After 30 days, t-NMOs exhibit compartmentalized neural and muscular components that establish functional interactions, allowing muscle contraction. We demonstrate the model's potential by creating Duchenne Muscular Dystrophy patient-specific t-NMOs, that recapitulate the reduced skeletal muscle contraction and altered calcium dynamics typical of the disease. Altogether, our study presents a tissue-engineered organoid that model the human neuromuscular system (dys)function, highlighting the potential of applying the ECM in organoid engineering.

DOI: https://doi.org/10.1038/s42003-025-08484-z
Sci Adv. 2025 Jul 25. 11(30): eadx1357

M6A-dependent RNA condensation underlies FUS autoregulation and can be harnessed for ALS therapy development.

Wan-Ping Huang, Vedanth Kumar, Karen Yap, Haiyan An, Sabin J John, Rachel E Hodgson, Anna Sanchez Avila, Emily Day, Brittany C S Ellis, Tek Hong Chung, Jenny Lord, Michaela Müller-McNicoll, Eugene V Makeyev, Tatyana A Shelkovnikova.

Mutations in the FUS gene cause aggressive amyotrophic lateral sclerosis (ALS-FUS). Beyond mRNA, FUS generates partially processed transcripts retaining introns 6 and 7. We demonstrate that these FUSint6&7-RNA molecules form nuclear condensates, scaffolded by the highly structured intron 7 and associated with nuclear speckles. Using hybridization-proximity labeling proteomics, we show that the FUSint6&7-RNA condensates are enriched for splicing factors and the N6-methyladenosine (m6A) reader YTHDC1. These ribonucleoprotein structures facilitate posttranscriptional FUS splicing and depend on m6A/YTHDC1 for integrity. In cells expressing mutant FUS, FUSint6&7-RNAs become hypermethylated, which in turn stimulates their condensation and splicing. We further show that FUS protein is repelled by m6A. Thus, ALS-FUS mutations may cause abnormal activation of FUS posttranscriptional splicing through altered RNA methylation. Notably, ectopic expression of FUS intron 7 sequences dissolves endogenous FUSint6&7-RNA condensates, down-regulating FUS mRNA and protein. Our findings reveal a condensation-dependent mechanism regulating FUS splicing, with possible therapeutic implications for ALS.

DOI: https://doi.org/10.1126/sciadv.adx1357
Curr Issues Mol Biol. 2025 Jun 10. pii: 442. [Epub ahead of print]47(6):

Dicer Is Involved in Cytotoxicity and Motor Impairment Induced by TBPH Deficiency.

Xiang Long, Yijie Wang, Hongrui Meng.

  TDP-43 is an RNA-binding protein linked to amyotrophic lateral sclerosis (ALS), possibly associated with a role in miRNA biogenesis, which is still not fully understood. Herein we investigated the impact of the Drosophila homolog of TDP-43, TBPH, on genes related to miRNA biogenesis. A TBPH knockout significantly reduced mRNA transcription and protein levels of DCR-1 and DCR-2, whereas an overexpression of DCR-1 and DCR-2 in a TBPH knockdown background exacerbated compound eye damage, with variations in severity that were sex-dependent. Neuronal TBPH RNAi consistently shortened lifespan, with males and females exhibiting distinct survival profiles. DCR-1 and DCR-2 knockdown worsened the locomotor defects induced by TBPH deficiency, thus reinforcing the functional link between TBPH and DCR. In TBPH-deficient flies, the pharmacological activation of Dicer promoted reverse locomotion behavior, with a preference for backward movement. Overall, we show that TBPH is a key regulator of DCR protein expression, highlighting its conserved role in miRNA dysregulation associated with motor function and cytotoxicity in ALS-like pathology in Drosophila models.

Keywords:  Dicer; Drosophila; TBPH; amyotrophic lateral sclerosis

DOI:  https://doi.org/10.3390/cimb47060442
J Biochem Mol Toxicol. 2025 Aug;39(8): e70404

CircRNA_26782 Regulates Axonal Growth via Inhibiting the Autophagy Pathway in a Rat Model of Spinal Cord Injury.

Xiaowei Qian, Wei Zhang, Dexia Kong, Chenyi Huang, Yan Liu, Mei Liu, Hongjian Chen, Ronghua Wu.

  Circular RNAs (circRNAs), a class of endogenous noncoding RNAs, play crucial roles in various physiological and pathological processes. This study aimed to investigate the role and underlying mechanisms of circRNA_26782 in spinal neurons. We analyzed the differential expression profiles of circRNAs in a rat model of spinal cord injury and identified circRNA_26782 as being downregulated. Fluorescence in situ hybridization assay demonstrated that circRNA_26782 is primarily situated in the neuronal cytoplasm. Knockdown of circRNA_26782 remarkably increased axonal length. RNA sequencing identified miR-19b-2-5p as a key miRNA upregulated following circRNA_26782 depletion. Axonal growth was significantly enhanced by either overexpressing miR-19b-2-5p or downregulating its target gene, Rab1b. Co-silencing of circRNA_26782 and miR-19b-2-5p indicated that miR-19b-2-5p inhibition rescued the increased axon length induced by circRNA_26782 knockdown. Additionally, the autophagy pathway was inhibited upon circRNA_26782 knockdown, miR-19b-2-5p overexpression, or Rab1b downregulation in rat spinal neurons. This study is the first to demonstrate that circRNA_26782 promotes axonal growth by inhibiting the autophagy pathway through the miR-19b-2-5p/Rab1b axis. These findings offer new insights into the molecular mechanisms regulating axonal growth, and potentially informing therapeutic strategies for spinal cord injury.

Keywords:  Rab1b; autophagy; axonal growth; circRNA_26782; miRNA‐19b‐2‐5p

DOI:  https://doi.org/10.1002/jbt.70404
Stem Cell Res Ther. 2025 Jul 22. 16(1): 395

Xenotransplantation of Human Umbilical Mesenchymal Stromal Cells Derived from Wharton's Jelly Mitigates Mouse Amyotrophic Lateral Sclerosis.

Chun-Fu Lin, Yu-Hui Chen, Chang-Ching Yeh, Sanford P C Hsu, Yu-Show Fu.

   BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a motor neuron disease characterized by progressive degeneration of motor neurons in the cerebral cortex, brainstem, and spinal cord, eventually leading to paralysis, respiratory failure, and death. Currently, no effective treatment exists for ALS.
METHODS: This study examined the therapeutic potential of human umbilical cord mesenchymal stromal cells (HUMSCs) by transplanting 2 × 10⁶ HUMSCs into the spinal canal of transgenic mice expressing mutant human superoxide dismutase 1 (SOD1) at 8 weeks of age.
RESULTS: Survival analysis showed that the SOD1 group lived up to 171 days, while the SOD1 + HUMSCs group survived up to 199 days, extending lifespan by 17 days on average. Motor function tests, including rotarod performance, grip strength, open field activity, and balance beam tests, demonstrated that while the SOD1 group experienced progressive decline, the SOD1 + HUMSCs group showed improvement. Electrophysiological assessments at 20 weeks of age revealed weak muscle action potential in the SOD1 group, whereas the SOD1 + HUMSCs group exhibited noticeable improvements. Histological analysis indicated significant spinal cord atrophy in the SOD1 group, while HUMSCs transplantation mitigated this degeneration. Moreover, HUMSCs reduced blood-spinal cord barrier leakage and T lymphocyte infiltration, alleviating inflammation. The number and size of activated microglia and astrocytes increased in the SOD1 group but were reduced with HUMSCs treatment. Additionally, HUMSCs preserved more motor neurons in the anterior horns.
CONCLUSION: Collectively, transplantation of HUMSCs effectively reduced inflammatory reaction in spinal cord, decreased loss of neurons, ameliorated disease deterioration, and extended life span, suggesting that it could serve as a new direction of ALS treatment to improve patients' quality of life or behavioral function.

Keywords:  ALS; Amyotrophic lateral sclerosis; Cell transplantation; Neuronal inflammation; SOD1; Umbilical mesenchymal stromal cells

DOI:  https://doi.org/10.1186/s13287-025-04485-1
Integr Zool. 2025 Jul 21.

Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids.

Zheng Dong, Chen Wang, Shukai Dong, Yicheng Peng, Jierui Guo, Chuchu Zhang, Zhaopeng Xu, Zixiang Wu, Bo Wang, Qingming Qu.

  Seahorses and their relatives (syngnathids) exhibit remarkable diversity in morphology and function, characterized by their distinctive body shapes and specialized feeding mechanisms. Despite recent advances in uncovering the genetic basis of some traits, the genotype-phenotype map in syngnathids remains incomplete. In this study, we employed forward-genomic approaches and developed a method to enrich for human disease amino acid loci at a genomic scale. Our aim was to identify genetic loci associated with fin size reduction, tooth loss, and spinal curvature in syngnathids. Intriguingly, we identified a convergent amino acid change in the lat4a gene shared by syngnathids and some flying fishes, with in vitro analysis confirming its role in fin size evolution in both lineages. While genes critical for tooth development are conserved in syngnathids, the absence of key regulatory elements, such as pitx2, likely contributes to tooth loss. Additionally, we implicated col6a3 in spinal curvature development in seadragons. These findings reveal novel genetic signatures and developmental constraints underlying syngnathid diversity, demonstrating the utility of comparative genomics and targeted gene enrichment in exploring vertebrate evolution.

Keywords:  amino acid change; comparative genomic; syngnathids

DOI:  https://doi.org/10.1111/1749-4877.13018
Brain. 2025 Jul 19. pii: awaf269. [Epub ahead of print]

Neurodegenerative disease in C9orf72 repeat expansion carriers: population risk and effect of UNC13A.

Jiali Gao, Andrew G L Douglas, Christos V Chalitsios, Jakub Scaber, Kevin Talbot, Martin R Turner, Alexander G Thompson.

  The C9orf72 hexanucleotide repeat expansion (HRE) is the most common monogenetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Neurodegenerative disease incidence in C9orf72 HRE carriers has been studied using cohorts from disease-affected families or by extrapolating from population disease incidence, potentially introducing bias. Age-specific cumulative incidence of ALS and dementia was estimated using Kaplan-Meier and competing risk models in C9orf72 HRE carriers compared to matched controls in UK Biobank. Risk modification by UNC13A genotype was examined. Of 490,331 individuals with valid genetic data, 701 had >100 repeats in C9orf72 (median age 55 [IQR 48-62], follow-up 13.4 years [12.3-14.1]). The cumulative incidence of ALS or dementia was 66% [95% CI 57-73%] by age 80 in C9orf72 HRE carriers versus 5.8% [4.5-7.0%] in controls, or 58% [50-64%] versus 5.1% [4.1-6.4%] accounting for the competing risk of other-cause mortality. Forty-one percent of dementia incidence accrued between age 75-80. C-allele homozygosity at rs12608932 in UNC13A increased ALS or dementia risk in C9orf72 HRE carriers (hazard ratio 1.81 [1.18 - 2.78]). C9orf72 HRE disease was incompletely penetrant in this population-based cohort, with risk modified by UNC13A genotype. This has implications for counselling at-risk individuals and modelling expected phenoconversion for prevention trials.

Keywords:  C9orf72; UNC13A; amyotrophic lateral sclerosis; frontotemporal dementia; neurodegeneration

DOI:  https://doi.org/10.1093/brain/awaf269
Sci Rep. 2025 Jul 23. 15(1): 26738

Effects of SLC6A8 mutation-induced creatine deficiency on cellular function in fibroblasts.

Shingo Ito, Tatsuki Uemura, Ayaka Miyano, Hiroko Shimbo, Takeshi Masuda, Tomohide Goto, Hitoshi Osaka, Takahito Wada, Sumio Ohtsuki.

  Creatine transporter deficiency (CTD) caused by mutations in SLC6A8 encoding the creatine transporter (CRT), leads to cerebral creatine deficiency syndromes; however, the cellular impact of CRT loss remains unclear. In this study, we investigated the consequences of the G561R mutation by examining fibroblasts using proteomics and functional assays. We observed severe intracellular creatine deficiency (> 90% reduction), leading to impaired energy metabolism (low ATP and high ADP/ATP). Proteomic analysis revealed significant alterations in the mitochondrial and extracellular vesicle pathways. Our investigation revealed impaired mitochondrial oxidative phosphorylation, reduced spare respiratory capacity, elevated oxidative stress, and significant alterations in amino acid transporter activity. Protein misfolding associated with G561R exacerbated these deficits compared to the deletion model. These findings elucidate the key pathological mechanisms induced by the CRT-G561R mutation-including energy metabolic reprogramming, mitochondrial dysfunction, and cellular stress-which significantly contribute to our understanding of the pathogenesis of creatine transporter deficiency and suggest potential therapeutic targets.

Keywords:  ATP production; Creatine transporter; Extracellular vesicles; Fibroblast; Mitochondrial function; SLC6A8

DOI:  https://doi.org/10.1038/s41598-025-11386-z
Cell Biochem Funct. 2025 Jul;43(7): e70105

Role of Mitochondria-Associated ER in Apoptosis.

Mudan Sang, Xindong Li, Mi Chen, Xiaoli Ren, Sheng Kang, Zhenyu Chang, Qingxia Wu.

  Apoptosis represents a critical noninflammatory mechanism for cell clearance in both physiological and pathological contexts, precisely regulated through the balance between proapoptotic and antiapoptotic signaling. Three well-characterized apoptotic pathways have been identified: (1) the intrinsic (mitochondria-mediated) pathway, (2) the extrinsic (death receptor-mediated) pathway, and (3) the endoplasmic reticulum (ER)-stress pathway. These processes are coordinated through the mitochondria-associated ER membrane (MAMs), which serves as a vital coupling platform between mitochondria and the ER. MAMs play pivotal roles in maintaining Ca²⁺ homeostasis and regulating apoptosis through dynamic alterations in architecture (e.g., gap width, contact number) that influence Ca²⁺ trafficking and tethering protein expression. Key protein complexes localized at MAMs (including the IP3Rs-Grp75-VDAC1 complex, Mfn1/Mfn2 complex, and PTPIP51-containing complex) regulate apoptosis through three primary mechanisms: Ca²⁺ homeostasis maintenance, lipid synthesis and transport, and mitochondrial morphology and dynamics. Furthermore, MAMs-mediated mitochondrial dynamics, particularly mitochondrial fission and cristae remodeling, contribute to apoptosis by facilitating Bax/Drp1 dimerization. This review systematically examines: how MAMs' structural dynamics influence Ca²⁺ signaling and tethering protein expression, the roles of MAMs-tethered proteins and their regulators in Ca²⁺ homeostasis, lipid metabolism, and mitochondrial dynamics, and the impact of mitochondrial dynamics on Bax/Drp1 dimerization during apoptosis.

Keywords:  Bcl‐2 family proteins; apoptosis; mitochondrial dynamics; mitochondria‐associated ER; tether proteins

DOI:  https://doi.org/10.1002/cbf.70105
Stem Cell Res. 2025 Jul 19. pii: S1873-5061(25)00131-X. [Epub ahead of print]87 103781

CRISPR/Cas9-mediated generation of two isogenic CEP290-mutated iPSC lines.

Joana Figueiro-Silva, Melanie Eschment, Michelle Mennel, Affef Abidi, Beatrice Oneda, Anita Rauch, Ruxandra Bachmann-Gagescu.

CEP290 is an important human disease gene, as mutations are implicated in a broad spectrum of autosomal recessive ciliopathies, including Leber congenital amaurosis and Joubert, Meckel, Senior-LØken or Bardet Biedl syndromes. To create isogenic mutant human induced pluripotent stem cell (hiPSC) lines for disease modeling, we employed CRISPR/Cas9 to introduce disease-relevant mutations into the control hiPSC line HMGU1 (ISFi001-A). Thorough characterization of the lines, including the effect of the mutation at the mRNA and protein level, shows that these CEP290-mutant lines provide a useful resource for studying ciliopathy disease mechanisms and cilia biology through differentiation into diverse cell types and organoids.

DOI: https://doi.org/10.1016/j.scr.2025.103781
Curr Issues Mol Biol. 2025 Apr 08. pii: 259. [Epub ahead of print]47(4):

Protein Misfolding and Aggregation as a Mechanistic Link Between Chronic Pain and Neurodegenerative Diseases.

Nebojsa Brezic, Strahinja Gligorevic, Aleksandar Sic, Nebojsa Nick Knezevic.

  Chronic pain, defined by persistent pain beyond normal healing time, is a pervasive and debilitating condition affecting up to 30-50% of adults globally. In parallel, neurodegenerative diseases (NDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by progressive neuronal loss and cognitive or motor decline, often underpinned by pathological protein misfolding and aggregation. Emerging evidence suggests a potential mechanistic link between chronic pain and NDs, with persistent pain contributing to neuroinflammatory states and protein homeostasis disturbances that mirror processes in neurodegeneration. This review explores the hypothesis that protein misfolding and aggregation serve as a mechanistic bridge between chronic pain and neurodegeneration. We systematically examine molecular pathways of protein misfolding, proteostasis dysfunction in chronic pain, and shared neuroimmune mechanisms, highlighting prion-like propagation of misfolded proteins, chronic neuroinflammation, and oxidative stress as common denominators. We further discuss evidence from experimental models and clinical studies linking chronic pain to accelerated neurodegenerative pathology-including tau accumulation, amyloid dysregulation, and microglial activation-and consider how these insights open avenues for novel therapeutics. Targeting protein aggregation, enhancing chaperone function, modulating the unfolded protein response (UPR), and attenuating glial activation are explored as potential strategies to mitigate chronic pain and possibly slow neurodegeneration. Understanding this intersection not only elucidates chronic pain's role in cognitive decline but also suggests that interventions addressing proteostasis and inflammation could yield dual benefits in pain management and neurodegenerative disease modification.

Keywords:  chronic pain; endoplasmic reticulum stress; neurodegenerative diseases; neuroinflammation; protein aggregation; protein misfolding; unfolded protein response

DOI:  https://doi.org/10.3390/cimb47040259
Brain Pathol. 2025 Jul 24. e70034

Dysregulation of the endosomal sorting complex III is linked to neurodegeneration in progressive multiple sclerosis.

Carmen Picon, Robertas Aleksynas, Marcelina Wojewska, Francesco de Virgiliis, Doron Merkler, Richard Reynolds.

  Multiple sclerosis (MS) is a chronic neuroinflammatory disease that progresses to a stage marked by irreversible neurological decline and widespread neurodegeneration. Necroptosis, a regulated form of cell death primarily triggered by tumor necrosis factor (TNF), has been implicated in neuronal loss in progressive MS. The Endosomal Sorting Complex Required for Transport (ESCRT) machinery, essential for plasma membrane repair and vesicle trafficking, is known to counteract necroptosis in non-neural cells. In this study, we investigated whether ESCRT dysfunction contributes to neurodegeneration in the MS cortex. We identified a significant dysregulation of ESCRT-III complex components, particularly VPS4B and CHMP2A, in neurons of MS cortical grey matter. This dysregulation correlated with reduced neuronal density and increased meningeal inflammation. Notably, both demyelinated and normal-appearing grey matter showed decreased VPS4B, while CHMP2A loss was more restricted to areas of demyelination. These findings suggest that impaired ESCRT-III function may increase neuronal vulnerability to necroptosis and contribute to disease progression in MS. Our results highlight a novel pathway linking neuroinflammation, ESCRT dysfunction, and neuronal death, with potential therapeutic implications for neuroprotection in progressive MS.

Keywords:  endosomal sorting; multiple sclerosis; necroptosis; neurodegeneration; neuroinflammation

DOI:  https://doi.org/10.1111/bpa.70034
STAR Protoc. 2025 Jul 21. pii: S2666-1667(25)00351-X. [Epub ahead of print]6(3): 103945

Protocol for CRISPR-based manipulation and visualization of endogenous α-synuclein in cultured mouse hippocampal neurons.

Leonardo A Parra-Rivas, Rohan Sharma, Trinity E Rust, Hannah O Bazick, Jared Carlson-Stevermer, Mark J Zylka, Yuki Ogawa, Subhojit Roy.

  CRISPR-Cas9 technology enables acute gene knockdown and endogenous tagging to study single-synapse function. Here, we present a protocol for depleting alpha-synuclein (α-syn) or visualizing native α-syn with an endogenously inserted fluorescent tag in cultured mouse hippocampal neurons. We describe detailed steps, including CRISPR design, virus packaging/transduction (delivery), and validation of on-/off-target editing. This protocol should be useful for assigning precise function to contentious synaptic proteins and for visualizing protein trafficking without overexpression in cultured hippocampal neurons-an established model system for synaptic biology. For complete details on the use and execution of this protocol, please refer to Parra-Rivas et al.1.

Keywords:  CRISPR; Cell Biology; Cell culture; Microscopy; Molecular Biology; Neuroscience

DOI:  https://doi.org/10.1016/j.xpro.2025.103945
Sci Rep. 2025 Jul 23. 15(1): 26821

Early and non-destructive prediction of the differentiation efficiency of human induced pluripotent stem cells using imaging and machine learning.

Miki Arai Hojo, Taku Tsuzuki, Yosuke Ozawa, Toshiyuki Araki, Hidetoshi Sakurai.

  The reproducibility and robustness of many directed differentiation protocols from human induced pluripotent stem cells (hiPSCs) remain low, and the long differentiation induction period significantly limits protocol optimization. To address this, we developed an early and non-destructive prediction system for the differentiation induction efficiency of hiPSCs using bioimage informatics. We employed a directed differentiation protocol for muscle stem cells (MuSCs), a promising cell source for the regenerative therapy of muscular dystrophy. Biological analyses suggested that days 14-38 are positive for forecasting the induction efficiency on day 82. Therefore, we conducted six independent experiments, inducing MuSC differentiation in a total of 34 wells, and captured a total of 5,712 phase contrast cell images between days 14 and 38. We selected Fast Fourier transform (FFT) as the feature extraction method and confirmed that it captures the characteristics of cells during differentiation. By classifying images on each day using extracted features and machine learning, we found that samples with high and low induction efficiency could be predicted at approximately 50 days before the end of induction. This system is expected to contribute to regenerative therapy through effective protocol optimization.

Keywords:  Bioimage informatics; Directed differentiation; Early and non-destructive prediction; Human induced pluripotent stem cells (hiPSCs); Machine learning; Muscle stem cells (MuSCs)

DOI:  https://doi.org/10.1038/s41598-025-11108-5
J Orthop Translat. 2025 Sep;54 26-36

Synovial organoids: From fundamental construction to groundbreaking applications in arthritic disorders.

Xin Jin, Lin Huang, Xueyan Wang, Yun Tan, Miao Huang, Haijing Fu, Chengping Wen, Mingqian Zhou.

  As an emerging three-dimensional (3D) cell culture model, synovial organoids can highly mimic the structure and function of synovial tissue in vivo, providing a new and powerful tool for the research of synovial-related diseases. This article elaborated in detail on the construction of synovial organoids from the cell sources, culture systems, and construction techniques. Meanwhile, it comprehensively reviewed the application progress of synovial organoids in arthritic diseases including rheumatoid arthritis and osteoarthritis such as disease pathogenesis, drug development, and personalized therapy. Additionally, it explores current challenges and future directions for synovial organoids, providing a reference for further research and applications in related-diseases. The Translational Potential of this Article Synovial organoids enable direct modeling of the human synovial joint, offering a physiologically relevant platform for high-throughput drug screening. Patient-derived organoids not only facilitate the development of personalized medicine but also reduce reliance on animal studies for preclinical validation. This approach addresses ethical challenges and species-specific limitations while enhancing the translational relevance to human disease mechanisms.

Keywords:  Arthritis; Osteoarthritis; Rheumatoid arthritis; Synovial organoids

DOI:  https://doi.org/10.1016/j.jot.2025.07.004
Sci Rep. 2025 Jul 19. 15(1): 26217

TFEB overexpression alleviates autophagy-lysosomal deficits caused by progranulin insufficiency.

Wren O Nader, Kaylan S Brown, Nicholas R Boyle, Azariah K Kaplelach, Shaimaa M Abdelaziz, Skylar E Davis, Qays Aljabi, Ahmad R Hakim, Amelia G Davidson, Giacynta A Vollmer, Leah C Wright, J Bailey Echols, Joelle Saad, Nicholas S Pena, Andrew E Arrant.

  Progranulin is a pro-protein that is necessary for maintaining lysosomal function. Loss-of-function progranulin (GRN) mutations are a dominant cause of frontotemporal dementia (FTD). Brains of people with FTD due to GRN mutations accumulate lysosomal storage material and exhibit increased expression of lysosomal transcripts, which may be driven by TFEB and related transcription factors. While this may be a compensatory response to lysosomal impairment, overproduction of lysosomal proteins may also contribute to FTD pathogenesis. To investigate how TFEB may contribute to disease in people with GRN mutations, we analyzed the effects of TFEB overexpression in progranulin-insufficient cells and mice. We generated GRN knockout HEK-293 cells (GRN KO cells), which exhibited increased nuclear localization of TFEB and expression of lysosomal transcripts, but impaired autophagy. TFEB overexpression in GRN KO cells further increased lysosomal transcripts and partially normalized autophagy. We next injected an AAV vector expressing mouse Tfeb (AAV-TFEB) into the thalamus of Grn-/- mice, which accumulates lysosomal storage material. AAV-TFEB increased lysosomal transcripts and reduced immunoreactivity for SCMAS, a marker of lysosomal storage material, in Grn-/- thalamus. These data show that TFEB activity alleviates some autophagy-lysosomal deficits caused by progranulin insufficiency, suggesting potential utility of lysosome-based therapies for GRN-associated diseases.

Keywords:  Autophagy; Lysosomes; Progranulin; TFEB

DOI:  https://doi.org/10.1038/s41598-025-12268-0
Biochim Biophys Acta Mol Basis Dis. 2025 Jul 22. pii: S0925-4439(25)00339-4. [Epub ahead of print] 167991

The emerging role of eIF5A hypusination as a unique and underexplored mechanism in proteinopathies and neurological diseases.

Rohan Desai, Daniel C Lee, Maj-Linda B Selenica.

  Eukaryotic Translation Initiation Factor 5A (eIF5A) undergoes a unique post-translational modification of hypusination, converting a lysine 50 residue to hypusine (hypK50). While a few studies have investigated the role of the spermidine-hypusine-eIF5A axis in neurodegenerative diseases, including the pathological accumulation of tau and TAR DNA-binding protein 43 (TDP-43), the role of the hypusine pathway in neurological diseases remains vastly understudied. Thus, the focus of this review is highlighting emerging research on the mechanisms by which aberrant and chronic increases in hypusinated eIF5A (eIF5AhypK50) govern nucleocytoplasmic transport, stress granule dynamics, and protein aggregation to encourage further research of this pathway in multi-etiology dementia.

Keywords:  Hypusination; Neurodegeneration; Proteinopathy; TDP-43; eIF5A

DOI:  https://doi.org/10.1016/j.bbadis.2025.167991
Mol Brain. 2025 Jul 24. 18(1): 66

Unraveling the mystery: How autophagy deficiency in dopaminergic neurons drives human Parkinson's disease.

Sachiko Noda, Nobutaka Hattori.

  Alpha-synuclein (α-synuclein), a key component of Lewy body pathology, is a classical hallmark of Parkinson's disease. In previous studies, our group has examined dopaminergic neuron-specific Atg7 autophagy-deficient mice, observing α-synuclein aggregation in vivo. This pathological process led to dopamine neuron loss and age-related motor impairments. Further, in a recent study, we developed a new mouse model by crossing human α-synuclein bacterial artificial chromosome transgenic mice with dopaminergic neuron-specific Atg7 conditional knockout mice to further investigate these mechanisms. These model mice exhibited accelerated Lewy body-like pathology and motor dysfunction, providing additional evidence that autophagy deficiency exacerbates synuclein toxicity in vivo. This nano-review provides essential clues that autophagy deficiency in dopamine neurons may contribute to the onset of human synuclein diseases.

Keywords:  Autophagy; Dopaminergic neurons; Parkinson’s disease; Α-synuclein

DOI:  https://doi.org/10.1186/s13041-025-01235-5
Cells. 2025 Jul 10. pii: 1058. [Epub ahead of print]14(14):

Hypergravity and ERK Inhibition Combined Synergistically Reduce Pathological Tau Phosphorylation in a Neurodegenerative Cell Model.

Valerio Mignucci, Ivana Barravecchia, Davide De Luca, Giacomo Siano, Cristina Di Primio, Jack J W A van Loon, Debora Angeloni.

  This study evaluates the effects of hypergravity (HG) on a neurodegenerative model in vitro, looking at how HG influences Tau protein aggregation in Mouse Hippocampal Neuronal Cells (HT22) induced by neurofibrillary tangle seeds. Overall, 50× g significantly, synergistically, reduced the Tau aggregate Area when combined with ERK-inhibitor PD-0325901, correlating with decreased phosphorylation at critical residues pS262 and pS396. These findings suggest HG treatments may help mitigate cytoskeletal damage linked to Tau aggregation.

Keywords:  European Space Agency (ESA); PD-0325901; hypergravity; large diameter centrifuge (LDC); neurodegeneration; tauopathies

DOI:  https://doi.org/10.3390/cells14141058
Methods Protoc. 2025 Jul 07. pii: 76. [Epub ahead of print]8(4):

A Model-Based Approach to Neuronal Electrical Activity and Spatial Organization Through the Neuronal Actin Cytoskeleton.

Ali H Rafati, Sâmia Joca, Regina T Vontell, Carina Mallard, Gregers Wegener, Maryam Ardalan.

  The study of neuronal electrical activity and spatial organization is essential for uncovering the mechanisms that regulate neuronal electrophysiology and function. Mathematical models have been utilized to analyze the structural properties of neuronal networks, predict connectivity patterns, and examine how morphological changes impact neural network function. In this study, we aimed to explore the role of the actin cytoskeleton in neuronal signaling via primary cilia and to elucidate the role of the actin network in conjunction with neuronal electrical activity in shaping spatial neuronal formation and organization, as demonstrated by relevant mathematical models. Our proposed model is based on the polygamma function, a mathematical application of ramification, and a geometrical definition of the actin cytoskeleton via complex numbers, ring polynomials, homogeneous polynomials, characteristic polynomials, gradients, the Dirac delta function, the vector Laplacian, the Goldman equation, and the Lie bracket of vector fields. We were able to reflect the effects of neuronal electrical activity, as modeled by the Van der Pol equation in combination with the actin cytoskeleton, on neuronal morphology in a 2D model. In the next step, we converted the 2D model into a 3D model of neuronal electrical activity, known as a core-shell model, in which our generated membrane potential is compatible with the neuronal membrane potential (in millivolts, mV). The generated neurons can grow and develop like an organoid brain based on the developed mathematical equations. Furthermore, we mathematically introduced the signal transduction of primary cilia in neurons. Additionally, we proposed a geometrical model of the neuronal branching pattern, which we described as ramification, that could serve as an alternative mathematical explanation for the branching pattern emanating from the neuronal soma. In conclusion, we highlighted the relationship between the actin cytoskeleton and the signaling processes of primary cilia. We also developed a 3D model that integrates the geometric organization unique to neurons, which contains soma and branches, such that the mathematical model represents the interaction between the actin cytoskeleton and neuronal electrical activity in generating action potentials. Next, we could generalize the model into a cluster of neurons, similar to an organoid brain model. This mathematical framework offers promising applications in artificial intelligence and advancements in neural networks.

Keywords:  actin cytoskeleton; action potential; mathematical modeling; neuronal signaling; organoid brain; primary cilia

DOI:  https://doi.org/10.3390/mps8040076
Cells. 2025 Jul 18. pii: 1109. [Epub ahead of print]14(14):

A High-Throughput ImmunoHistoFluorescence (IHF) Method for Sub-Nuclear Protein Analysis in Tissue.

Kezia Catharina Oxe, Kristoffer Staal Rohrberg, Ulrik Lassen, Dorthe Helena Larsen.

  The current understanding of cellular protein distribution in clinical samples is limited. This is partially due to the complexity and heterogeneity of tissues combined with the qualitative nature of analysis by immunohistochemistry (IHC). The common use of manual assessment in the clinic is time-consuming and restricts both the complexity of scoring and the scale of patient tissue analysis. This has limited the transfer of biological observations into pathology and their integration into diagnostics. Immunofluorescence (IF) techniques allow detailed and high-throughput investigation of proteins in cell models, but their application to tissues has been hindered by poor antibody penetration, autofluorescence artefacts, and weak signals. With a growing focus on precision medicine, scalable techniques to investigate and analyse proteins are critically important. To address this, we generated a high-throughput ImmunoHistoFluorescence (IHF) approach, applying IF to tissue samples followed by automated acquisition and artificial intelligence (AI)-based analysis of sub-nuclear protein distribution to enable precise investigation of complex protein localization patterns. This advancement offers a method to transfer in vitro findings into human tissues to analyse protein localization patterns in physiologically relevant contexts for improved understanding of disease-driving mechanisms in patients, identification of new biomarkers, and acceleration of translational research.

Keywords:  ImmunoHistoFluorescence; sub-nuclear protein analysis; tissue analysis

DOI:  https://doi.org/10.3390/cells14141109
Adv Healthc Mater. 2025 Jul 23. e04817

3D-Printed Scaffolds Promote Enhanced Spinal Organoid Formation for Use in Spinal Cord Injury.

Guebum Han, Nicolas S Lavoie, Nandadevi Patil, Olivia G Korenfeld, Hyunjun Kim, Manuel Esguerra, Daeha Joung, Michael C McAlpine, Ann M Parr.

  The transplantation of regionally specific spinal neural progenitor cells (sNPCs) has shown promise for functional restoration after spinal cord injury (SCI) by forming connections with host neural circuits. Here, 3D-printed organoid scaffolds for transplantation using clinically relevant human induced pluripotent stem cell-derived regionally specific sNPCs is developed. Scaffolds with microscale channels are printed, and sNPCs are subsequently printed within these channels. The scaffolds direct axonal projections along the channels and guide the cells to simulate in vivo-like conditions, leading to more effective cell maturation and the development of neuronal networks crucial for restoring function after SCI. The scaffolds, with organoids assembled along their lengths, are transplanted into the transected spinal cords of rats. This significantly promotes the functional recovery of the rats. At 12 weeks post-transplantation, the majority of the cells in the scaffolds differentiate into neurons and integrate into the host spinal cord tissue. These results demonstrate their potential to create a relay system along the spinal cord and form synapses in both the rostral and caudal directions relative to the scaffold. It is envisioned that combining sNPCs, organoid assembly, and 3D printing strategies can ultimately lead to a transformative treatment approach for SCI.

Keywords:  3D‐printed scaffold; functional recovery; human induced pluripotent stem cells; spinal cord organoids; spinal neural progenitor cells

DOI:  https://doi.org/10.1002/adhm.202404817