bims-axbals 2025-07-13 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2025–07–13
thirty-six papers selected by
TJ Krzystek

Autophagic stress activates distinct compensatory secretory pathways in neurons.
Absence of the axon initial segment in sensory neuron enhances resistance to amyotrophic lateral sclerosis.
TDP-43 Proteinopathies in ALS and FTLD: Mechanistic Insights and Therapeutic Approaches.
Integrated genomic and molecular insights into astrocyte- and oligodendrocyte-derived amyotrophic lateral sclerosis: focus on miRNAs and extracellular vesicles.
TIA1-mediated stress granules promote neurodegeneration by sequestering HSP70 mRNA in C9orf72 mice.
Inhibiting Clarinet/CLA-1 restores function to injured motor neurons.
Activation of endogenous PRKN by structural derepression is linked to increased turnover of the E3 ubiquitin ligase.
Glial phagocytosis for synapse and toxic proteins in neurodegenerative diseases.
A Hybrid 2D/3D Approach for Neural Differentiation Into Telencephalic Organoids and Efficient Modulation of FGF8 Signaling.
Integrated phenotypic and transcriptomic characterization of desmin-related cardiomyopathy in hiPSC-derived cardiomyocytes and machine learning-based classification of disease features.
Tofersen: A Review in Amyotrophic Lateral Sclerosis Associated with SOD1 Mutations.
Identification of Transcriptomic Differences in Induced Pluripotent Stem Cells and Neural Progenitors from Amyotrophic Lateral Sclerosis Patients Carrying Different Mutations: A Pilot Study.
Deleterious Sequestosome 1 mutations G262R and P438L in amyotrophic lateral sclerosis cause autophagy and oxidative stress imbalance.
Induced Pluripotent Stem Cells for the Treatment of Lysosomal Storage Disorders.
Whole-mount Retinal Organoid Visualization with Cellular Resolution.
Super-resolution microscopy of mitochondrial mRNAs.
An Unstable ATG2A Variant Causes a Neurodegenerative Disorder via Impaired Autophagy and Proteotoxic Stress in Brain Atrophy.
The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence.
Glycogen supports glycolytic plasticity in neurons.
Increased BNIP3-mediated mitophagy attenuates GDAP1 loss of function - implications for Charcot-Marie-Tooth disease 4A.
Inhibition of PTPRS function does not affect the survival or regeneration of dopaminergic neurons but alters synaptic function in the nigrostriatal pathway.
Lysosomal changes caused by nicotine exposure in human epithelial tongue cells.
Nondisruptive inducible labeling of ER-membrane contact sites using the Lamin B receptor.
Mutant α-synuclein takes down autophagy.
PINK1 Loss of Function Selectively Alters the Mitochondrial-Derived Vesicle Pathway.
The Fragile Balance: Autophagy's Role in Neurodegenerative Disease Progression.
Nonmuscle myosin II regulates presynaptic actin and neuronal mechanobiology in Drosophila.
Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function.
FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites.
Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets.
Organoids as powerful models of endometrium epithelium in transcriptomic, cellular and functional mimicry.
Implications of mitochondrial phosphatidylethanolamine in neuronal health and neurodegeneration.
TDP-43 loss-of-function triggers mitochondrial dysfunction and metabolic imbalance.
Patient-derived induced pluripotent stem cell models reveal mechanistic links between aberrant mitochondrial dynamics and cardiomyopathy.
Organelles share the load.
Identification of Cytosol-Facing Organelle Membrane-Proximal Proteins via Proximity-Dependent Biotinylation.

Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2421886122

Autophagic stress activates distinct compensatory secretory pathways in neurons.

Sierra D Palumbos, Jacob Popolow, Juliet Goldsmith, Erika L F Holzbaur.

  Autophagic dysfunction is a hallmark of neurodegenerative disease, leaving neurons vulnerable to the accumulation of damaged organelles and aggregated proteins. However, the late onset of diseases suggests that compensatory quality control mechanisms may be engaged to delay these deleterious effects. Neurons expressing common familial Parkinson's disease-associated mutations in the leucine-rich repeat kinase 2 (LRRK2) exhibit defective autophagy. Here, we demonstrate that both primary murine neurons and human induced Pluripotent Stem Cells (iPSC)-derived neurons harboring pathogenic LRRK2 upregulate the secretion of extracellular vesicles. We used unbiased proteomics to characterize the secretome of LRRK2G2019S neurons and found that autophagic cargos including mitochondrial proteins were enriched. Based on these observations, we hypothesize that autophagosomes are rerouted toward secretion when cell-autonomous degradation is compromised to mediate clearance of undegraded cellular waste. Immunoblotting confirmed the release of autophagic cargos and live-cell imaging demonstrated that secretory autophagy is upregulated in LRRK2G2019S neurons. We also found that LRRK2G2019S neurons upregulate the release of exosomes containing microRNAs. Live-cell imaging confirmed that this upregulation of exosomal release is dependent on hyperactive LRRK2 activity, while pharmacological experiments indicate that this release staves off apoptosis. Finally, we show that markers of both vesicle populations are upregulated in plasma from mice expressing pathogenic LRRK2. In sum, we find that neurons expressing pathogenic LRRK2 upregulate secretory autophagy and the compensatory release of exosomes to mediate waste disposal and transcellular communication, respectively. We propose that this increased secretion contributes to the maintenance of cellular homeostasis, delaying neurodegenerative disease progression over the short term while potentially contributing to neuroinflammation over the longer term.

Keywords:  Parkinson’s disease; autophagy; neurodegeneration; secretion

DOI:  https://doi.org/10.1073/pnas.2421886122
Brain. 2025 Jul 07. pii: awaf182. [Epub ahead of print]

Absence of the axon initial segment in sensory neuron enhances resistance to amyotrophic lateral sclerosis.

Nguyen Thu Tra, Sumiko Kiryu-Seo, Haruku Kida, Koji Wakatsuki, Yoshitaka Tashiro, Motosuke Tsutsumi, Mitsutoshi Ataka, Yohei Iguchi, Tomomi Nemoto, Ryosuke Takahashi, Masahisa Katsuno, Hiroshi Kiyama.

  Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the selective loss of motor neurons. Proteasome dysfunction in ALS is considered to cause the accumulation of protein aggregates, which leads to motor neuron degeneration; however, the resilience of motor neurons to ALS pathology might be impaired long before the appearance of protein aggregates. Intriguingly, sensory dorsal root ganglion (DRG) neurons are not susceptible to ALS pathology despite their processes coexisting with axons of motor neurons in the same spinal nerves. Both DRG neurons and motor neurons in ALS model mice express activating transcription factor 3 (ATF3), a well-known marker of nerve injury and disease progression, suggesting that both types of neurons respond to ALS pathology. However, it remains unknown why only DRG neurons are resilient to ALS pathological damage. To address this issue, we used a nerve injury model in combination with unique injury-induced genetically engineered mice, in which genetic control with an Atf3 regulatory element enables proteasome ablation and mitochondrial visualization specifically in damaged neurons. Using the strategy, we found that DRG neurons are resistant to damage in proteasome-deficient conditions, whereas spinal motor neurons degenerate in the same conditions. This might be because DRG neurons lack the typical axon initial segment (AIS), which normally exists in mature neurons and acts as a gate for the selective transport of cargo to axons. The absence of a typical AIS in DRG neurons facilitated increased entry of mitochondria into the axon upon injury, with or without proteasome function. In contrast, damaged motor neurons lacking the proteasome failed to disassemble the AIS, which prevented increased mitochondrial influx into axons and led to energy depletion and degeneration. In the absence of the AIS, DRG neurons in the ALS mouse model are able to deliver sufficient mitochondria into the axon to prevent pathological damage. However, impaired proteasome function in ALS motor neurons results in retention of the AIS gate and failure of mitochondrial transport to axons. This is a possible reason why DRG neurons have greater resilience to ALS pathological damage compared with spinal motor neurons. Collectively, this study opens new directions for the understanding of neurodegenerative diseases at early stages of disturbed protein homeostasis.

Keywords:  Rpt3 (Pmsc4); amyotrophic lateral sclerosis; axonal transport; neurodegeneration; neuronal injury; proteostasis

DOI:  https://doi.org/10.1093/brain/awaf182
CNS Neurol Disord Drug Targets. 2025 Jul 03.

TDP-43 Proteinopathies in ALS and FTLD: Mechanistic Insights and Therapeutic Approaches.

Shilpi Chauhan, Preeti Maan, Archna Panghal.

  TAR DNA-binding protein 43 (TDP-43) is a vital RNA/DNA-binding protein involved in RNA metabolism, playing a key role in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Approximately 97% of sporadic ALS (sALS), familial ALS (fALS) and FTLD cases are associated with pathological inclusions of hyperphosphorylated and ubiquitinated TDP-43 and genetic mutations in TAR DNA binding protein (TARDBP). Besides TARDBP, mutations in other genes such as C9ORF72, SOD1, FUS, and NEK1 are also linked to other fALS cases. Cytoplasmic mislocalization, aberrant post-translational modifications, and amyloid- like aggregation characterize TDP-43 pathology. These pathological changes impair essential cellular processes, including gene expression, mRNA stability, and RNA metabolism. Mechanisms of TDP-43-induced toxicity include disruption of endocytosis, mitochondrial dysfunction, and progressive cellular damage. Additionally, liquid-liquid phase separation (LLPS) and prion-like propagation are emerging as central features of its pathological spread. This review summarizes advances in understanding TDP-43's physiological functions and pathological mechanisms in ALS and FTLD. It highlights key processes underlying TDP-43 toxicity, such as aggregation, selective neuronal vulnerability, and regional susceptibility. Finally, this review summarizes evolving therapeutic strategies aimed at mitigating TDP-43-related toxicity through disaggregation, targeting mislocalization, and addressing upstream dysfunctions and challenges faced in the development of effective therapies for ALS and FTLD.

Keywords:  TDP-43; TDP-43 toxicity.; amyotrophic lateral sclerosis; dementia; frontotemporal lobar degeneration; proteinopathy

DOI:  https://doi.org/10.2174/0118715273374466250617085832
Cell Mol Biol (Noisy-le-grand). 2025 Jul 06. 71(6): 1-8

Integrated genomic and molecular insights into astrocyte- and oligodendrocyte-derived amyotrophic lateral sclerosis: focus on miRNAs and extracellular vesicles.

Ehsan Asghari Jafari, Maryam Arabi, Ahmad Bereimipour.

Motor neurons in the brain and spinal cord begin to die off in Amyotrophic lateral sclerosis (ALS), a disease that can be fatal. Molecular pathways in neurological disease, especially ALS, remain a challenge in the medical sciences. In this disease, a disorder in both astrocytes and oligodendrocytes can cause the disease to progress. This study aimed to investigate the molecular mechanisms and find key elements between these two cells in ALS with a bioinformatics perspective. In this study, using integrated and continuous bioinformatics analytics by various tools and databases, we investigated genes, protein products, and miRNAs between astrocytes and oligodendrocytes. The obtained data were involved in the Cellular senescence, actin cytoskeleton, and cell cycle signaling pathways. Then, after careful evaluation of the information, TP53, MDM2, KRAS, PTPRC, and GSK proteins were candidates, which are regulated by hsa-miR-564, hsa-miR-496-5p, hsa-miR-324-5p, hsa-miR-296-5p, and hsa-miR-4258-3p miRNAs. Finally, the four genes had a more robust and better relationship in this study between astrocyte and oligodendrocyte-derived ALS.

DOI: https://doi.org/10.14715/cmb/2025.71.6.1
Brain. 2025 Jul 07. pii: awaf248. [Epub ahead of print]

TIA1-mediated stress granules promote neurodegeneration by sequestering HSP70 mRNA in C9orf72 mice.

Yan Wei, Dongmei Li, Rui Yang, Yanzhu Liu, Xuan Luo, Weiqiao Zhao, Hui Yang, Zhichao Chen, Chengyong Shen, Ying Wang, Zhihui Huang.

  Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease with progressive loss of motor neurons in the central nervous system. Recent studies have reported that there are mutations at the T cell antigen-1 (TIA1) domain site in some ALS patients. TIA1 is a key component of stress granules (SGs), but its role and mechanism in ALS pathogenesis remain unclear. In this study, we found that TIA1 was upregulated in the motor cortex of postmortem ALS patients as well as in the motor cortex neurons of C9orf72-poly-GA mice (ALS mice). TIA1 knockout in the central nervous system (TIA1Nestin-CKO mice) alleviated motor neuron loss, neuroinflammation and motor dysfunction in C9orf72-poly-GA mice. Mechanistically, RNA-sequencing combined with the C9orf72-ALS/FTD patient (snRNA-seq) database revealed that mRNA of heat shock protein 70 (HSP70) family member genes such as HSPa1b were up-regulated in the motor cortex of TIA1Nestin-CKO ALS mice. We further found that TIA1-mediated SGs formation was increased during ALS pathogenesis, leading to HSP70 mRNA being sequestered into SGs. This reduced HSP70 expression, impairing the degradation of poly-GA aggregates by the UBQLN2-HSP70 pathway and exacerbating C9orf72-ALS progression. Taken together, these findings highlight a previously unrecognized role of TIA1-mediated SGs in promoting ALS pathogenesis by sequestering HSP70 mRNA, suggesting potential therapeutic targets for ALS treatment.

Keywords:  C9orf72; HSP70; TIA1; UBQLN2; amyotrophic lateral sclerosis; stress granules

DOI:  https://doi.org/10.1093/brain/awaf248
bioRxiv. 2025 Jul 06. pii: 2025.07.05.663315. [Epub ahead of print]

Inhibiting Clarinet/CLA-1 restores function to injured motor neurons.

Wenjia Huang, Eli Min, Alexandra Byrne.

To regain function, injured axons must both regenerate and reform synapses with appropriate postsynaptic cells. We found that inhibiting the scaffolding protein Clarinet/CLA-1, a C. elegans ortholog of Piccolo and Fife, robustly improves axon regeneration. Despite the importance of CLA-1 during synapse development, disrupting the medium isoform of CLA-1 increases the number of axons that regenerate to the neuromuscular junction without significantly influencing synapse reformation. Consequently, the axons that do regenerate are capable of regaining function. Mechanistically, the enhanced axon regeneration observed in cla-1(-) mutants depends on the function of PTRN-1, a microtubule minus-end binding protein. Our data supports a model where loss of CLA-1 promotes PTRN-1 function, which speeds trafficking of injury-related cargo to and from the lesion, thus improving repair. Together, our results reveal a highly conserved synaptic active zone protein that can be manipulated to enhance axon regeneration without sacrificing the function of the repaired axons.

DOI: https://doi.org/10.1101/2025.07.05.663315
Autophagy. 2025 Jul 07.

Activation of endogenous PRKN by structural derepression is linked to increased turnover of the E3 ubiquitin ligase.

Fabienne Fiesel, Bernardo Bustillos, Jens Watzlawik, Carol Chen, Martin Berryer, Jiazhen Zhang, Paige Boneski, Caleb Hayes, Jenny Bredenberg, Eric Deneault, Zhipeng You, Narges Abdien, Nathalia Aprahamian, Taylor Goldsmith, Zahra Baninameh, Liam Cocker, Haonan Zhang, Matthew Goldberg, Edward Fon, Jean-François Trempe, Satpal Virdee, Thomas Durcan, Wolfdieter Springer.

  Loss-of-function mutations in the PINK1 and PRKN genes are the most common cause of early-onset Parkinson disease (PD). The encoded enzymatic pair selectively identifies, labels, and targets damaged mitochondria for degradation via the macroautophagy/autophagy-lysosome system (mitophagy). This pathway is cytoprotective and efforts to activate mitophagy are pursued as therapeutic avenues to combat PD and other neurodegenerative disorders. When mitochondria are damaged, the ubiquitin kinase PINK1 accumulates and recruits PRKN from the cytosol to activate the E3 ubiquitin ligase from its auto-inhibited conformation. We have previously designed several mutations that effectively derepress the structure of PRKN and activate its enzymatic functions in vitro. However, it remained unclear how these PRKN-activating mutations would perform endogenously in cultured neurons or in vivo in the brain. Here, we gene-edited neural progenitor cells and induced pluripotent stem cells to express PRKN-activating mutations in dopaminergic cultures. All tested PRKN-activating mutations indeed enhanced the enzymatic activity of PRKN in the absence of exogenous stress, but their hyperactivity was linked to their own PINK1-dependent degradation. Strikingly, in vivo in a mouse model expressing an equivalent activating mutation, we find the same relationship between PRKN enzymatic activity and protein stability. We conclude that PRKN degradation is the consequence of its structural derepression and enzymatic activation, thus resulting only in a temporary gain of activity. Our findings imply that pharmacological activation of endogenous PRKN will lead to increased turnover and suggest that additional considerations might be necessary to achieve sustained E3 ubiquitin ligase activity for disease treatment.

Keywords:  Autophagy; PINK1; Parkin; mitophagy; parkinson’s disease

DOI:  https://doi.org/10.1080/15548627.2025.2531025
Mol Neurodegener. 2025 Jul 09. 20(1): 81

Glial phagocytosis for synapse and toxic proteins in neurodegenerative diseases.

Yeseong Choi, Won-Suk Chung.

Glia, as resident immune and supportive cells of the central nervous system, play a critical role in maintaining brain homeostasis. One of their key homeostatic functions is phagocytic capacity in pruning synapses and removing cellular debris/protein aggregates, a process vital for synaptic plasticity and brain maintenance. However, these phagocytic functions are often dysregulated with aging and in neurodegenerative diseases (NDs), such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and frontotemporal dementia. This review aims to examine the phagocytic roles of glia under both physiological and pathological conditions, with a special focus on their interactions with misfolded protein aggregates, including amyloid beta, tau, alpha synuclein, prion, huntingtin, and TAR DNA-binding protein 43. We also explore the fate of ingested molecules after being phagocytosed by glia-whether they are degraded, accumulate intracellularly, or are transferred between cells-and their implications for disease progression. Finally, we review current therapeutic strategies and the potential approaches for modulating glial phagocytosis to mitigate several NDs. We believe that understanding the exact mechanisms of glial phagocytosis and clearance will serve as key elements in developing future treatments for NDs.

DOI: https://doi.org/10.1186/s13024-025-00870-9
Bio Protoc. 2025 Jun 20. 15(12): e5354

A Hybrid 2D/3D Approach for Neural Differentiation Into Telencephalic Organoids and Efficient Modulation of FGF8 Signaling.

Michele Bertacchi, Gwendoline Maharaux, Michèle Studer.

  Human brain development relies on a finely tuned balance between the proliferation and differentiation of neural progenitor cells, followed by the migration, differentiation, and connectivity of post-mitotic neurons with region-specific identities. These processes are orchestrated by gradients of morphogens, such as FGF8. Disruption of this developmental balance can lead to brain malformations, which underlie a range of complex neurodevelopmental disorders, including epilepsy, autism, and intellectual disabilities. Studying the early stages of human brain development, whether under normal or pathological conditions, remains challenging due to ethical and technical limitations inherent to working with human fetal tissue. Recently, human brain organoids have emerged as a powerful in vitro alternative, allowing researchers to model key aspects of early brain development while circumventing many of these constraints. Unlike traditional 2D cultures, where neural progenitors and neurons are grown on flat surfaces, 3D organoids form floating self-organizing aggregates that better replicate the cellular diversity and tissue architecture of the developing brain. However, 3D organoid protocols often suffer from significant variability between batches and individual organoids. Furthermore, few existing protocols directly manipulate key morphogen signaling pathways or provide detailed analyses of the resulting effects on regional brain patterning. • To address these limitations, we developed a hybrid 2D/3D approach for the rapid and efficient induction of telencephalic organoids that recapitulate major steps of anterior brain development. Starting from human induced pluripotent stem cells (hiPSCs), our protocol begins with 2D neural induction using small-molecule inhibitors to achieve fast and homogenous production of neural progenitors (NPs). After dissociation, NPs are reaggregated in Matrigel droplets and cultured in spinning mini-bioreactors, where they self-organize into neural rosettes and neuroepithelial structures, surrounded by differentiating neurons. Activation of the FGF signaling pathway through the controlled addition of FGF8 to the culture medium will modulate regional identity within developing organoids, leading to the formation of distinct co-developing domains within a single organoid. Our protocol combines the speed and reproducibility of 2D induction with the structural and cellular complexity of 3D telencephalic organoids. The ability to manipulate signaling pathways provides an additional opportunity to further increase system complexity, enabling the simultaneous development of multiple distinct brain regions within a single organoid. This versatile system facilitates the study of key cellular and molecular mechanisms driving early human brain development across both telencephalic and non-telencephalic areas. Key features • This protocol builds on the method established by Chambers et al. [1] for generating 2D neural progenitors, followed by dissociation and reaggregation into 3D brain organoids. • For optimal growth and maturation, telencephalic organoids are cultured in spinning mini-bioreactors [2] or on orbital shakers. • The protocol enables the generation of telencephalic neural progenitors in 10 days and produces 3D telencephalic organoids containing neocortical neurons within one month of culture. • Addition of morphogens in the culture medium (example: FGF8) enhances cellular heterogeneity, promoting the emergence of distinct brain domains within a single organoid.

Keywords:  Brain organoids; Brain patterning; FGF8; Neural differentiation; Telencephalic organoids; hiPSCs

DOI:  https://doi.org/10.21769/BioProtoc.5354
Eur J Cell Biol. 2025 Jul 01. pii: S0171-9335(25)00027-5. [Epub ahead of print]104(3): 151502

Integrated phenotypic and transcriptomic characterization of desmin-related cardiomyopathy in hiPSC-derived cardiomyocytes and machine learning-based classification of disease features.

Vivien Batoumeni, Yeranuhi Hovhannisyan, Bénédicte Gobert, Keyhan Alvandipour, Jennifer Arthur Ataam, Ombline Conrad, David Hoffmann, Nicolas Wiest-Daesslé, Jochen Dobner, José Américo Nabuco Leva Ferreira Freitas, Hakim Hocini, Zhenlin Li, Laurent Brino, Andrea Rossi, Onnik Agbulut, Peter Sommer, Pierre Joanne, Konstantinos Gkatzis.

  Desmin-related diseases are characterized by skeletal muscle weakness, cardiomyopathy, and respiratory dysfunction due to mutations in the desmin gene (DES), which encodes a protein essential for muscle cell integrity. This study investigates the effects of a pathogenic desmin mutation (DESE439K) in human cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) obtained from a patient carrying the DESE439K mutation, compared to cardiomyocytes derived from hiPSCs of three healthy donors. To further validate our findings a genome edited cell line has been obtained following the insertion of the mutation in a control hiPSC line. Using advanced technologies, including transcriptomics and phenotypic machine learning algorithms, we analyzed how this mutation disrupts cellular function and contributes to disease phenotypes. Our findings reveal that cardiomyocytes carrying DESE439K exhibit cytoplasmic protein aggregation, mitochondrial and sarcomere defects, and contractile dysfunctions, highlighting key phenotypic defects in desmin-related cardiomyopathy. Finaly, we developed a machine learning prediction model to classify cellular phenotypes, which can be used for translational research, including drug candidate screening. This research opens new avenues for understanding the molecular mechanisms of desmin-related cardiomyopathies and fosters the development of novel therapeutic strategies.

Keywords:  Cardiomyocyte; Desminopathy; Dilated Cardiomyopathy; Disease Modeling; Machine Learning; Myofibrillar Myopathy

DOI:  https://doi.org/10.1016/j.ejcb.2025.151502
CNS Drugs. 2025 Jul 10.

Tofersen: A Review in Amyotrophic Lateral Sclerosis Associated with SOD1 Mutations.

Aisling McGuigan, Hannah A Blair.

Tofersen (QALSODY®) is the first drug approved for the treatment of amyotrophic lateral sclerosis (ALS) associated with superoxide dismutase 1 (SOD1) mutations. Tofersen is an antisense oligonucleotide that induces SOD1 mRNA degradation. In the 28-week, placebo-controlled, multinational, phase III VALOR trial, intrathecally administered tofersen reduced plasma concentrations of neurofilament proteins (biomarker for neuro-axonal injury) and total SOD1 protein in cerebrospinal fluid in patients with SOD1 mutation-associated ALS. These reductions were sustained in a long-term, open-label extension study. The decline in functional outcomes was not significantly reduced with tofersen treatment compared with placebo in the 28-week phase III trial, although in the longer-term open-label study, early tofersen initiation was associated with slowed functional decline versus delayed tofersen initiation. Tofersen had an acceptable tolerability profile in clinical trials with a favourable benefit-to-risk balance. In summary, tofersen is a new disease-modifying therapy for patients with ALS attributed to an SOD1 mutation, offering reductions in levels of a biomarker associated with neurodegeneration and disease progression, with an acceptable tolerability profile.

DOI: https://doi.org/10.1007/s40263-025-01204-5
Cells. 2025 Jun 23. pii: 958. [Epub ahead of print]14(13):

Identification of Transcriptomic Differences in Induced Pluripotent Stem Cells and Neural Progenitors from Amyotrophic Lateral Sclerosis Patients Carrying Different Mutations: A Pilot Study.

Chiara Sgromo, Martina Tosi, Cristina Olgasi, Fabiola De Marchi, Francesco Favero, Giorgia Venturin, Beatrice Piola, Alessia Cucci, Lucia Corrado, Letizia Mazzini, Sandra D'Alfonso, Antonia Follenzi.

  Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease affecting motor neurons with a phenotypic and genetic heterogeneity and elusive molecular mechanisms. With the present pilot study, we investigated different genetic mutations (C9orf72, TARDBP, and KIF5A) associated with ALS by generating induced pluripotent stem cells (iPSCs) from peripheral blood of ALS patients and healthy donors. iPSCs showed the typical morphology, expressed stem cell markers both at RNA (OCT4, SOX2, KLF4, and c-Myc) and protein (Oct4, Sox2, SSEA3, and Tra1-60) levels. Moreover, embryoid bodies expressing the three germ-layer markers and neurospheres expressing neural progenitor markers were generated. Importantly, the transcriptomic profiles of iPSCs and neurospheres were analyzed to highlight the differences between ALS patients and healthy controls. Interestingly, the differentially expressed genes (DEGs) shared across all ALS iPSCs are linked to extracellular matrix, highlighting its importance in ALS progression. In contrast, ALS neurospheres displayed widespread deficits in neuronal pathways, although these DEGs were varied among patients, reflecting the disease's heterogeneity. Overall, we generated iPSC lines from ALS patients with diverse genetic backgrounds offering a tool for unravelling the intricate molecular landscape of ALS, paving the way for identifying key pathways implicated in pathogenesis and the disease's phenotypic variability.

Keywords:  Amyotrophic lateral sclerosis; RNA-seq; induced pluripotent stem cells; neural progenitor cells; transcriptomic analysis

DOI:  https://doi.org/10.3390/cells14130958
Neuroscience. 2025 Jul 07. pii: S0306-4522(25)00773-0. [Epub ahead of print]

Deleterious Sequestosome 1 mutations G262R and P438L in amyotrophic lateral sclerosis cause autophagy and oxidative stress imbalance.

Nidhi Singh, Dibyakanti Mishra, James Gomes.

  Amyotrophic Lateral Sclerosis (ALS) is a severe neurodegenerative disease (NDD) prevalent across the world. It is known that mutations in ALS associated genes can cause imbalances between cellular processes such as apoptosis, necroptosis, autophagy and proteasomal degradation that remove dysfunctional and aggregating proteins. Two rare missense variants namely G262R (G > A) and P438L (C > T) in Sequestosome 1 (SQSTM1), were identified by our group in a cohort of Indian ALS patients. SQSTM1 codes for p62, which is an autophagy adaptor protein involved in several signaling pathways. In this study, we investigated how these SQSTM1 mutations affect autophagy and the oxidative stress response pathway in SH-SY5Y cells through quantitative RT-PCR, immunoblotting and confocal microscopy. In addition, we examined how changes in the downstream signaling pathways alters nuclear-cytoplasmic localization of TDP-43 protein, a marker protein usually found in cytoplasmic inclusions in ALS patient tissues. We observed up-regulation of autophagy marker proteins LC3-II and ubiquitin, and down-regulation of oxidative stress marker protein Nrf2. Along with LC3-II, p-OPTN and ATG5, proteins that are also associated with autophagy were up-regulated. We also observed an increase in cytoplasmic localization of TDP-43 protein in cells expressing these p62 mutant proteins. Overall, our study provides evidence that the G262R (G > A) and P438L (C > T) mutations are deleterious through mechanisms that increase cytoplasmic localization of TDP-43, and adversely affect the autophagy and oxidative stress response pathway.

Keywords:  Amyotrophic Lateral Sclerosis; Autophagy; G262R/P438L mutations; Oxidative stress; Sequestosome 1; TDP-43

DOI:  https://doi.org/10.1016/j.neuroscience.2025.07.011
J Inherit Metab Dis. 2025 Jul;48(4): e70064

Induced Pluripotent Stem Cells for the Treatment of Lysosomal Storage Disorders.

Maryann Lorino, Bei Qiu, Brian Bigger.

Lysosomal disorders (LSDs) are a group of rare metabolic disorders, with an overall incidence of 1:4800 to 1:8000 live births. LSDs are primarily caused by dysfunctional lysosomal enzymes, which typically lead to the progressive accumulation of substrates within cellular lysosomes. As a result, patients experience a wide array of somatic symptoms such as visceromegaly, cardiopulmonary abnormalities, and respiratory and urinary infections. Additionally, over two-thirds of LSD subtypes have a neurological component, and without treatment, patients experience neurodegeneration, cognitive decline, and life expectancies spanning infancy to adulthood. At present, there is no therapy that rescues the degenerative neuropathology of LSDs, and current developments, such as brain-targeted enzyme replacement therapy, hematopoietic stem cell transplantation, and even gene therapy, can only prevent further neurodegeneration. However, recent advancements involving induced pluripotent stem cells (iPSCs) have demonstrated that stem cells may harbor the potential to both recapitulate the phenotype of neuropathic LSDs in vitro, as well as serve as a vector for regeneration in vivo, by replacing cells and neurons damaged by disease progression. This review reports the current state of iPSC technology in LSD research, and the pathway by which iPSCs are translated from disease modeling to serving as a regenerative therapeutic for neuropathic LSDs in the clinic.

DOI: https://doi.org/10.1002/jimd.70064
J Vis Exp. 2025 Jun 20.

Whole-mount Retinal Organoid Visualization with Cellular Resolution.

Marina Cunquero, Helena Isla-Magrané, Maria Marsal, Maddalen Zufiaurre-Seijo, José García-Arumí, Miguel Ángel Zapata, Anna Duarri, Pablo Loza-Alvarez.

Retinal organoids derived from human induced pluripotent stem cells are intricate 3D structures that mimic the human retina, offering a powerful platform for studying retinal development, disease mechanisms, and potential therapeutic strategies. Moreover, as they are derived from patients, they are becoming increasingly popular as they hold great promise as a tool for personalized medicine. Unlike conventional 2D cell cultures, retinal organoids preserve the native 3D architecture of the retina, allowing for a more realistic representation and enabling more physiologically relevant studies. However, their structural complexity, high cellular density, and diverse composition present significant challenges for characterization. To address these challenges and enhance our understanding of retinal organoid maturation while preserving the 3D context, we combined optical clearing methods with immunolabeling to visualize the entire structure of whole-mount organoids with confocal microscopy. For this, we employed a clearing method compatible with low- and high-numerical-aperture objectives, facilitating full-volume imaging and capturing certain regions of interest with cellular resolution. Using this approach, we identified the morphology and distribution in 3D of the three main neuron paths responsible for the visual information transmission: cone and rod photoreceptors, bipolar and ganglion cells. Our findings shed more light on the visualization techniques to address the spatial organization of retinal cells within the organoid.

DOI: https://doi.org/10.3791/68384
Nat Commun. 2025 Jul 10. 16(1): 6391

Super-resolution microscopy of mitochondrial mRNAs.

Stefan Stoldt, Frederike Maass, Michael Weber, Sven Dennerlein, Peter Ilgen, Jutta Gärtner, Aysenur Canfes, Sarah V Schweighofer, Daniel C Jans, Peter Rehling, Stefan Jakobs.

Mitochondria contain their own DNA (mtDNA) and a dedicated gene expression machinery. As the mitochondrial dimensions are close to the diffraction limit of classical light microscopy, the spatial distribution of mitochondrial proteins and in particular of mitochondrial mRNAs remains underexplored. Here, we establish single-molecule fluorescence in situ hybridization (smFISH) combined with STED and MINFLUX super-resolution microscopy (nanoscopy) to visualize individual mitochondrial mRNA molecules and associated proteins. STED nanoscopy reveals the spatial relationships between distinct mRNA species and proteins such as the RNA granule marker GRSF1, demonstrating adaptive changes in mRNA distribution and quantity in challenged mammalian cells and patient-derived cell lines. Notably, STED-smFISH shows the release of mRNAs during apoptosis, while MINFLUX reveals the folding of the mRNAs into variable shapes, as well as their spatial proximity to mitochondrial ribosomes. These protocols are transferable to various cell types and open new avenues for understanding mitochondrial gene regulation in health and disease.

DOI: https://doi.org/10.1038/s41467-025-61577-5
Clin Genet. 2025 Jul 09.

An Unstable ATG2A Variant Causes a Neurodegenerative Disorder via Impaired Autophagy and Proteotoxic Stress in Brain Atrophy.

S Rehan Ahmad, Md Zeyaullah, Abdullah M AlShahrani, Danish Qavi, Abdelrhman A G Altijani, Mohammad Suhail Khan, Khursheed Muzammil.

  Autophagy is a critical cellular process for maintaining proteostasis and neuronal health. Disruption of this pathway is increasingly recognized in pediatric neurodegenerative disorders. Here, we study a novel previously uncharacterized homozygous and autosomal recessive missense variant, c.1372G>C (p.Gly433Ala), in the autophagy gene ATG2A, identified in a 3-year-old female proband presenting with developmental regression, seizures, cerebellar ataxia, and MRI-confirmed diffuse cerebral and cerebellar atrophy. The affected residue, Gly433, is evolutionarily conserved across eukaryotes and predicted to be structurally and functionally critical. Computational modeling and molecular dynamics simulations revealed that the G433A substitution induces local β-sheet extension, increased protein flexibility, higher aggregation propensity, and global structural destabilization. Proband-derived fibroblasts expressing ATG2A-G433A showed normal transcript and protein levels, but exhibited mislocalization of ATG2A to the cytosol, reduced colocalization with LC3B, loss of autophagosome formation, and a marked increase in protein aggregates. Proteotoxic stress was further evidenced by significant accumulation of Proteostat- and SQSTM1-positive granules. Additionally, transcript levels of unfolded protein response markers (GRP78, PERK, ATF4, and CHOP) were significantly upregulated, suggesting increased ER stress signaling. Cell cycle analysis revealed a substantial increase in cell death in proband fibroblasts. Overall, our findings identify ATG2A as a potentially novel disease gene and its G433A variant as a pathogenic substitution that disrupts autophagy and proteostasis, driving neurodegeneration via aggregation-prone misfolding and autophagy failure. This work depicts the first clinical spectrum of ATG2A-related neurodegenerative disorders and highlights the importance of autophagy maintenance in pediatric neurodevelopmental processes.

Keywords:  ATG2A; autophagy; neurodegeneration; pediatric seizure; protein aggregation

DOI:  https://doi.org/10.1111/cge.70019
Elife. 2025 Jul 07. pii: RP101984. [Epub ahead of print]13

The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence.

Fan Zhang, Yuan Wang, Luyang Zhang, Chunjie Wang, Deping Chen, Haibo Liu, Ren Xu, Cole M Haynes, Jae-Hyuck Shim, Xianpeng Ge.

  The dysfunction of the cellular endolysosomal pathway, such as in lysosomal storage diseases, can cause severe musculoskeletal disorders. However, how endolysosomal dysfunction causes musculoskeletal abnormalities remains poorly understood, limiting therapeutic options. Here, we report that CHMP5, a member of the endosomal sorting complex required for transport (ESCRT)-III protein family, is essential to maintain the endolysosomal pathway and regulate bone formation in osteogenic lineage cells. Genetic ablation of Chmp5 in mouse osteogenic cells increases bone formation in vivo and in vitro. Mechanistically, Chmp5 deletion causes endolysosomal dysfunction by decreasing the VPS4A protein, and CHMP5 overexpression is sufficient to increase the VPS4A protein. Subsequently, endolysosomal dysfunction disturbs mitochondrial functions and increases mitochondrial ROS, ultimately resulting in skeletal cell senescence. Senescent skeletal cells cause abnormal bone formation by combining cell-autonomous and paracrine actions. Importantly, the elimination of senescent cells using senolytic drugs can alleviate musculoskeletal abnormalities in Chmp5 conditional knockout mice. Therefore, our results show that cell senescence represents an underpinning mechanism and a therapeutic target for musculoskeletal disorders caused by the aberrant endolysosomal pathway, such as in lysosomal storage diseases. These results also uncover the function and mechanism of CHMP5 in the regulation of cell senescence by affecting the endolysosomal-mitochondrial pathway.

Keywords:  CHMP5; bone; cell biology; cell senescence; endolysosomal pathway; medicine; mouse; musculoskeletal disease; skeletal stem cell

DOI:  https://doi.org/10.7554/eLife.101984
Proc Natl Acad Sci U S A. 2025 Jul 15. 122(28): e2509003122

Glycogen supports glycolytic plasticity in neurons.

Milind Singh, Aaron D Wolfe, Anjali A Vishwanath, Anastasia Tsives, Ian J Gonzalez, Sarah E Emerson, Richard Goodman, Daniel Colón-Ramos.

  Glycogen is the largest energy reserve in the brain, but the specific role of glycogen in supporting neuronal energy metabolism in vivo is not well understood. We established a system in Caenorhabditis elegans to dynamically probe glycolytic states in single cells of living animals via the use of the glycolytic sensor HYlight and determined that neurons can dynamically regulate glycolysis in response to activity or transient hypoxia. We performed an RNAi screen and identified that PYGL-1, an ortholog of the human glycogen phosphorylase, is required in neurons for glycolytic plasticity. We determined that neurons employ at least two mechanisms of glycolytic plasticity: glycogen-dependent glycolytic plasticity (GDGP) and glycogen-independent glycolytic plasticity. We uncover that GDGP is employed under conditions of mitochondrial dysfunction, such as transient hypoxia or in mutants for mitochondrial function. We find that the loss of GDGP impairs glycolytic plasticity and is associated with defects in synaptic vesicle recycling during hypoxia. Together, our study reveals that, in vivo, neurons can directly use glycogen as a fuel source to sustain glycolytic plasticity and synaptic function.

Keywords:  C. elegans; glycogen utilization; glycolytic biosensor; glycolytic plasticity; neuronal metabolism

DOI:  https://doi.org/10.1073/pnas.2509003122
Neurobiol Dis. 2025 Jul 04. pii: S0969-9961(25)00235-9. [Epub ahead of print]213 107019

Increased BNIP3-mediated mitophagy attenuates GDAP1 loss of function - implications for Charcot-Marie-Tooth disease 4A.

Li Zhang, Alireza Pouya, Janina Kopetzky, Sara Bitar, Christina Wolf, Federica Dal Bello, David Gomez-Zepeda, Stefan Tenzer, Axel Methner.

  Charcot-Marie-Tooth disease type 4 A ((CMT4A), an autosomal recessive neuropathy, is caused by mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1). GDAP1 resides in the outer mitochondrial membrane facing the cytosol and is involved in mitochondrial dynamics and function. Its perturbation affects mitochondrial shape, contact sites, redox homeostasis and cellular metabolism. In response to GDAP1 knockdown in a human neuronal cell line, we found increased mitochondrial turnover, biogenesis and mitophagy. This was associated with more lysosomal proteins in mitochondrial fractions including BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3) and its homolog BNIP3-like (BNIP3L) - proteins involved in the recruitment of autophagy machinery via direct interaction. Flies with neural Gdap1 knockdown also exhibited upregulated levels of the sole BNIP3 ortholog. Neural expression of human BNIP3 reduced the detrimental effects of Gdap1 knockdown on eclosion and climbing ability in adult flies, while simultaneous knockdown of both genes was detrimental. These findings suggest that increased BNIP3-driven mitophagy may act as a protective mechanism, partially counteracting the cellular dysfunction caused by GDAP1 loss of function, and highlight the potential of targeting mitophagy pathways as a therapeutic strategy for CMT4A.

Keywords:  BNIP3; Charcot-Marie-tooth (CMT) disease; Drosophila; GDAP1; Mitophagy

DOI:  https://doi.org/10.1016/j.nbd.2025.107019
Neurobiol Dis. 2025 Jul 05. pii: S0969-9961(25)00239-6. [Epub ahead of print]213 107023

Inhibition of PTPRS function does not affect the survival or regeneration of dopaminergic neurons but alters synaptic function in the nigrostriatal pathway.

Joshua Peter, Kaejaren C N Caldwell, Lucas McClain, Jason Tchieu, Ashley E Ross, Yu Luo.

  Parkinson's Disease (PD) is characterized by midbrain dopaminergic (mDA) neuron degeneration in the ventral midbrain, contributing to debilitating motor symptoms. This study investigated whether Protein Tyrosine Phosphatase Receptor Sigma (PTPRS), a known inhibitor of axonal growth through chondroitin sulfate proteoglycan (CSPG) interaction, plays a role in mDA neuron survival, function, and regeneration in PD. Our data show that inhibition of PTPRS using intracellular sigma peptide (ISP) enhances human mDA neuron neurite outgrowth in vitro, suggesting an inhibitory role of this receptor in the differentiation of human embryonic stem cell (hESC)-derived mDA neurons in vitro. However, genetic deletion and pharmacological inhibition of PTPRS does not affect mDA neuron survival, axon density, or motor behavior in 6-OHDA unilateral partially lesioned mice. Similarly, mDA-specific deletion of Ptprs does not affect the basal behavioral measurement in cKO mice, including general locomotion and motor learning. Interestingly, however, Ptprs deletion led to a reduced response in the behavior sensitization to repeated methamphetamine (METH) exposure in cKO mice, suggesting a dampened response in synaptic function in cKO mice under these conditions. Ex vivo voltammetry recording in the striatum indeed shows altered parameters of dopamine (DA) release upon stimulation. These findings indicate that the inhibition of PTPRS function in human mDA neuron progenitors might be a promising strategy for enhancing neurite outgrowth or incorporation in host tissues in transplantation therapies. Finally, our data support that inhibition of PTPRS function in mDA neurons in adult mice in vivo could inhibit METH induced plasticity and behavioral sensitization.

Keywords:  Dopaminergic neurons; PTPRS; Parkinson's disease; Synapses

DOI:  https://doi.org/10.1016/j.nbd.2025.107023
Toxicol Lett. 2025 Jul 05. pii: S0378-4274(25)00131-6. [Epub ahead of print]

Lysosomal changes caused by nicotine exposure in human epithelial tongue cells.

S Uvsløkk, T Tanner, R Becher, H Valen, J T Samuelsen.

  Nicotine is an addictive substance and has been associated with several harmful effects on health. Many previous studies have focused on the receptor-mediated mechanisms of nicotine. However, non-receptor mediated effects of nicotine, such as effects on the lysosomes have also been reported. Well-functioning lysosomes are essential for cellular degradation pathways like the autophagic, phagocytic, and endocytic pathways. This study aimed to investigate nicotine's direct effect on lysosomes and lysosome-dependent activities in vitro. Cells from the immortalized human epithelial tongue cell line PE/CA-PJ49 were exposed to nicotine (5mM) alone or in combination with bafilomycin A1 (10nM; an inhibitor of lysosomal activity). Cell viability was measured using the MTT assay. Morphological changes were studied in a phase contrast microscope. Lysosomal activity was measured using flow cytometry and western blotting was used to quantify selected autophagy-related proteins. Only nicotine in combination with bafilomycin A1 resulted in decreased cell viability. However, morphological changes (vacuolization) were only observed in the cells exposed to nicotine. Apart from control, all exposures decreased lysosomal activity and increased the levels of the autophagy-related proteins p62/SQSTM1 and LC3-II. In conclusion, nicotine caused cellular vacuolization, reduced lysosomal activity, and increased levels of autophagy-related proteins indicating impaired autophagic flux.

Keywords:  Autophagy; Lysosomes; Nicotine

DOI:  https://doi.org/10.1016/j.toxlet.2025.07.001
PLoS Biol. 2025 Jul;23(7): e3003249

Nondisruptive inducible labeling of ER-membrane contact sites using the Lamin B receptor.

Laura Downie, Nuria Ferrandiz, Elizabeth Courthold, Megan Jones, Stephen J Royle.

Membrane contact sites (MCSs) are areas of close proximity between organelles that allow the exchange of material, among other roles. The endoplasmic reticulum (ER) has MCSs with a variety of organelles in the cell. MCSs are dynamic, responding to changes in cell state, and are, therefore, best visualized through inducible labeling methods. However, existing methods typically distort ER-MCSs, by expanding contacts or creating artificial ones. Here, we describe a new method for inducible labeling of ER-MCSs using the Lamin B receptor (LBR) and a generic anchor protein on the partner organelle. Termed LaBeRling, this versatile, one-to-many approach allows labeling of different types of ER-MCSs (mitochondria, plasma membrane, lysosomes, early endosomes, lipid droplets, and Golgi), on-demand, in interphase or mitotic human cells. LaBeRling is nondisruptive and does not change ER-MCSs in terms of the contact number, extent or distance measured; as determined by light microscopy or a deep-learning volume electron microscopy approach. We applied this method to study the changes in ER-MCSs during mitosis and to label novel ER-Golgi contact sites at different mitotic stages in live cells.

DOI: https://doi.org/10.1371/journal.pbio.3003249
Sci Signal. 2025 Jul 08. 18(894): eaea2255

Mutant α-synuclein takes down autophagy.

Leslie K Ferrarelli.

Parkinson's disease-associated α-synuclein impairs autophagy by hijacking the cell's acetylation machinery.

DOI: https://doi.org/10.1126/scisignal.aea2255
FASEB Bioadv. 2025 Jul;7(7): e70030

PINK1 Loss of Function Selectively Alters the Mitochondrial-Derived Vesicle Pathway.

Charlotte L Collier, Colleen Ruedi, Naomi J Thorne, David A Tumbarello.

  Cell homeostasis and metabolic control require the efficient function of mitochondria and implementation of quality control pathways following damage. Cells have various discrete pathways of mitochondrial quality control (mitoQC) to maintain the healthy network. PINK1 and Parkin are two key players in mitoQC, most highly associated with the ubiquitin-dependent capture and degradation of whole mitochondria by autophagy. However, these proteins have alternative roles in repair routes directing locally damaged cargo to the lysosome, such as the mitochondrial-derived vesicle (MDV) pathway. We aimed to clarify the role of PINK1 and determine how its loss of function impacts mitochondrial dynamics and quality control. Results indicate PINK1 knockout (KO) has little impact on whole mitochondrial turnover in response to damage in SH-SY5Y cells, whereas both PINK1 and Parkin KO cells have healthy mitochondrial networks with efficient ATP production. However, TOM20 positive outer-membrane and damage-induced PDH-positive inner-membrane MDVs are elevated in PINK1 KO cells. Although, in contrast to Parkin KO, this is not due to a defect in trafficking to a LAMP1-positive compartment and may instead indicate increased damage-induced flux. In comparison, loss of Atg5-dependent mitophagy has no effect on whole mitochondrial turnover and only results in a limited elevation in inner-membrane MDVs in response to damage, indicating autophagy-independent mechanisms of whole mitochondrial turnover and a minor compensatory increase in damage-induced MDVs. Therefore, these data suggest PINK1 and Parkin are dispensable for whole mitochondrial turnover, but following their perturbation have disparate effects on the MDV pathway.

Keywords:  Parkinson's; lysosome; membrane trafficking; mitochondria; mitochondrial quality control; vesicle transport

DOI:  https://doi.org/10.1096/fba.2024-00200
Curr Neuropharmacol. 2025 Jul 03.

The Fragile Balance: Autophagy's Role in Neurodegenerative Disease Progression.

Bharat Bhushan, Meenakshi Dhanawat, Garima, Kashish Wilson, Sumeet Gupta, Samrat Chauhan.

  Autophagy relates to the mechanism underlying the intracellular constituents' breakdown by lysosomes. Autophagy plays an essential role in preserving and regulating cellular homeostasis by mediating the degradation of intracellular components and recycling their decomposition products. It was demonstrated that autophagy operates in-vivo in the starving reaction, initial growth, internal control of quality, and cell division. Autophagy malfunction is perhaps connected with cancer and neurological conditions, as demonstrated by current research. In conjunction with the identification of specific mutations associated with autophagy-related disorders and deeper knowledge of the pathophysiology of disorders caused by aberrant disintegration of particular autophagy substrates, autophagy activation serves a vital part in prolonging lifespans and suppressing the process of aging. To safeguard the homeostasis within a cell, cells have developed sophisticated quality-control procedures for organelles and proteins. These quality-control mechanisms maintain cellular integrity through degradation by the autophagy-lysosome or ubiquitin-proteasome systems, as well as through protein folding assistance (or refolding of misfolded proteins) provided by molecular chaperones. A great deal of neurodegenerative illnesses are indicated by the development of intracellular inclusions formed from misfolded proteins, which are believed to be an outcome of defective autophagy. Additionally, it was recently discovered that neurodegenerative illnesses are also linked with mutations in key autophagy-related genes. However, pathogenic proteins like α-synuclein and amyloid β cause damage to the autophagy system. This paper examines the recent advancements in our understanding of the link between autophagic abnormalities and the development of neurological disorders, and proposes that activating autophagy could serve as a potential therapeutic strategy.

Keywords:  Autophagy; autophagy-related gene; cancer; heart disease; liver disease; neurodegenerative disease.; protein aggregates

DOI:  https://doi.org/10.2174/011570159X377552250627113915
J Cell Biol. 2025 Sep 01. pii: e202501211. [Epub ahead of print]224(9):

Nonmuscle myosin II regulates presynaptic actin and neuronal mechanobiology in Drosophila.

Biljana Ermanoska, Jonathan Baets, Avital A Rodal.

Neuromuscular junctions (NMJs) are evolutionarily ancient, specialized contacts between neurons and muscles. They experience lifelong strain, yet the mechanism preserving their integrity under mechanical load remains unclear. Here, we identify a novel actomyosin structure at Drosophila larval NMJs, consisting of a long-lived, low-turnover presynaptic actin core that colocalizes with nonmuscle myosin II (NMII) and becomes disorganized upon manipulating neuronal NMII levels or activity. Intriguingly, neuronal NMII depletion altered postsynaptic NMII levels and organization near synapses, suggesting transsynaptic propagation of actomyosin rearrangements. Under these conditions, integrin adhesion receptors were reduced on both sides of the synapse, indicating disrupted neuron-muscle connections. Notably, axon severing mimics these effects, while axonal stretching reorganizes integrins without disrupting the actin core, suggesting that presynaptic actomyosin and integrin organization are highly sensitive to mechanical cues and dynamically adjust to both loss and gain of tension. Our study reveals a presynaptic actomyosin assembly that maintains mechanical continuity between neurons and muscle, potentially enabling mechanotransduction at the NMJ through integrin-mediated adhesion.

DOI: https://doi.org/10.1083/jcb.202501211
bioRxiv. 2025 Jul 04. pii: 2025.07.01.662163. [Epub ahead of print]

Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function.

Kaylee D Tutrow, Jade Harkin, Laurna Varghese, Melody Hernandez, Kang-Chieh Huang, Yue Fang, Parker Wilcox, Logan Bedford, Tsai-Yu Lin, Chi Zhang, Cátia Gomes, Shweta Puntambekar, Stephanie Bissel, Bruce T Lamb, Jason S Meyer.

The involvement of microglia in neurodegenerative diseases has drawn increasing attention, as many genetic risk factors are preferentially expressed in microglia. Microglial fractalkine receptor (CX3CR1) signaling regulates many key microglial functions, and the CX3CR1-V249I single nucleotide polymorphism (SNP) has been associated with increased risk for multiple neurodegenerative conditions, including Alzheimer's disease, yet its functional consequences in human microglia remain unexplored. In this study, we generated iPSC-derived human microglia-like cells (hMGLs) and found that the CX3CR1-V249I variant increased susceptibility to starvation-induced cell death, reduced amyloid-beta uptake, altered microglial morphology, and impaired migration, with more pronounced effects in homozygous cells. Co-culture with neurons demonstrated that hMGLs with the CX3CR1-V249I variant misregulated neuronal properties, including abnormal neuronal growth as well as an induction of neuronal hyperexcitability. These findings highlight the critical role of CX3CR1 in regulating microglial function and implicate the V249I variant in driving pathogenic microglial states relevant to neurodegeneration.

DOI: https://doi.org/10.1101/2025.07.01.662163
Nucleic Acids Res. 2025 Jul 08. pii: gkaf665. [Epub ahead of print]53(13):

FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites.

Hana Antonicka, Ana Vučković, Woranontee Weraarpachai, Seungwoo Hong, Michele Brischigliaro, Ahram Ahn, Antoni Barrientos, Hauke S Hillen, Eric A Shoubridge.

The first post-transcriptional step in mammalian mitochondrial gene expression, required for the synthesis of the 13 polypeptides encoded in mitochondrial DNA (mtDNA), is endonucleolytic cleavage of the primary polycistronic transcripts. Excision of the mtDNA-encoded transfer RNAs (tRNAs) releases most mature RNAs; however, processing of three noncanonical messenger RNAs (mRNAs) not flanked by tRNAs (CO1, CO3, and CYB) requires FASTKD5. To investigate the molecular mechanism involved, we created knockout human cell lines to use as assay systems. The absence of FASTKD5 produced a severe OXPHOS assembly defect due to the inability to translate two unprocessed noncanonical mRNAs and predicted altered folding patterns specifically at the 5'-end of the CO1 coding sequence. Structural features 13-15 nt upstream of the CO1 and CYB cleavage sites suggest FASTKD5 recognition mechanisms. Remarkably, a map of essential FASTKD5 amino acid residues revealed RNA substrate specificity; however, a key, putative active site residue was required for processing all three noncanonical pre-RNAs. Mutating this site did not significantly alter the binding of any client RNA substrate. A reconstituted in vitro system showed that wild-type, but not mutant, FASTKD5, was able to cleave client substrates correctly. These results establish FASTKD5 as the missing piece of biochemical machinery required to completely process the primary mitochondrial transcript.

DOI: https://doi.org/10.1093/nar/gkaf665
Commun Biol. 2025 Jul 07. 8(1): 1015

Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets.

Thomas Funck, Konrad Wagstyl, Claude Lepage, Mona Omidyeganeh, Paule-Joanne Toussaint, Ting Xu, Katrin Amunts, Alexander Thiel, Nicola Palomero-Gallagher, Alan C Evans.

Mesoscale maps of brain architecture are important tools for characterizing the chemo- and cytoarchitectonic organization of the brain. These maps are essential for advancing our understanding of normal and pathologic brain function because they provide a bridge between neuron-level micro-scale imagining and macro-level population brain imaging. Here we introduce a method and software package called BrainBuilder for reconstructing 3-dimensional cortical maps from data sets of 2-dimensional post-mortem serial brain sections processed for the visualization of multiple different biological features. This pipeline can be applied to the brains from different species, without the strict need for a corresponding reference volume from the brain donor. As a proof of principle, we reconstruct data showing the distribution of multiple neurotransmitter receptor binding sites, and cell and myelin stained sections in the human and macaque brain. We show that BrainBuilder can serve as the basis for the development of future mesoscale 3D atlases.

DOI: https://doi.org/10.1038/s42003-025-08267-6
Cell Mol Life Sci. 2025 Jul 07. 82(1): 272

Organoids as powerful models of endometrium epithelium in transcriptomic, cellular and functional mimicry.

Martina Ciprietti, Celine Bueds, Hugo Vankelecom, Joris Vriens.

  Organoids have emerged as revolutionary biomimetic systems that offer a physiologically relevant in vitro model to study the specific tissue or organ of origin. In the field of female reproductive biology, endometrial organoids have proven their high value in the exploration of intricate physiological processes of the endometrium such as hormonal differentiation (decidualization) and embryo-receptivity, as well as to understand the pathophysiology of diseases associated with endometrial deficits. Moreover, organoid-based adhesion models have emerged as appropriate in vitro platform that faithfully reproduces the receptive endometrium. These in vitro models offer new tools to explore the molecular mechanisms of the early embryo-endometrium interaction and to bypass the barrier of ethical restrictions. This review highlights recent advances in the endometrial research domain, focusing on endometrial epithelial organoid models that closely replicate the cellular, transcriptomic and functional characteristics of the native tissue. A comprehensive overview of the transcriptomic changes during the menstrual cycle is provided, as well as of the detailed comparison between the different cell populations of the endometrium and the endometrial organoid model. Here, we provide evidence that endometrial organoids mimic the native endometrial tissue and offer relevant tools to advance our understanding of endometrial (patho)biology, enabling us to gain insights into molecular pathways.

Keywords:  Endometrium; Ion channels; Organoids; Transcriptomics

DOI:  https://doi.org/10.1007/s00018-025-05807-5
Neural Regen Res. 2025 Jul 05.

Implications of mitochondrial phosphatidylethanolamine in neuronal health and neurodegeneration.

Yantao Zuo, Niharika Amireddy, Qian Cai.

  Phosphatidylethanolamine is a major phospholipid class abundant in the brain, particularly in the inner leaflet of the plasma and mitochondrial membranes. Although it is primarily synthesized from phosphatidylserine via decarboxylation in mitochondria or from ethanolamine via the cytidine diphosphate-ethanolamine pathway in the endoplasmic reticulum, phosphatidylethanolamine that resides in mitochondria is preferentially produced locally and is distinct and separate from the pool of phosphatidylethanolamine made in the endoplasmic reticulum. Mitochondria-derived phosphatidylethanolamine is not only essential for mitochondrial integrity but also is exported to other organelles to fulfill diverse cellular functions. Neurons are highly enriched with phosphatidylethanolamine, and the importance of phosphatidylethanolamine metabolism in neuronal health has recently been recognized following its reported links to Alzheimer's disease, Parkinson's disease, and hereditary spastic paraplegia, among other neurological disorders. Indeed, disturbances in mitochondrial function and phosphatidylethanolamine metabolism and the resulting neuronal dysfunction are the common features of individuals suffering from these diseases, highlighting the great importance of maintaining proper phosphatidylethanolamine homeostasis in neurons. In this review, we summarize the current knowledge of phosphatidylethanolamine metabolism and its role in neuronal function with a special emphasis on the phosphatidylethanolamine biosynthetic pathway in mitochondria. We then review findings on how phosphatidylethanolamine biosynthesis is affected in major neurodegenerative diseases. Finally, we highlight promising future research areas that will help advance the understanding of neuronal phosphatidylethanolamine mechanisms and identify phosphatidylethanolamine-targeted therapeutic strategies for combating such brain diseases.

Keywords:  ; Alzheimer's disease; Parkinson's disease; autophagy; cognitive dysfunction; hereditary spastic paraplegia; neuronal phospholipid trafficking; phosphatidylserine decarboxylase; phosphatidylserine transport; tauopathy

DOI:  https://doi.org/10.4103/NRR.NRR-D-25-00201
Neural Regen Res. 2025 Jul 05.

TDP-43 loss-of-function triggers mitochondrial dysfunction and metabolic imbalance.

Miriam Ceron-Codorniu, Anna Fernàndez-Bernal, Reinald Pamplona, Manuel Portero-Otín.

DOI: https://doi.org/10.4103/NRR.NRR-D-25-00167
Pediatr Res. 2025 Jul 09.

Patient-derived induced pluripotent stem cell models reveal mechanistic links between aberrant mitochondrial dynamics and cardiomyopathy.

Chrishan J Ramachandra.

IMPACT: DNM1L mutations impair mitochondrial fission, leading to cardiomyocyte energy deficits and contractile dysfunction, and reveal a cardiac role for DNM1L beyond neurological disease. iPSC-cardiomyocytes derived from patients with DNM1L mutations demonstrate mitochondrial defects and cardiomyopathy phenotypes, offering a robust model to dissect disease mechanisms and identify personalised therapies. Disrupted mitochondrial dynamics directly lead to calcium mishandling and contractile dysfunction, positioning fission/fusion pathways as promising therapeutic targets in cardiomyopathy treatment.

DOI: https://doi.org/10.1038/s41390-025-04278-5
Science. 2025 Jul 10. 389(6756): 130-131

Organelles share the load.

Marc Fransen.

Peroxisome-mitochondria contact sites manage mitochondrial oxidative stress.

DOI: https://doi.org/10.1126/science.adz0109
Methods Mol Biol. 2025 ;2953 189-203

Identification of Cytosol-Facing Organelle Membrane-Proximal Proteins via Proximity-Dependent Biotinylation.

Xinyue Bao, Xiaoyan Zhang, Huifang Jia, Xiaohong Zhu.

  Organelle membrane (OM)-resident or -proximal proteins that face the cytosol play a critical role in the import and exchange of ions, metabolites, and proteins between subcellular compartments, thereby regulating organelle biogenesis and function. However, the identification and functional characterization of these proteins pose challenges due to their dynamic spatial and temporal nature. We introduce a proximity labeling system using biotin ligase-mediated protein biotinylation in live Arabidopsis thaliana cells. This chapter outlines a detailed step-by-step protocol for identifying cytosol-facing OM-resident or -proximal proteins of mitochondria, chloroplasts, and peroxisomes in plant cells. This protocol can be adapted to identify cytosol-facing OM-resident and/or proximal proteins of any subcellular compartments of interest, as well as to map their spatiotemporal profiles under various stress conditions. The protocol described includes the following key steps: (1) sample preparation; (2) optimization of biotin labeling conditions; (3) enrichment of biotinylated proteins for liquid chromatography-tandem mass spectrometry (LC-MS/MS); (4) validation of identified candidate proteins.

Keywords:  Arabidopsis thaliana; Biotin protein ligase; Organellar quality control; Organelle membrane proximal protein; Organelle membrane proximity labeling; Proximity labeling

DOI:  https://doi.org/10.1007/978-1-0716-4694-6_12