bims-axbals 2026-07-05 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2026–07–05
38 papers selected by
TJ Krzystek

TDP-43 proteinopathy as a biomarker and therapeutic target in amyotrophic lateral sclerosis.
Therapeutic targeting of the conserved region within the low-complexity domain of TDP-43 is neuroprotective and extends survival in amyotrophic lateral sclerosis mice.
Neural Organoid Models as a Platform for Studying Disease Mechanisms in Amyotrophic Lateral Sclerosis.
Lysophagy protects against ANXA11 amyloid fibril toxicity and propagation in FTLD.
A PARK9 iPSC-Derived Dopaminergic Neuron Model Enables Drug Screening Targeting Autophagy-Lysosome Pathway Dysfunction in Parkinson's Disease.
The SQSTM1 L341V Variant Associated With Sporadic ALS Promotes the Accumulation of Enlarged Ubiquitin-Positive SQSTM1 Bodies.
A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical-like and dopaminergic-like induced neurons.
Leucettinib-21 decreases dosage effects of DYRK1A in human trisomy 21 induced pluripotent stem cell-derived neural cells.
Rescue of mitochondrial and neurite pathology in SPG7 hereditary spastic paraplegia patient-derived cortical neurons.
LRRK2 mutations: at the crossroads of dopamine, iron, and calcium imbalance in Parkinson's disease.
Nanoscale morphological and structural analysis of round and donut oligomers formed by C-terminal domain of TDP-43.
Disentangling the response to lysosomal damage.
Advancing the monitoring of organelle contact sites in vitro and in vivo.
The role of ATF4 in neurons under mitochondrial stress.
Proteostasis and unfolded protein response dynamics in human neuron/mouse glia co-cultures reveal a cell-specific maturation response.
Assessing upper motor neuron dysfunction in ALS: from TMS-EEG and EMG neurophysiology to a combined tFUS-TMS translational framework.
Advances in neural organoids: structural organization, disease modeling, and applications in gene therapy.
ADAR2-Mediated RNA Editing Promotes TDP-43 Nuclear Export and Alters RNA Binding.
Topological modeling of gene expression in the brain with Huntington's disease reveals selective disruption of co-expression network.
Nuclear RNA clusters are dynamic structural entities in Huntington's disease.
Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders.
Differentiation of human induced pluripotent stem cells into cardiac valve cells using 2D and 3D differentiation protocols.
VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair.
Targeting neurodevelopmental miR132-3p promotes neuroprotection and axon regeneration after optic nerve injury in mice.
Tau protein as a regulator of mitochondrial function and dynamics.
SGK1-mediated deficits in microglial phagocytosis drive pathological progression in amyotrophic lateral sclerosis.
Simple input-output dependencies explain neuronal activity.
Potentiated Maturation of hPSC-Derived Dopaminergic Neurons via Convergent Genetic and Small Molecule Modulation.
Parkinson's Disease Cell Transplantation Therapy: A New Dawn With Pluripotent Stem Cell-Based Therapy.
Targeted Photodegradation of Misfolded Proteins via Self-photosensitizing with Molecularly Produced Light.
Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data.
From iPSC to manufactured iNK cells using CombiCult® screening platform.
Two-photon 3D imaging of optically stimulated neural activity at 100 Hz.
PTEN Subcellular Localization Dictates Function.
Releasing the neuronal brake: Inhibiting AhR to enhance axon regeneration.
Kinematic-calcium loops unravel impaired excitation-contraction coupling in MELAS-affected cardioids.
Mitochondrial Calcium Transport in Amino Acid Metabolism: From nutritional responses to metabolic regulation.
COPII meets autophagy at the ER membrane.

Biochem Soc Trans. 2026 Jul 29. 54(7): 901-913

TDP-43 proteinopathy as a biomarker and therapeutic target in amyotrophic lateral sclerosis.

Eleni Christoforidou, Emily McFagan, Martha McLaughlin, Majid Hafezparast.

  Amyotrophic lateral sclerosis (ALS) is the most common form of adult-onset motor neuron disease, characterised by the degeneration of upper and lower motor neurons. The cytoplasmic aggregation of TDP-43 (TAR DNA-binding protein 43), an RNA-binding protein, is considered a hallmark of ALS pathology, found in nearly all postmortem cases of ALS. TDP-43 is normally primarily nuclear, where it has a widespread role in gene regulation. Mutations, extrinsic stressors, and alterations in RNA homeostasis in ALS lead to nuclear depletion of TDP-43 and the formation of cytosolic TDP-43 aggregates. This causes multiple downstream effects on neuronal function and degeneration as well as gene expression. TDP-43 is a promising target as a biomarker, as it is found to be elevated in the biofluids of ALS patients, and its cytoplasmic aggregation can also be observed in peripheral tissues; however, methodological variability and technical limitations currently preclude the establishment of TDP-43 as a standalone biomarker. There are also promising therapeutic strategies in development targeting TDP-43 pathology, but a critical challenge that remains is achieving a balance between eliminating toxic aggregates and preserving the essential functions of TDP-43. In summary, with further research, considering TDP-43 pathology in ALS gives hope for finding future novel diagnostics and therapeutics for ALS.

Keywords:  ALS; Amyotrophic Lateral Sclerosis; MND; Motor Neuron Disease; TARDBP; TDP-43

DOI:  https://doi.org/10.1042/BST20260896
Nat Aging. 2026 Jul 03.

Therapeutic targeting of the conserved region within the low-complexity domain of TDP-43 is neuroprotective and extends survival in amyotrophic lateral sclerosis mice.

Ju Gao, Devanshi Shukla, Mao Ding, Siyue Qin, Fan Tang, Evelyn Guerrero, Lauren Vicuna, Jiawei Xu, Hongling Li, Masaru Miyagi, Pan P Li, Jingjing Liang, Xinglong Wang.

Autosomal dominant mutations in TARDBP, encoding TAR DNA-binding protein 43 (TDP-43), cause amyotrophic lateral sclerosis (ALS), and TDP-43 pathology is a hallmark of multiple aging-associated neurodegenerative diseases. Despite its pathological role, effective therapies remain limited by the lack of safe, potent molecules targeting TDP-43 neurotoxicity. Here we show that the conserved α-helical region spanning residues 320-340 (conserved region or CR) is a therapeutically actionable target for TDP-43 neurotoxicity. Deletion of CR markedly suppressed TDP-43-induced neuronal death. Structure-based virtual screening identified XL20, a brain-penetrant small molecule that engages CR and confers neuroprotection without affecting TDP-43 splicing activity. XL20 alleviated motor neuron loss, extended survival in TDP-43 p.Ala315Thr ALS mice and enhanced neuronal function in p.Gln331Lys induced pluripotent stem cell-derived human ALS motor neurons. Mechanistically, targeting CR suppressed TDP-43 mitochondrial localization and restored mitochondrial function, likely through liquid-liquid phase separation. Our findings highlight CR as a therapeutic target for TDP-43-associated neurodegeneration and support CR-binding small molecules as therapeutic candidates.

DOI: https://doi.org/10.1038/s43587-026-01166-3
J Neurochem. 2026 Jul;170(7): e70513

Neural Organoid Models as a Platform for Studying Disease Mechanisms in Amyotrophic Lateral Sclerosis.

Kristel N Eigenhuis, Roberto Montoro Ferrer, R Jeroen Pasterkamp.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder affecting upper and lower motor neurons leading to muscle wasting. However, structural and molecular abnormalities, including cortical thinning and TDP-43 pathology, extend into frontal, parietal, and temporal areas, pointing to defects across broader cortical regions. The advent of human induced pluripotent stem cell (hiPSC) technology has enabled the generation of human-specific brain cell types in vitro. Here, we provide an overview of the three-dimensional (3D) hiPSC-derived neural organoid platforms used to model cortical structures and to study cortical ALS-associated phenotypes. We review which pathological hallmarks have been recapitulated in these organoids and discuss disease phenotypes reported to date. Further, we comprehensively cover different neural organoid models and experimental strategies, including patient-derived hiPSC models and exogenous pathology induction, while addressing current technical challenges. Together, these advances position neural organoids as an emerging tool to study cell-type-specific and circuit-level mechanisms related to cortical changes in ALS.

DOI: https://doi.org/10.1111/jnc.70513
Transl Neurodegener. 2026 Jun 28. pii: 29. [Epub ahead of print]15(1):

Lysophagy protects against ANXA11 amyloid fibril toxicity and propagation in FTLD.

Honglin Zheng, Haiyang Luo, Yongting Lu, Yapei Yuan, Na Zhang, Suying Duan, Zongping Xia, Yuming Xu.

   BACKGROUND: Accumulation of Annexin A11 (ANXA11) aggregates is a distinct pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While genetic studies have linked ANXA11 mutations (e.g., D40G) to disease, the precise molecular events converting aggregation into neurotoxicity and intercellular propagation remain elusive. We hypothesize that lysosomal integrity serves as a critical checkpoint in ANXA11 proteinopathy and that its failure drives disease progression.
METHODS: To model the human pathology of ANXA11, we generated pre-formed fibrils (PFFs) of wild-type and FTLD/ALS-linked D40G mutant ANXA11. Human iPSC-derived neurons, 3D cerebral organoids, and bulk RNA-sequencing were employed to investigate neurotoxicity. High-resolution imaging, lentiviral knockdown, and biochemical assays were performed to delineate the lysosomal damage response and the subsequent "prion-like" spreading of aggregates.
RESULTS: The internalized ANXA11 fibrils accumulated in lysosomes, triggering lysosomal membrane permeabilization (LMP). The D40G mutation exacerbated this toxicity, leading to severe LMP, mitochondrial depolarization, and specific transcriptional downregulation of the dynactin subunit ACTR10. Mechanistically, we identified a protective signaling axis involving p38 MAPK, MK2, and HSP27 that senses ANXA11-induced lysosomal damage and initiates lysophagy. Notably, in human cerebral organoids, failure of this lysophagic clearance facilitated the cytoplasmic escape of ANXA11, thereby accelerating its seeding activity and propagation to neighboring cells. Pharmacological or genetic modulation of this pathway significantly altered neuronal survival.
CONCLUSIONS: Our study established lysosomal rupture as a primary driver of ANXA11-associated neurodegeneration and validated the p38/MK2/HSP27 axis as a crucial defense mechanism in human neural tissue. These findings provide a novel mechanistic link between lysosomal quality control and ANXA11 propagation, highlighting that enhancing lysophagic flux represents a promising translational strategy to halt the progression of FTLD and ALS.

Keywords:  Annexin A11; Cerebral organoids; Frontotemporal lobar degeneration; Lysophagy; Lysosomal membrane permeabilization; Prion-like propagation

DOI:  https://doi.org/10.1186/s40035-026-00561-5
J Neurochem. 2026 Jul;170(7): e70515

A PARK9 iPSC-Derived Dopaminergic Neuron Model Enables Drug Screening Targeting Autophagy-Lysosome Pathway Dysfunction in Parkinson's Disease.

Kei-Ichi Tsukiboshi, Kei-Ichi Ishikawa, Akihiro Yamaguchi, Kimihito Arai, Kazuaki Kanai, Taiji Tsunemi, Hideyuki Okano, Nobutaka Hattori, Wado Akamatsu.

Parkinson's disease (PD) is a neurodegenerative disease characterized by dopaminergic neuronal degeneration in the substantia nigra, in which lysosomal dysfunction and impaired autophagy-lysosome pathway activity are increasingly recognized as important pathogenic mechanisms. However, disease-modifying therapies targeting this pathway remain unavailable. Here, we generated induced pluripotent stem cells (iPSCs) from a PARK9 patient carrying an ATP13A2 mutation and established mutation-corrected isogenic control iPSCs. PARK9 iPSC-derived neurons recapitulated lysosomal dysfunction-associated cellular phenotypes, including impaired lysosomal acidification, reduced mature cathepsin D levels, CD63-positive vesicle accumulation, LC3B-positive autophagosome accumulation, cytoplasmic pSer129 α-synuclein accumulation, and increased cleaved caspase-3 signals. These phenotypes were ameliorated in mutation-corrected neurons, supporting the contribution of ATP13A2 dysfunction to these abnormalities. We then performed high-content imaging-based compound screening targeting LC3B-positive autophagosome accumulation in PARK9 neurons. A three-step workflow identified 19 candidate compounds that reduced autophagosome accumulation consistent with partial improvement of lysosome-dependent downstream autophagosome processing rather than simple suppression of autophagosome formation. Among these, paroxetine, Ro 25-6981, amisulpride, and PK11195 showed additional, compound-dependent effects on PARK9-associated phenotypes, including lysosomal acidification, CD63-positive vesicle accumulation, cytoplasmic pSer129 α-synuclein signals, and cleaved caspase-3 signals. These findings establish PARK9 iPSC-derived neurons as a useful model of lysosomal dysfunction-associated PD pathology and provide a practical screening platform for identifying candidate compounds that modulate autophagy-lysosome pathway-related cellular phenotypes.

DOI: https://doi.org/10.1111/jnc.70515
Genes Cells. 2026 Jul;31(4): e70134

The SQSTM1 L341V Variant Associated With Sporadic ALS Promotes the Accumulation of Enlarged Ubiquitin-Positive SQSTM1 Bodies.

Kento Shimakura, Akira Oka, Haruka Yudahira, Yutaro Hama, Asako Otomo, Shinji Hadano.

  SQSTM1 is one of the causative genes of neurodegenerative disorders, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The SQSTM1 protein regulates the degradation of polyubiquitinated proteins and autophagosome formation through its interaction with microtubule-associated protein light chain 3 (MAP1LC3/LC3). However, the molecular mechanisms by which SQSTM1-LC3 binding regulates the autophagy-endolysosomal system (APELS) remain unclear. To elucidate the spatiotemporal role of SQSTM1, we transiently expressed wild-type SQSTM1 or missense mutants carrying mutations in the LC3-interacting region (LIR), fused with the photoconvertible fluorescent protein Dendra2. Live-cell fluorescence imaging and co-localization analyses with markers of the APELS were then performed. Particle analysis of photoconverted or non-photoconverted SQSTM1-positive structures in live cells revealed that the pathogenic L341V variant formed larger structures than the wild-type. Co-localization analyses further showed that both the L341V and artificial LIR3A mutants accumulated in large ubiquitin-positive structures, likely due to impaired localization to autophagosomes. These results suggest that mutations within the LIR differentially affect autophagosome formation and cargo degradation within APELS-related compartments, highlighting the importance of SQSTM1 structural integrity in ALS/FTD pathogenesis.

Keywords:  ALS; Dendra2; FTD; LC3; SQSTM1; autophagy‐endolysosomal system (APELS)

DOI:  https://doi.org/10.1111/gtc.70134
Proc Natl Acad Sci U S A. 2026 Jul 07. 123(27): e2609132123

A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical-like and dopaminergic-like induced neurons.

Felix Kraus, Yuchen He, Yizhi Jiang, Delong Li, Yohannes A Ambaw, Federico M Gasparoli, Joao A Paulo, Tobias C Walther, Robert V Farese, Steven P Gygi, Florian Wilfling, J Wade Harper.

  Lysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy and by recycling building blocks for organelle biogenesis. Lysosomal storage disorders (LSDs) comprise a group of diseases affecting diverse lysosomal functions. To facilitate molecular phenotyping across diverse LSD gene classes, we are developing a library of human embryonic stem cells engineered to lack individual LSD genes as a resource for the field. Here, we report our initial stem cell toolkit lacking one of 23 LSD genes, including the majority of genes associated with sphingolipidoses and neuronal ceroid lipofuscinoses, and its use in the generation of a proteomic resource for induced cortical-like and midbrain dopaminergic-like neurons. In-depth abundance and correlation profiling across organelles and suborganelle components revealed potential vulnerabilities that reflect distinct patterns of proteome alterations across both genotypes and neuronal cell types. We characterize alterations in the mitochondrial proteome associated with GBA1 and ASAH1 deficiency and identify synaptic and mitochondrial defects in ASAH1-/- induced neurons that correlate with defects in neuronal firing rates. Moreover, we developed an informatic pipeline for proteome-wide identification of individual protein-protein interactions and protein complexes that may be disrupted as a result of LSD gene deficiency. Finally, we visualized structural alterations of ASAH1-deficient endolysosomes in situ using cryoelectron tomography, revealing swollen organelles that were largely devoid of dense internal membranes characteristic of wild-type cells, but containing numerous intralumenal vesicle compartments. This toolkit and associated proteomic landscapes provide a resource for defining molecular signatures associated with LSD gene dysfunction and organelle vulnerability.

Keywords:  iNeurons; lysosome; organelle; protein interactions; proteomics

DOI:  https://doi.org/10.1073/pnas.2609132123
Dis Model Mech. 2026 Jun 01. pii: dmm052740. [Epub ahead of print]19(6):

Leucettinib-21 decreases dosage effects of DYRK1A in human trisomy 21 induced pluripotent stem cell-derived neural cells.

Nicole R West, Mattias F Lindberg, Julien Dairou, Shawn MacGregor, Sahith Puthireddy, Laurent Meijer, Anita Bhattacharyya.

  Dosage imbalance of dual specificity tyrosine phosphorylation regulated kinase 1A (DYRK1A) is a feature of several neurodevelopmental and neurodegenerative diseases, including Down syndrome, DYRK1A syndrome, autism spectrum disorders, Alzheimer's disease and Parkinson's disease. Thus, manipulating DYRK1A activity in the brain has emerged as a potential therapeutic target for neurological disorders. Several DYRK1A inhibitors have shown promise for improving cognition in rodent models of Down syndrome and Alzheimer's disease, for example, but the ability of these inhibitors to affect DYRK1A levels or activity in relevant human cells has not been established. We filled this gap by testing the effects of a new DYRK1A inhibitor on trisomy 21 induced pluripotent stem cell (iPSC)-derived neural progenitor cells and neurons, in which DYRK1A expression and activity are increased. Our results demonstrated that Leucettinib-21, a potent and selective low-molecular-mass pharmacological inhibitor of DYRK1A, decreases DYRK1A activity in human trisomy 21 iPSC-derived neural progenitor cells and cortical neurons. Leucettinib-21 reduces DYRK1A activity in a relevant human disease model, supporting future human trials.

Keywords:  Cell proliferation; DYRK1A; DYRK1A inhibitors; Down syndrome; Induced pluripotent stem cells; Tau phosphorylation

DOI:  https://doi.org/10.1242/dmm.052740
Brain Commun. 2026 ;8(3): fcag219

Rescue of mitochondrial and neurite pathology in SPG7 hereditary spastic paraplegia patient-derived cortical neurons.

David Neubauer, Carlotta Kaißer, Laura Krumm, Tom Boerstler, Klara Metzner, Thamer Al Hamad, Martin Böttcher, Simon Geißler, Iryna Prots, Philipp Arnold, Dimitrios Mougiakakos, Jürgen Winkler, Beate Winner, Martin Regensburger.

  Biallelic pathogenic variants in SPG7 are a frequent cause of hereditary spastic paraplegia leading to progressive disability due to a length-dependent degeneration of cerebellar and cortical projection neurons. While underlying mechanisms have been linked to impaired mitochondrial function, no disease-modifying therapy is available. We generated induced pluripotent stem cell-derived cortical neurons from SPG7 patients with non-sense or truncating variants and from matched controls. We performed detailed phenotyping of neuronal differentiation, as well as mitochondrial and neuritic morphology and function. We explored the effects of Bz-423, a modulator of the mitochondrial permeability transition pore, as a potential rescue of SPG7-specific cellular phenotypes. We successfully differentiated SPG7 patient-derived neurons, without quantitative differences in differentiation compared with controls. However, we delineate neurite-specific aberrations of mitochondrial morphology and ultrastructure. Moreover, anterograde axonal mitochondrial transport was impaired in SPG7. Exposure to Bz-423 rescued ultrastructural and functional phenotypes. In summary, our data show impaired neuritic mitochondria in a patient-specific human model, and we here demonstrate for the first time beneficial effects of Bz-423 on neuritic ultrastructure and function in a human neuronal SPG7 system. Moreover, we identify the mitochondrial permeability transition pore as a molecular target to rescue phenotypes also in carriers of non-sense or truncating SPG7 variants.

Keywords:  SPG7; cortical motor neuron; hereditary spastic paraplegia (HSP); induced pluripotent stem cells; mitochondria

DOI:  https://doi.org/10.1093/braincomms/fcag219
Acta Neurobiol Exp (Wars). 2026 Apr 24. 86(2): 93-108

LRRK2 mutations: at the crossroads of dopamine, iron, and calcium imbalance in Parkinson's disease.

Weronika Skarżyńska, Aleksandra Moskal, Jacek Kuźnicki.

  Parkinson's disease (PD) is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons. The G2019S mutation in the leucine‑rich repeat kinase 2 (LRRK2) gene is the most common genetic cause of familial and sporadic PD. In dopaminergic neurons, increased kinase activity caused by LRRK2‑G2019S mutation impairs synaptic vesicle recycling and dopamine storage, increasing cytosolic dopamine, which is prone to oxidation and generates reactive oxygen species. Simultaneously, the mutation alters iron metabolism through Rab misregulation, increasing iron uptake and lysosomal dysfunction, further amplifying oxidative stress and creating a pro‑ferroptotic environment. At the same time, dysregulated calcium signaling, driven by the enhanced activity of L‑type calcium channels and impaired mitochondrial calcium buffering via the mitochondrial calcium uniporter, enhances mitochondrial dysfunction. This minireview integrates current evidence linking LRRK2‑G2019S to these pathological pathways, highlighting this mutation's role in dopamine, iron, and calcium imbalance. Understanding this molecular interplay may provide novel insights into PD pathogenesis and guide the development of targeted neuroprotective therapies.

Keywords:  LRRK2; Parkinson’s disease; calcium; dopamine; iron

DOI:  https://doi.org/10.55782/kre63y59
Phys Chem Chem Phys. 2026 Jul 02.

Nanoscale morphological and structural analysis of round and donut oligomers formed by C-terminal domain of TDP-43.

Davis Pickett, Yana Purvinsh, Joshua T Skrehot, Daniel Warren, Dmitry Kurouski.

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), limbic predominant age-related TDP-43 encephalopathy (LATE), and Parkinson's disease are associated with an abrupt aggregation of TAR DNA-binding protein 43 (TDP-43). Although molecular mechanisms of this pathological aggregation remain unclear, accumulated evidence suggests that the C-terminus domain (C-terminal domain (CTD)) is the trigger of TDP-43 self-assembly into toxic oligomers and fibrils. While the secondary structure and morphology of protein fibrils have been well documented, very little is known about TDP-43 oligomers. This is primarily because of the transient nature and low concentrations of these protein species. In the current study, we utilize nano-infrared spectroscopy, also known as atomic force microscopy-infrared (AFM-IR) spectroscopy, to investigate the morphology and secondary structure of CTD of TDP-43 oligomers formed at the early and middle stages of protein aggregation. This innovative technique allows us to resolve both morphology and secondary structure of individual protein aggregates. We found that at the early stage of protein aggregation, CTD of TDP-43 formed two morphologically different protein aggregates: donut-like (DO) and round (RO) oligomers. DO yielded fibrillar species, while RO persisted throughout the entire course of CTD TDP-43 self-assembly.

DOI: https://doi.org/10.1039/d6cp01760f
J Cell Sci. 2026 Jul 01. pii: jcs264806. [Epub ahead of print]139(13):

Disentangling the response to lysosomal damage.

Hemmo Meyer, Akiko Kuma, Shuhei Nakamura.

  The limiting membrane of lysosomes is prone to damage that can have deleterious consequences for cellular homeostasis. Cells respond to this damage with an array of molecular countermeasures, ranging from membrane repair mechanisms to elimination of terminally damaged lysosomes by selective macroautophagy. The various elements of this response therefore need to be carefully assessed in the context of the specific pathological or experimental conditions being studied. Emerging evidence has revealed further complexity within the lysosomal damage response, such as processes that contribute to initial membrane resealing as well as lysosome regeneration required to restore the lysosomal system. These mechanisms involve unusual ubiquitylation, non-canonical ATG8 lipidation, or modifications that govern lysosome tubulation or microlysophagy pathways. Therefore, caution is advised when using previously established lysosome damage reporters that might confound interpretation of the underlying events and outcomes. This Opinion article seeks to shed light on the emerging regulatory mechanisms of lysosomal regeneration and evaluate the appropriateness of various reporters and assays for studying the lysosomal damage response.

Keywords:  ATG8; ESCRT; Lysosomes; Membrane permeabilization; Microautophagy; Ubiquitin

DOI:  https://doi.org/10.1242/jcs.264806
Biochem Soc Trans. 2026 Jul 29. 54(7): 887-899

Advancing the monitoring of organelle contact sites in vitro and in vivo.

Lucia Barazzuol, Caterina Peggion, Marisa Brini, Yusuke Nasu, Tito Calì.

  Organelle contact sites are highly dynamic and specialized regions where distinct organelles come into proximity, enabling direct inter-organelle communication. These structures play fundamental roles in cellular homeostasis by coordinating the exchange of lipids, metabolites, and ions, as well as regulating key processes such as organelle dynamics, mitochondrial fission, autophagy, and metabolic integration. Alterations in contact site architecture and function have been increasingly associated with a wide range of human diseases, including neurodegeneration, metabolic disorders, and cancer. Despite their biological relevance, the nanoscale nature and dynamic behaviour of contact sites have historically posed significant challenges for their accurate detection and functional characterization. Here, we provide a comprehensive overview of the methodologies currently available to study organelle contact sites, ranging from classical approaches such as electron microscopy and biochemical fractionation to advanced imaging techniques and genetically encoded reporters. We discuss recent developments in high-resolution and live-cell microscopy that have improved the spatial and temporal resolution of contact site analysis, as well as emerging tools designed to selectively label, quantify, and manipulate these interfaces. Attention is given to the next generation of engineered reporters capable of sensing molecular and ionic exchanges at contact sites, thereby moving beyond structural description toward functional interrogation. By critically evaluating the strengths and limitations of existing approaches, we aim to provide a framework for selecting appropriate tools and to highlight future directions in the field. Ultimately, advancing our ability to monitor and dissect organelle contact sites will be essential for understanding their contribution to cellular physiology and disease.

Keywords:  Organelle contact sites; SPLICS; genetically encoded reporters

DOI:  https://doi.org/10.1042/BST20250371
NAR Genom Bioinform. 2026 Sep;8(3): lqag069

The role of ATF4 in neurons under mitochondrial stress.

Maria Bilen, Yubing Liu, Imane Chakroun, Mohamed Ariff Iqbal, Bensun C Fong, Jingwei Chen, Smitha Paul, Alexandre Blais, Ruth S Slack.

Mitochondrial dysfunction and fragmentation are observed in various circumstances, such as neurodegeneration and aging. Studies have shown that altered mitochondrial function activates the integrated stress response (ISR), with ATF4 serving as a major mediator of adaptation to stress. Presently, little is known about the role of ATF4 in neurons under mitochondrial stress. Using primary cortical neurons, we demonstrate that inhibiting ATF4 under OPA1-mediated mitochondrial stress accelerates the impairment of neuronal differentiation, as evidenced by smaller dendrites and lower dendritic spine density. To better understand the role of ATF4 in this context, we investigated the global binding sites of ATF4 using chromatin immunoprecipitation sequencing (ChIP-seq) and examined the chromatin accessibility changes that occur following the loss of ATF4 in neurons under conditions of mitochondrial stress. We found that ATF4 binds to a wide range of targets and alters the chromatin accessibility of genes involved in metabolism, neuronal fate, and neuron maturation. The downstream targets of ATF4 identified in this study can reveal novel and direct targets of ATF4 in neuronal survival and maturation. These adaptations are the hallmarks of stress response in mitochondrial dysfunction-mediated neurodegeneration.

DOI: https://doi.org/10.1093/nargab/lqag069
Proc Natl Acad Sci U S A. 2026 Jul 07. 123(27): e2521663123

Proteostasis and unfolded protein response dynamics in human neuron/mouse glia co-cultures reveal a cell-specific maturation response.

Lea A Barny, Sarah K Garcia, Aiden J Houcek, Burak Uzay, Minsoo Kim, Ege T Kavalali, Lars Plate.

  Proteostasis, or protein homeostasis, is a tightly regulated network of cellular pathways essential for maintaining proper protein folding, trafficking, and degradation. Neurons are particularly vulnerable to proteostasis collapse due to their postmitotic and long-lived nature and thus represent a unique cell type to understand the dynamics of proteostasis throughout development and maturation. Here, we utilized a dual-species co-culture model of human excitatory neurons and mouse glia to recapitulate and investigate cell type-specific, maturation-related changes in the proteostasis network using data-independent acquisition LC-MS/MS proteomics. We quantified branch-specific unfolded protein response (UPR) activation by monitoring curated effector proteins downstream of the ATF6, IRE1/XBP1s, and PERK pathways, enabling a comprehensive, unbiased evaluation of UPR dynamics during in vitro neuronal maturation between 30 d and 60 d. Species-specific analysis revealed that mature neurons largely preserved proteostasis, although they showed some signs of collapse, primarily in endoplasmic reticulum (ER)-to-Golgi transport mechanisms. However, these changes were accompanied by upregulation of proteostasis-related machinery and activation of the ATF6 branch, as well as maintenance of the XBP1s and PERK branches of the UPR over time. In contrast, glia exhibited broad downregulation of proteostasis factors and UPR components, independent of neuronal presence. Furthermore, we quantified stimulus-specific modulation of select UPR branches in matured neurons exposed to pharmacologic ER stressors. These findings highlight distinct, cell-type-specific stress adaptations during in vitro maturation and provide a valuable proteomic resource for dissecting proteostasis and UPR regulation in human neurons.

Keywords:  activating transcription factor 6; data-independent acquisition (DIA) mass spectrometry; inositol requiring enzyme 1; neuronal maturation; protein kinase R-like ER kinase

DOI:  https://doi.org/10.1073/pnas.2521663123
Front Neurol. 2026 ;17 1798525

Assessing upper motor neuron dysfunction in ALS: from TMS-EEG and EMG neurophysiology to a combined tFUS-TMS translational framework.

Ahmadreza Keihani, Mahsa Hassani, Seyed Saman Sajadi, Seyedeh Atena Modarresi, Marziyeh Khoshkholgh, Mahdi Haresabadi, Kiana Amani, Zahra Jourahmad, Fabio Ferrarelli.

  Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterized by the progressive loss of upper motor neurons (UMNs) and lower motor neurons (LMNs). Despite significant advances in molecular and neuroimaging biomarkers, the initial site of pathology and the causal contribution of UMN dysfunction to disease progression remain undetermined. Accumulating neurophysiological evidence points to cortical hyperexcitability as an early and potentially upstream mechanism, raising the possibility that UMN pathology drives LMN degeneration through an anterograde dying-forward process. In this review, we synthesize findings from noninvasive brain stimulation (NIBS) studies, with particular emphasis on transcranial magnetic stimulation (TMS)-based neurophysiological markers of UMN dysfunction. We review evidence from TMS-electromyography (TMS-EMG) and TMS-electroencephalography (TMS-EEG) paradigms demonstrating cortical disinhibition and excitatory-inhibitory imbalance in ALS, consistent with impaired GABAergic interneuronal dysfunction and supportive of a cortical onset hypothesis. Finally, we propose integrating transcranial focused ultrasound (tFUS) with TMS as a novel experimental and translational framework to directly examine and modulate cortical hyperexcitability and test the causal role of UMN dysfunction in ALS. The combination of targeted neuromodulation with sensitive neurophysiological readouts in controlled experimental designs offers a promising avenue to advance mechanistic insight, refine biomarkers, and inform mechanism-based therapeutic strategies. Together, these approaches position noninvasive neurophysiology as a powerful tool for elucidating UMN dysfunction in ALS.

Keywords:  ALS; TMS; cortical onset theory; hyperexcitability; tFUS; upper motor neuron

DOI:  https://doi.org/10.3389/fneur.2026.1798525
Mol Biol Rep. 2026 Jun 30. pii: 1064. [Epub ahead of print]53(1):

Advances in neural organoids: structural organization, disease modeling, and applications in gene therapy.

Evelina Nasybullina, Elvira Akhmetzyanova, Albert Rizvanov, Yana Mukhamedshina.

  Neural organoids and assembloids have emerged as advanced in vitro models that reproduce the cytoarchitecture and functional complexity of the human brain. This review focuses on recent applications of these three-dimensional systems for modeling neurodegenerative diseases and assessing the efficacy of gene therapy, particularly using adeno-associated viral vectors. The development of induced pluripotent stem cell technology enables the creation of patient-specific organoids that reflect individual genetic backgrounds and disease phenotypes. Neural organoids have been used to model Alzheimer's, Parkinson's, and Huntington's diseases, reproducing hallmark features such as protein aggregation, neuroinflammation, and synaptic dysfunction. They have also served as test systems for evaluating AAV-mediated gene delivery, revealing serotype-specific tropism and supporting optimization of vector design and gene expression. Further advances include integration of immune and vascular components and the construction of multi-regional assembloids that replicate inter-regional neuronal communication and complex network dynamics. Ongoing standardization and scalability of neural organoid systems, combined with bioengineering and analytical innovations, are expected to enhance reproducibility and translational relevance. The convergence of organoid models with gene therapy testing frameworks may accelerate preclinical validation and contribute to the development of precision approaches in neurology.

Keywords:  AAV vectors; Assembloids; Gene therapy; Neural organoids; Neurodegeneration; iPSCs models

DOI:  https://doi.org/10.1007/s11033-026-12236-5
bioRxiv. 2026 Jun 25. pii: 2026.06.22.730622. [Epub ahead of print]

ADAR2-Mediated RNA Editing Promotes TDP-43 Nuclear Export and Alters RNA Binding.

Stephen Moore, Dominic L Julian, Eric Alsop, Lauren M Gittings, Ileana Lorenzini, Michael McMillan, Sam Macklin-Isquierdo, Erik Lehmkuhl, Petr Kalab, Danielle de Paula Moreira, Lindsey Hayes, Christopher Donnelly, Sami J Barmada, Daniela C Zarnescu, Kendall Van Keuren-Jensen, Rita Sattler.

BACKGROUND: TAR DNA binding protein - 43 (TDP-43) nuclear loss is a pathological hallmark of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and related neurodegenerative disorders. While the consequences of TDP-43 dysfunction have been well-characterized, the mechanisms driving TDP-43 mislocalization remain poorly understood. Previous observations of altered localization and function of the adenosine-to-inosine (A-to-I) RNA editing enzyme adenosine deaminase acting on RNA 2 (ADAR2) in ALS/FTD tissue prompted us to investigate whether dysregulated RNA editing contributes to pathological TDP-43 nucleocytoplasmic trafficking.
METHODS: TDP-43 cytoplasmic mislocalization was assessed following ADAR2 and TDP-43 co-overexpression in HEK293T cells and a Drosophila model co-overexpressing human TDP-43 and dADAR in motor neurons. We further evaluated TDP-43 mislocalization through both HeLa cell assays and interspecies heterokaryon assays. Next, we assessed TDP-43 binding to A-to-I edited RNA oligomers through electrophoretic mobility shift assays (EMSAs), and investigated inosine-containing RNAs in vivo via TDP-43 RNA immunoprecipitation followed by sequencing (RIP-seq) datasets from human TDP-43-expressing Drosophila . Finally, RNAseq and enhanced cross-linking and immunoprecipitation (eCLIP-seq) were performed in SH-SY5Y cells overexpressing three ADAR2 variants with differing editing activity to identify editing-related transcriptional alterations and RNAs differentially bound to TDP-43.
RESULTS: ADAR2 overexpression reduced the nucleocytoplasmic (N:C) ratio of TDP-43 in HEK293T cells in a ADAR2 catalytic activity- and TDP-43 RNA-binding capacity-dependent manner. Drosophila motor neurons overexpressing dADAR also exhibited decreased nuclear TDP-43. Interspecies heterokaryons and permeabilized HeLa cell assays demonstrated that catalytically active ADAR2 and synthetic inosine-containing RNA oligomers, respectively, enhance nuclear export of endogenous TDP-43. EMSAs revealed preferential binding of TDP-43 to inosine-containing RNAs relative to unedited RNAs, and analysis of Drosophila RIP-seq datasets demonstrated enrichment of edited transcripts within TDP-43-bound RNAs. Finally, RNAseq and eCLIP-seq analyses identified editing-dependent alterations in gene expression and TDP-43 RNA-binding profiles in SH-SY5Y cells overexpressing active ADAR2 variants.
CONCLUSIONS: Together, our findings identify A-to-I RNA editing as a previously unrecognized regulator of TDP-43 localization and RNA interactions. These results support a model where altered RNA editing modifies TDP-43-RNA interactions, promoting increased nuclear export of TDP-43. Broadly, our work highlights RNA editing dysregulation as a potential contributor to early pathogenic mechanisms underlying TDP-43 proteinopathies.

DOI: https://doi.org/10.64898/2026.06.22.730622
Sci Rep. 2026 Jun 30. pii: 18328. [Epub ahead of print]16(1):

Topological modeling of gene expression in the brain with Huntington's disease reveals selective disruption of co-expression network.

Yuko Okamura-Oho, Kazuro Shimokawa, Satoshi Oota, Atsushi Yoshiki, Masahiko Morita, Masaomi Nishimura, Sakiko Nakamura, Yuki Tsujimura, Shumpei Ishikawa, Hideo Yokota.

We applied transcriptome tomography to create a whole-brain model of early-stage Huntington's disease (HD) in R6/2 mice, which ubiquitously express truncated human mutant HTT containing approximately 150 CAG repeats. Medium spiny neuron (MSN)-related genes showed abnormal expression in the HD brain, in terms of expression similarity to wild-type Htt. Bdnf was the most probable upstream regulator of these genes. Smarca4, the Bdnf-regulator, was similarly expressed to wild-type Htt in the control brain; however, this was not observed in HD, implying a possible involvement of Smarca4 in glutamate excitotoxicity in HD. Lhx6, a master gene for MSN-related pathway development ordinarily conserved postnatally and in adulthood, was lost in the HD co-expression network. And a network hub node, Fcho1, was lost in connection involving Lhx6 and mitochondrial gene clusters. Loss of Smarca4, Lhx6, and Fcho1 in co-expression may contribute to spatiotemporally specific neuronal loss in HD.

DOI: https://doi.org/10.1038/s41598-026-56101-8
Commun Biol. 2026 Jun 29.

Nuclear RNA clusters are dynamic structural entities in Huntington's disease.

Sandra Fienko, Iulia M Nita, Ignacio Munoz-Munoz, Gillian P Bates.

Huntington's disease research has focused on either loss of normal huntingtin function or toxic gain-of-function of the mutant huntingtin protein as a key driver of pathology. The role of mutant HTT mRNA in vivo has been only partially studied and remains largely unexplored. Recently, we discovered that full-length human HTT mRNA is retained, together with the alternatively processed HTT1a transcript, in RNA nuclear clusters in YAC128 mouse brains. Here, we demonstrate that these clusters were present at the prenatal stage, indicating early developmental effects. Moreover, these clusters were confined to neurons, implying a neuron-specific mechanism of accumulation, and were colocalised with core spliceosomal proteins, suggesting an impact on nuclear homeostasis. HTT nuclear RNA clusters showed remarkable dynamics, rapidly dissolving when ionic interactions were disrupted or transcription and splicing were inhibited. This malleability underscores the importance of HTT mRNA accessibility to therapeutic interventions and may guide future design of HTT-targeting therapies.

DOI: https://doi.org/10.1038/s42003-026-10419-1
Cell. 2026 Jul 01. pii: S0092-8674(26)00700-2. [Epub ahead of print]

Recurrent patterns of TOP1-mediated neuronal genomic damage shared by major neurodegenerative disorders.

Zinan Zhou, Lovelace J Luquette, Guanlan Dong, Junho Kim, Jayoung Ku, Kisong Kim, Nandini Ramesh, Mingyun Bae, Ann Caplin, Diane D Shao, Bezawit Sahile, Kow Essuman, Eitan Goodman, Michael B Miller, August Yue Huang, William J Nathan, Andre Nussenzweig, Peter J Park, Clotilde Lagier-Tourenne, Eunjung Alice Lee, Christopher A Walsh.

  Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD) represent two major categories of neurodegenerative disorders-TAR DNA-binding protein 43 (TDP-43) and tau proteinopathies-for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 469 neurons from C9ORF72 ALS, C9ORF72 FTD, AD, and control brains revealed increased somatic single-nucleotide variants (sSNVs) and insertions/deletions (sIndels) in all three diseases. Mutational signature analysis identified a disease-associated sSNV signature consistent with oxidative damage and an sIndel process affecting 22% of ALS, 76% of FTD, and 61% of AD neurons-but only 2% of control neurons-resembling signature ID4, previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Rapid approach to DNA adduct recovery (RADAR) assays confirmed increased TOP1-DNA covalent complexes, and duplex sequencing confirmed the increased sIndels and identified single-strand events as likely precursor lesions. TOP1-associated sIndel mutagenesis and genome instability thus represent a mechanism shared by both TDP-43 and tau neurodegeneration.

Keywords:  Alzheimer’s disease; DNA damage; DNA strand breaks; amyotrophic lateral sclerosis; frontotemporal dementia; genomic instability; mutation signature; ribonucleotide excision repair; somatic mutation; topoisomerase 1

DOI:  https://doi.org/10.1016/j.cell.2026.06.013
Stem Cell Res Ther. 2026 Jul 02. pii: 239. [Epub ahead of print]17(1):

Differentiation of human induced pluripotent stem cells into cardiac valve cells using 2D and 3D differentiation protocols.

Z Farzaneh, A Brückner, B K Fleischmann, S Rieck.

   BACKGROUND: Given the high relevance of human cardiac valve disease, recent research aims to differentiate human induced pluripotent stem cells (hiPSCs) into valve endothelial-like cells (VELCs) and, through endothelial-to-mesenchymal transition (EndMT), into valve interstitial-like cells (VILCs).
METHODS: Here, we modified a 2D differentiation protocol demonstrating that VEGF can serve as the sole driver for differentiating cardiac progenitor cells (CPCs) into VELCs. Next, we utilized the so-called GiWi protocol (inhibition of glycogen synthase kinase, followed by inhibition of the Wnt pathway) to derive VELCs from 3D endocardial spheres. To this aim, hiPSCs were first differentiated into cardiac progenitor (CP) spheres using CHIR99021 (12 µM) and IWP2 (5 µM). Subsequent treatment with E8 medium containing high-dose FGF2 (100 ng/ml) resulted in endocardial spheres enriched for VELCs. For EndMT induction, endocardial spheres were MACS-sorted for PECAM1+ VELCs and transdifferentiated into ACTA2+/CDH5- VILCs using TGFβ1 (200 ng/ml).
RESULTS: Using VEGF as main driver to differentiate CPCs into VELCs in 2D, the generated VELCs appeared stable over time, can be maintained in vitro and transdifferentiated into ACTA2+ VILCs using FGF2 (100 ng/ml) and TGFβ1 (50 ng/ml). Besides, our novel 3D differentiation protocol yielded endocardial spheres, which were highly enriched with VELCs, as shown by the expression of GATA4 (≈ 83%), PECAM1 (≈ 69%), and nuclear NFATC1 (≈ 76%), along with typical functional characteristics such as network formation, LDL uptake and the ability to undergo EndMT.
CONCLUSIONS: Overall, we developed a 2D differentiation protocol that produces stable VELCs and a high percentage of VILCs upon EndMT induction. We also established a new, efficient, and cost-effective protocol for the 3D differentiation of endocardial spheres to better mimic a physiologically relevant environment, thereby enabling improved maturation.

Keywords:  Differentiation; Endocardial cells; Endothelial-to-mesenchymal transition; Human induced pluripotent stem cells; Valve endothelial-like cells

DOI:  https://doi.org/10.1186/s13287-026-05132-z
Nat Commun. 2026 Jul 02. pii: 5789. [Epub ahead of print]17(1):

VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair.

Oluwatobi Andrew Adeosun, Christian Schröer, Elisabeth Südhoff, Fabio Bergenthal, Katharina Sommer, Emely Döffinger, Britta Fiedler, Angelika Hilderink, Ann-Katrin Lehmann, Lea Sophie Pohle, Sergei M Korneev, Florian Fröhlich, Kenji Maeda, Rainer Kurre, Michael Holtmannspötter, Bianca M Esch, Joost C M Holthuis.

Perturbations in lysosome integrity are tightly linked to neurological disorders and ageing, but the underlying pathogenic mechanisms are incompletely understood. Using an unbiased proteomic approach, we here identified the bridge-like lipid transport protein VPS13C/PARK23 as a key component of a global early response pathway to lysosome damage. VPS13C readily binds lysosomes under mechanical or osmotic tension in anticipation of membrane lesions. The latter trigger a conformational change in the protein's C-terminus, involving its ATG2C domain acting as sensor of damage-induced lipid packing defects. We show that ER-lysosome contacts formed by VPS13C provide critical binding platforms for OSBP/ORPs to enable efficient ER wrapping of damaged lysosomes. A chemical approach to assess directional ER-to-lysosome lipid transport revealed that VPS13C is essential for large-scale lipid delivery to acutely damaged lysosomes to facilitate their repair. Our findings offer new mechanistic insights into how loss-of-function mutations in VPS13C may enhance the risk of Parkinson's disease.

DOI: https://doi.org/10.1038/s41467-026-75145-y
Brain Res. 2026 Jul 01. pii: S0006-8993(26)00310-0. [Epub ahead of print]1889 150450

Targeting neurodevelopmental miR132-3p promotes neuroprotection and axon regeneration after optic nerve injury in mice.

Clyde D'souza, Agnieszka Lukomska, Arnav J Balaji, Jacob Brady, Ephraim F Trakhtenberg.

  Micro-RNA (miRNA) miR-132 regulates the axonal elongation-to-branching switch in central nervous system (CNS) neurons during maturation, which coincides with the mammalian developmental loss of CNS projection neurons' intrinsic axon growth capacity. However, it is unknown whether experimental targeting of miR-132 in mature CNS neurons could activate elongation/regeneration of the axons severed by an injury. Here, we characterized miR-132 5p and 3p arm expression during maturation of a prototypical CNS projection neuron, the retinal ganglion cell (RGC), and then tested whether miR-132 arm-specific knockdown (KD) in the RGCs activates elongation/regeneration of axons severed by optic nerve crush (ONC) injury in vivo. We identified the miR132-3p arm as developmentally-upregulated in the RGCs and found that its KD modestly but significantly promoted RGC axon-regeneration and survival. We also gained insights into the miR132-3p KD-regulated biological processes by transcriptomic profiling of the treated injured RGCs, which showed enrichment of a developmental gene network for formation of axonal projections. Thus, neuronal miR132-3p plays a role in axon regeneration after optic nerve injury, and future studies should investigate the underlying mechanisms.

Keywords:  Axon regeneration; Gene therapy; Micro-RNAs; Optic nerve injury; Retinal ganglion cell

DOI:  https://doi.org/10.1016/j.brainres.2026.150450
Proc Natl Acad Sci U S A. 2026 Jul 07. 123(27): e2521642123

Tau protein as a regulator of mitochondrial function and dynamics.

Eleni Tsakiri, Carlos Campos-Marques, Christina Ploumi, Kalliopi Skourti, Antonis Roussos, Eirini Mytilinaiou, Anastasia Vamvaka Iakovou, Ildete Luísa Ferreira, Chrysoula Dioli, Despoina D Gianniou, Martina Samiotaki, Jonas Campos, Clarissa Waites, Nuno Sousa, Ioannis P Trougakos, Joana M Silva, A Cristina Rego, Ioannis Sotiropoulos, Konstantinos Palikaras.

  Mitochondrial damage is a shared hallmark of brain aging and neurodegeneration. While pathological Tau mutations disrupt mitochondrial dynamics and function, the physiological role of wild-type (WT) Tau in the maintenance of mitochondrial homeostasis remains poorly understood. Here, using Caenorhabditis elegans and mice lacking PTL-1, the nematode Tau-like homolog, and Tau respectively, we demonstrate that Tau deficiency promotes a shift toward a pro-fusion mitochondrial state associated with enhanced mitochondrial function and stress resistance. In both models, loss of Tau leads to increased mitochondrial activity and altered redox homeostasis, while it enhances resistance to heat and mitochondrial stress in C. elegans. Strikingly, loss of FZO-1, the mitofusin homolog, abolishes the beneficial phenotypes, whereas its overexpression phenocopies key aspects of Tau/PTL-1 deficiency. Together, our findings uncover a conserved role for WT Tau in restraining mitochondrial fusion and functional adaptation, highlighting its contribution to mitochondrial homeostasis and cellular stress responses.

Keywords:  Tau; mitochondria; mitochondrial dynamics; neurodegeneration; neuron

DOI:  https://doi.org/10.1073/pnas.2521642123
J Neuroinflammation. 2026 Jul 02.

SGK1-mediated deficits in microglial phagocytosis drive pathological progression in amyotrophic lateral sclerosis.

Meijun He, Chaoran Wu, Mengqiu Hu, Xiayi Shi, Ruiqi Liu, Yujie Tong, Heng Wang, Haoran Hu, Hong Liao.

  Alterations in microglial function and transcriptomic profiles are major pathological hallmarks of amyotrophic lateral sclerosis (ALS). However, the dynamics and regulatory mechanisms underlying microglial phagocytic activity during disease progression remain unclear. In this study, we observed stage-dependent alterations in microglial phagocytic activity during disease progression in SOD1G93A mice. Single-cell RNA sequencing suggested that this change was associated with a reduced abundance of microglial subpopulations enriched for phagocytosis-related pathways. Transcriptomic analysis identified serum- and glucocorticoid-regulated kinase 1 (SGK1) as a potential mediator of this process. Notably, sgk1 knockout in SOD1G93A mice was associated with improved microglial clearance of myelin debris and reduced aberrant engulfment of neuronal material after disease onset. Our results further showed that, after disease onset, the accumulation of myelin debris and apoptotic neurons induced SGK1 upregulation in microglia from SOD1G93A mice. Mechanistically, SGK1 appeared to promote lipid accumulation in microglia by suppressing lipophagy, thereby impairing the ability of microglia to clear cellular debris. Moreover, pharmacological inhibition of SGK1 with GSK650394 attenuated motor deficits and prolonged survival in SOD1G93A mice. Together, our findings provide evidence for a previously unrecognized role of SGK1 in regulating microglial phagocytosis in ALS models and support SGK1 as a potential therapeutic target in SOD1 mutation-associated ALS models.

Keywords:  ALS; Lysosomal dysfunction; Microglia; Motor deficits; Phagocytic activity; SGK1

DOI:  https://doi.org/10.1186/s12974-026-03925-w
Nat Phys. 2026 May 18.

Simple input-output dependencies explain neuronal activity.

Christopher W Lynn.

Our understanding of neural computation is founded on the assumption that neurons fire in response to a linear summation of inputs. However, experiments demonstrate that some neurons are capable of complex functions that require interactions between inputs. Here we show that direct dependencies - without interactions between inputs - explain most of the variability in neuronal activity. Neurons across multiple brain regions and species are quantitatively described by models that capture the measured dependence on each input individually but assume nothing about combinations of inputs. These minimal models, which are equivalent to logistic artificial neurons, predict complex higher-order dependencies and recover known features of synaptic connectivity. The inferred neural network is sparse, indicating a highly redundant neural code that is robust to perturbations. These results suggest that, despite intricate biophysical details, most neurons can be described by simple artificial models.

DOI: https://doi.org/10.1038/s41567-026-03306-3
Tissue Eng Regen Med. 2026 Jun 29.

Potentiated Maturation of hPSC-Derived Dopaminergic Neurons via Convergent Genetic and Small Molecule Modulation.

Sanghyun Park, Dongyun Kim, Seo Hyun Yoo, Gyu-Bum Yeon, Jaewook Lee, Myung Soo Cho, Dong-Wook Kim, Dae-Sung Kim.

   BACKGROUND: Ventral midbrain dopaminergic (vmDA) neurons derived from human pluripotent stem cells provide a powerful platform for modeling Parkinson's disease (PD) and developing therapeutic strategies. Although robust protocols exist for generating vmDA progenitors, maturation into functionally competent neurons typically requires prolonged culture periods and occurs with substantial heterogeneity in maturity, representing major bottlenecks.
METHODS: Building on established protocols for vmDA progenitor differentiation, we introduce a sequential strategy that specifically targets the subsequent phases of neuronal conversion and postmitotic maturation. Transient overexpression of the proneural transcription factor achaete-scute family bHLH transcription factor 1 (ASCL1) was applied to human embryonic stem cell-derived vmDA progenitors to induce neuronal commitment, followed by accelerated postmitotic maturation using the small-molecule cocktail GENtoniK. This approach was evaluated in CRISPR/Cas9-engineered human induced pluripotent stem cell (hiPSC) lines lacking either PINK1 or PRKN and their isogenic control hiPSCs.
RESULTS: Transient ASCL1 overexpression promoted rapid cell cycle exit and neuronal conversion of vmDA progenitors while preserving ventral midbrain identity and dopaminergic fate. Subsequent GENtoniK treatment enhanced postmitotic dopaminergic maturation and increased neurite complexity, synaptic organization, and dopaminergic neurotransmission without altering lineage specification. Consequently, within two weeks, our protocol yielded high-purity vmDA neurons with enhanced functional maturation from vmDA progenitors. Importantly, PINK1- and PRKN-deficient neurons generated from CRISPR/Cas9-engineered hiPSC lines using this strategy recapitulated key PD-associated mitochondrial phenotypes, including impaired mitophagy, mitochondrial dysfunction, and elevated oxidative stress.
CONCLUSION: Taken together, these findings address the central limitations of current dopaminergic differentiation paradigms by enabling the rapid and uniform acquisition of advanced functional maturity, thereby providing a robust platform for disease modeling and translational research in PD.

Keywords:   ASCL1 ; Dopaminergic neuron differentiation; Functional neuronal maturation; Human pluripotent stem cells; Parkinson’s disease modeling

DOI:  https://doi.org/10.1007/s13770-026-00820-6
J Neurochem. 2026 Jul;170(7): e70500

Parkinson's Disease Cell Transplantation Therapy: A New Dawn With Pluripotent Stem Cell-Based Therapy.

Etsuro Nakanishi, Hodaka Yamakado, Nobukatsu Sawamoto, Jun Takahashi, Ryosuke Takahashi.

  Parkinson's disease (PD), a prevalent neurodegenerative disorder, is characterized by progressive loss of dopaminergic neurons in the midbrain. While dopamine replacement therapy effectively manages early symptoms, its long-term use leads to motor complications, highlighting the urgent need for treatments that directly address the underlying pathological changes. Cell transplantation, which aims to replace the lost dopaminergic neurons, has emerged as a promising approach. Early attempts using fetal ventral mesencephalic (fVM) tissue showed proof-of-concept, with some patients experiencing long-term motor improvement. However, these trials have been hampered by inconsistent results, graft-induced dyskinesia (GID), and significant ethical and logistical issues related to tissue supply. These challenges have shifted the focus to pluripotent stem cells (PSCs), including human-induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs), which offer a stable, ethically sound, and scalable source of high-quality cells. Recent clinical trials using PSCs suggest a turning point. All reported clinical trials demonstrated the safety and feasibility of this approach. The need for long-term safety and efficacy data, patient stratification, and techniques to improve graft survival are key areas of future research. Nevertheless, recent clinical trial successes suggest that cell transplantation is moving beyond symptomatic relief to become a truly restorative therapy for PD.

Keywords:  Kyoto trial; Parkinson's disease; cell transplantation therapy; embryonic stem cell; fetal ventral mesencephalic; induced pluripotent stem cell

DOI:  https://doi.org/10.1111/jnc.70500
bioRxiv. 2026 Jun 22. pii: 2026.06.16.732486. [Epub ahead of print]

Targeted Photodegradation of Misfolded Proteins via Self-photosensitizing with Molecularly Produced Light.

Huizhe Wang, Shiju Gu, Jiang Yu, Jinwu Yan, Jing Zhang, Zhiyong Jiang, Caroline Shen, Jun Yang, Chongzhao Ran.

Misfolded proteins are tightly associated with various neurodegenerative diseases, and removing these misfolded proteins is one of the actively pursued approaches for seeking therapeutics for these diseases. In this study, we demonstrated that molecularly produced light (molecular light) from ADLumin-5, a self-photosensitizing chemiluminescence compound, could induce photo-oxidation and photodegradation of misfolded proteins, including beta-amyloid, tau, alpha-synucleins, and TDP-43 proteins in vitro. We validated the oxidation and degradation via LC-MS, MADLI-MS, and western blotting. Using beta-amyloid as a showcase, we demonstrated that, upon photo-oxidation and photodegradation, the toxicities of this misfolded protein were significantly reduced. To investigate the therapeutic effects of ADLumin-5 in vivo, we used the 5xFAD mouse model for longitudinal treatment for 4 months. In vivo molecular imaging results indicated that ADLumin-5 could reduce the accumulation of beta-amyloid proteins. Our study presents a novel approach to seek therapeutics for neurodegenerative disease via molecular light-induced degradation of misfolded proteins. In addition, because ADLumin-5 is dual-functional-enabling both photodegradation and in vivo imaging of misfolded protein changes-it can be considered a photo-theranostic agent for neurodegenerative diseases, representing a novel approach to drug discovery for neurodegenerative diseases.

DOI: https://doi.org/10.64898/2026.06.16.732486
Cell. 2026 Jun 30. pii: S0092-8674(26)00697-5. [Epub ahead of print]

Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data.

Eric Arkfeld, Zichen Wang, Hiroyuki Hakozaki, Johannes Schöneberg.

  We introduce a whole-cell digital twin framework that integrates four-dimensional (4D) (x, y, z, and t) lattice light-sheet microscopy with particle-based reaction-diffusion simulations in ReaDDy to model mesoscale intracellular organelle dynamics. Using fluorescence microscopy data from live Cal27 cells, we construct spatially resolved digital twins incorporating mitochondrial networks, microtubule networks, dynein and kinesin motors, the plasma membrane, and the nucleus. Mitochondrial dynamics include fusion/fission remodeling, diffusion, and motor-driven active transport along microtubules. Our simulations reproduce experimental trends in mitochondrial dynamics across control and two microtubule-perturbed conditions, demonstrating predictive capability without reparameterization. We then use stress-mimicking to predict emergent perinuclear mitochondrial clustering. Crucially, these simulations reveal that microtubule topology acts as a structural gate for this reorganization, demonstrating that upregulated retrograde motor kinetics alone are insufficient to drive clustering without permissive filament connectivity. This digital twin framework provides an approach for investigating intracellular dynamics and perturbation effects in an interpretable and biologically grounded manner.

Keywords:  ReaDDy; digital twin; lattice light-sheet microscopy; microtubule cytoskeleton; mitochondrial dynamics; mitochondrial fusion-fission; molecular motors; perinuclear clustering; reaction-diffusion simulation; whole-cell modeling

DOI:  https://doi.org/10.1016/j.cell.2026.06.010
Front Cell Dev Biol. 2026 ;14 1824021

From iPSC to manufactured iNK cells using CombiCult® screening platform.

Marina Tarunina, Sachin Luharia, Matthew Houppermans, Giuseppe D'Agostino, Lam Lam, Michelle Gestwa, Aleksandra Habich-Crayton, Marcia Mata, Juline Guenat, Molly Tregidgo, Patrick Statham, Charlotte Lee-Reeves, Mudith Jayawardena, Simona Zingaro, Limor Zwi-Dantsis, Aishwarya Nair, Alexandru-Robert Podovei, Vera Karels, Jahid Hasan, Tatyana Ponomaryov, Yen Choo.

   Background: Allogeneic cell-based immunotherapies generated from pluripotent stem cells show considerable promise for the treatment of oncological, autoimmune, and viral diseases, however discovery platforms for induced pluripotent stem cell (iPSC)-derived cell therapies do not translate well to scalable manufacturing platforms.
Methods: We applied a high-throughput combinatorial screening platform (CombiCult®) to identify novel, manufacturing-ready, feeder-free protocols for the generation of mature, functional NK cells from human iPSCs.
Results: We validated seven CombiCult®-derived differentiation protocols for the production of highly cytotoxic, phenotypically mature iPSC-derived NK (iNK) cells, which are comparable to donor-derived NK cells. Translation to a Stirred Tank Bioreactor (STR) system resulted in a 10x increase in productivity, from ∼20 to ∼190 iNK cells per starting iPSC. iNK cells demonstrate mature transcriptomic signatures, retained after translation to bioreactor-based production.
Conclusion: The three-dimensional, bead-based screening approach enables seamless translation to bioreactor-based production of iNK cells exhibiting high cytotoxic activity against a range of cancer cell types.

Keywords:  human iPSc; immuno-oncology; manufacturing, STR; natural killer cells; off-the-shelf therapy

DOI:  https://doi.org/10.3389/fcell.2026.1824021
Light Sci Appl. 2026 Jul 03. pii: 303. [Epub ahead of print]15(1):

Two-photon 3D imaging of optically stimulated neural activity at 100 Hz.

Dongli Xu, Fuu-Jiun Hwang, Jun B Ding, Leilei Peng.

Understanding how neurons integrate synaptic inputs requires imaging techniques capable of capturing rapid, three-dimensional dendritic events. These processes occur on millisecond timescales and submicron spatial scales, exceeding the speed of conventional two-photon microscopy (2PM). We developed dual-view Bessel two-photon projection microscopy (dv-B2PM), a high-speed volumetric imaging approach that achieves 100 Hz whole-volume acquisition with synaptic-level resolution. dv-B2PM simultaneously records two orthogonal projections of the same 3D volume, preserving spatial information while minimizing ambiguity from structural overlap. Combining dv-B2PM with two-photon glutamate uncaging, we visualized 3D Ca²⁺ dynamics in neurons following localized stimulation. Multi-timescale analysis revealed dendrite-to-soma Ca²⁺ signal propagation, back propagated Ca²⁺ signal from the soma, and multi-frequency (5-40 Hz) Ca²⁺ transients activated along apical dendrites at speeds from ten of microns per second to millimeters per seconds. These findings demonstrate dv-B2PM as a powerful tool for direct visualization of 3D calcium dynamics associated with dendritic integration across extended neuronal structures, bridging the gap between optical imaging and the dynamic biophysics of neuronal integration.

DOI: https://doi.org/10.1038/s41377-026-02395-2
bioRxiv. 2026 Jun 18. pii: 2026.06.16.732743. [Epub ahead of print]

PTEN Subcellular Localization Dictates Function.

Nicole M Desmet, Cheyenne F Griffin, Helena Seo, Annaliese OuYang, Penelope Tir, Mackenzi L Prina, Wei Wang, Meijie Li, Bryan W Luikart.

Mutations in phosphatase and tensin homolog (PTEN) drive unregulated activation of the phosphatidylinositol-3-kinase (PI3K) pathway, resulting in neuronal hypertrophy, and are strongly associated with autism spectrum disorder (ASD). Several PTEN mutations alter subcellular localization, yet how localization governs PTEN function in developing neurons remains unclear. Although PTEN has been reported broadly distributed throughout neurons, here, live imaging of HaloTagged PTEN reveals dynamically regulated localization, suggesting spatial control of its signaling. We then used retroviral-mediated genetic manipulation to delete endogenous Pten in developing hippocampal neurons while simultaneously expressing PTEN fused to defined localization motifs, allowing us to directly test how subcellular targeting regulates neuronal morphology. Loss of Pten produces neurons characterized by enlarged somata, more elaborate dendritic arbors, and increased spine density, length, and head area. Nuclear-excluded PTEN fully rescued these phenotypes, whereas targeting PTEN to filopodia via fusion to the FBAR domain of srGAP3 or to the postsynaptic density via Homer1C corrected or corrected all morphological abnormalities in PTEN-deficient neurons and simplified dendritic arborization compared to wild-type. In contrast, nuclear-localized PTEN produced only partial rescue, normalizing soma size and spine head area but not dendritic complexity or spine density. These findings indicate that PTEN acts locally to restrain growth and structural connectivity, whereas regulation of spine head size can be mediated by PTEN both inside and outside the nucleus, potentially through transcriptional or splicing-dependent mechanisms. Together, our results identify subcellular localization as a critical determinant of PTEN function and reveal spatially distinct mechanisms through which PTEN sculpts neuronal development.

DOI: https://doi.org/10.64898/2026.06.16.732743
Clin Transl Med. 2026 Jul;16(7): e70733

Releasing the neuronal brake: Inhibiting AhR to enhance axon regeneration.

Daniel Halperin, Hongyan Zou.

DOI: https://doi.org/10.1002/ctm2.70733
J Physiol. 2026 Jul 01.

Kinematic-calcium loops unravel impaired excitation-contraction coupling in MELAS-affected cardioids.

Margherita Burattini, Annalinda Pisano, Maria Gemma Pignataro, Giulia d'Amati, Silvana Pinelli, Minh Long Hoang, Francesco Paolo Lo Muzio, Michele Miragoli.

  Impaired Ca2+ handling, and in particular leakage from the sarcoplasmic reticulum, is a critical mechanism in metabolic diseases affecting the heart. Phase-plane loop analysis provides an integrated assessment of excitation-contraction coupling (ECC) by capturing the dynamic relation between Ca2 + transients and mechanical contraction, exceeding standard time analysis limitations. Here, we investigated how mitochondrial encephalopathy, lactic acidosis and stroke-like episodes metabolic disorder (MELAS) impairs the ECC using cardiac spheroids from diseased human induced pluripotent stem cells (m3243A>G mutation) and matched control (mtDNA mutation <10%). High-speed dual-mode imaging at 200 fps enabled simultaneous acquisition of Ca2 + dynamics and spheroid kinematics. To uncover disease-specific mechanisms, supra-threshold electric field stimulation was applied to simulate increased energy demand. After signal extraction, we built our interpretation of phase-plane loops, comprising kinematic-calcium (Ki-Ca) loops, to quantify ECC efficiency. Time-domain analysis demonstrated that MELAS cardiac spheroids showed significant reduction in beat duration at kinematics (1.068 ± 0.066 s vs. 0.775 ± 0.094 s), as well as decreased Ca2+ transient duration (0.984 ± 0.049 s vs. 0.664 ± 0.042 s). Critically, Ki-Ca loop analysis provided a more complete picture where MELAS samples displayed visibly different loops and a significant reduction of their area compared to controls (0.129 ± 0.056 vs. 0.082 ± 0.163). These findings demonstrate that Ki-Ca loops provide a sensitive and integrative metric for detecting ECC dysfunction in human in vitro cardiac models. This approach offers mechanistic insight into how mitochondrial metabolic disorders, such as MELAS, compromise the coupling between Ca2 + cycling and contractility. KEY POINTS: Phase-plane Ki-Ca loops effectively contribute to understanding the excitation-contraction coupling (ECC) efficiency. Mitochondrial encephalopathy, lactic acidosis and stroke-like episodes metabolic disorder (MELAS) impairs ECC in cardioid models. Cardiac challenge pacing protocol highlights beating anomaly in MELAS spheroids, uncovering ECC failure.

Keywords:  Ki‐Ca loops; MELAS; calcium signalling; computer vision; excitation–contraction coupling; hiPSCs; kinematics

DOI:  https://doi.org/10.1113/JP290473
Am J Physiol Cell Physiol. 2026 Jul 02.

Mitochondrial Calcium Transport in Amino Acid Metabolism: From nutritional responses to metabolic regulation.

Marcos Vinícius Caetano, Vitor de Miranda Ramos, Alicia J Kowaltowski.

  Mitochondrial calcium (Ca2+) transport is a central regulator of cellular metabolism, linking bioenergetics, signaling, and organelle function. While its role in controlling oxidative phosphorylation and cell fate is well established, emerging evidence indicates that mitochondrial 2+ handling is also tightly connected to amino acid metabolism and nitrogen balance. In this review, we integrate classical and recent findings to examine how mitochondrial 2+ transporters, including the mitochondrial calcium uniporter complex (MCUc), Na+/2+ exchangers, and H+/Ca2+ exchange systems, respond to nutritional cues and contribute to metabolic adaptation. We discuss how variations in amino acid availability and dietary protein intake may modulate the expression and activity of Ca2+ transport machinery, and explore the emerging role of mitochondrial proteases in regulating transporter turnover and activity, highlighting unexplored questions and future prospects in the field. We discuss how mitochondrial Ca2+ fluxes influence amino acid-sensitive processes including autophagy, mitochondrial morphology, and substrate utilization, while also potentially modulating the urea cycle through effects on key enzymes and metabolite transporters. Overall, we find that mitochondrial Ca2+ transport is a dynamic interface between nutrient availability and metabolic regulation, with implications for physiology and metabolic disease, but significant gaps remain regarding specific mechanisms within the integration of Ca2+ signaling with amino acid-sensing pathways.

Keywords:  amino acid metabolism; mTORC1; mitochondrial calcium; mitochondrial proteases; urea cycle

DOI:  https://doi.org/10.1152/ajpcell.00212.2026
Nat Rev Mol Cell Biol. 2026 Jun 30.

COPII meets autophagy at the ER membrane.

Lisa Heinke.

DOI: https://doi.org/10.1038/s41580-026-00997-7