bims-axbals Biomed News
on Axonal biology and ALS
Issue of 2026–03–08
twenty-one papers selected by
TJ Krzystek
  1. Coupling of functionality to trafficking of KCNQ2/3 potassium channels at the axon initial segment.
  2. A guide to selecting high-performing antibodies for STXBP1 (UniProt ID: P61764) for use in western blot, immunoprecipitation, and immunofluorescence.
  3. Imaging interorganelle membrane contact sites using dimerization-dependent fluorescent proteins.
  4. Brain Organoids as Emerging Platforms for Modeling Neurodegenerative Diseases: Progress, Challenges, and Future Directions.
  5. N-acetyl-l-leucine lowers α-synuclein levels and improves synaptic function in Parkinson's disease models.
  6. TDP-43 phosphorylation: Exploring kinases, phosphatases, and therapeutic potential in neurodegeneration.
  7. Role of LRRK2 in physiological activities, diseases, and therapy.
  8. Dual targeting of the UPS and autophagy as a novel therapy for neurodegenerative proteinopathies.
  9. Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress.
  10. Neighbors who talk: Mitochondria-lysosome crosstalk in homeostasis.
  11. Voltage-gating and neuronal signalling in neurodegeneration: From neuropathology to therapeutic opportunities in motor neuron disease.
  12. Modeling the growth of cytosolic TDP-43 inclusion bodies and accumulated neurotoxicity of misfolded oligomers in neurons.
  13. Proteostasis, disease and the ageing neuron: Compartmental complexity in non-renewing cells.
  14. In Vitro retinal ganglion cell differentiation and enrichment under the scope: do subtypes matter?
  15. Imaging and quantifying organelle contact sites using a reversible splitFAST complementation system.
  16. Guided and unguided neural organoids play complementary roles in studying neurodevelopment and neuroinflammation.
  17. Constitutive neuronal expression and disease-associated upregulation of chitinases in amyotrophic lateral sclerosis.
  18. The TBCK-PPP1R21-FERRY3/C12orf4 complex: a RAB5-GAP brake essential for endo-lysosomal homeostasis.
  19. Applications of in vitro transporter assays for mechanistic characterization and prediction of clinical drug-drug interactions.
  20. Tubulin transforms Tau and α-synuclein condensates from pathological to physiological.
  21. A guide to selecting high-performing antibodies for MMP7 (UniProt ID: P09237) for use in western blot and immunoprecipitation.
  1. Proc Natl Acad Sci U S A. 2026 Mar 10. 123(10): e2527749123
    Coupling of functionality to trafficking of KCNQ2/3 potassium channels at the axon initial segment.
    Daisuke Yoshioka, Yasushi Okamura.
      KCNQ2/3, a major voltage-gated potassium channel at the axon initial segment (AIS), plays a crucial role in controlling neuronal excitability. While the functionality of KCNQ2/3 is regulated by conformational changes from voltage sensing, the AIS localization of KCNQ2/3 is regulated by ankyrinG (ankG). However, the potential coupling between the mechanisms governing channel functionality and trafficking remains unresolved. Here, we combine genetic engineering of channel functionality with advanced imaging techniques of channel trafficking to uncover a coupling of KCNQ2/3 functionality to trafficking. Single-molecule imaging reveals that reduced KCNQ3 functionality alters the entire trafficking pathway, including exo/endocytosis and lateral diffusion, reducing AIS localization of KCNQ2/3. Furthermore, we develop a live-cell assay to quantify the interactions between full-length KCNQ3 and ankG, demonstrating that the active conformation of KCNQ3 is essential for the stable ankG binding. Our findings establish a mechanistic basis for the integration of KCNQ2/3 gating and trafficking in regulating neuronal excitability.
    Keywords:  ankyrinG; axon initial segment; epilepsy; single-molecule imaging; voltage-gated potassium channel
    DOI:  https://doi.org/10.1073/pnas.2527749123
  2. F1000Res. 2024 ;13 1557
    A guide to selecting high-performing antibodies for STXBP1 (UniProt ID: P61764) for use in western blot, immunoprecipitation, and immunofluorescence.
    NeuroSGC/YCharOS/EDDU collaborative group
      The Syntaxin-binding protein 1, STXBP1, is a protein involved in docking and fusion of synaptic vesicles, a crucial event for neurotransmitters release into the synapse. Here we have characterized twelve STXBP1 commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.
    Keywords:  MUNC18-1; P61764; STXBP1; Syntaxin-binding protein 1; antibody characterization; antibody validation; immunofluorescence; immunoprecipitation; western blot
    DOI:  https://doi.org/10.12688/f1000research.160174.1
  3. Methods Enzymol. 2026 ;pii: S0076-6879(26)00032-7. [Epub ahead of print]727 321-354
    Imaging interorganelle membrane contact sites using dimerization-dependent fluorescent proteins.
    Victoria H Williams, Chih-Hsuan Hsu, Gregory E Miner, Sarah Cohen.
      Membrane contact sites (MCSs), sites of close apposition between membrane-bound organelles, mediate key intracellular processes to coordinate organelle function and are implicated in a wide range of human diseases. Because MCSs can span as little as 10 nm of distance, the limited resolution of light microscopy can hamper the ability to study these structures in live cells. Dimerization-dependent fluorescent proteins consist of a weakly fluorescent and non-fluorescent monomer that produce greater signal when the two monomers interact, thereby allowing the user to identify sites of proximity through protein-protein interaction. Here, we describe a protocol using Contact-FP - our suite of organelle-targeted dimerization-dependent fluorescent proteins - to study MCSs using confocal or Airyscan microscopy in live cells. The protocol includes guidance for transfection, imaging, and analysis of Contact-FP biosensors. It includes instructions on how to leverage this tool to study a single MCS type, identify two MCSs involving the same organelle, or induce MCSs using high levels of transfection of Contact-FP probes. We also suggest troubleshooting steps for transfection, imaging, and analysis. This protocol provides a specific example for using this tool in U-2 OS osteosarcoma cells but is amenable to adjustment for other cell types.
    Keywords:  Biosensors; Endoplasmic reticulum; Fluorescent proteins; Lipid droplets; Lysosomes; Membrane contact sites; Mitochondria; Organelles; Peroxisomes; Plasma membrane
    DOI:  https://doi.org/10.1016/bs.mie.2026.01.024
  4. J Neurochem. 2026 Mar;170(3): e70395
    Brain Organoids as Emerging Platforms for Modeling Neurodegenerative Diseases: Progress, Challenges, and Future Directions.
    Yesim Kaya, Kevser Kübra Kırboğa.
      Neurodegenerative diseases are a group of disorders (such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis) characterized by loss of function and death of neurons in different parts of the nervous system. These pathologies constitute a global burden, especially for aging populations. This circumstance leads to an increasing demand for understanding the fundamental mechanisms and development of therapeutic strategies. Conventional models, including two-dimensional cell culture and animal models, postmortem brain tissue provide an overview about neurodegenerative disorders but do not completely recapitulate cellular and molecular mechanisms of the human brain. Although three-dimensional (3D) brain organoids exhibit similar properties with physiological and pathological conditions of human brain, including interaction of neuronal, glial cells and self-organizing structure, protein aggregation, neuroinflammation, and neuronal degeneration. The integration of reprogrammed human induced pluripotent stem cells (iPSCs) with 3D brain organoid systems provides a clinical platform as a bridge between bench to bedside. Brain organoids have been used to elucidate novel insights into the molecular and genetic mechanisms underlying neurodegenerative diseases. Furthermore, brain organoids serve as a tool for in vitro disease modeling, drug screening and emergence of new treatments. Despite these clinical benefits, there are various limitations such as incomplete tissue maturation, lack of vascularization and incomplete cellular diversity in this 3D culture system. This review describes in detail the advantages and disadvantages of brain organoids usage in modeling neurodegenerative diseases from a contemporary perspective.
    Keywords:  3D disease modeling; brain organoids; induced pluripotent stem cells; neurodegenerative diseases
    DOI:  https://doi.org/10.1111/jnc.70395
  5. J Clin Invest. 2026 Mar 02. pii: e196137. [Epub ahead of print]136(5):
    N-acetyl-l-leucine lowers α-synuclein levels and improves synaptic function in Parkinson's disease models.
    Pingping Song, Chuyu Chen, Rossella Franchini, Bryan Duong, Yi-Zhi Wang, Robert Coukos, Zhong Xie, Jeffrey N Savas, Yueqin Zhou, Mariarita Bertoldi, D James Surmeier, Loukia Parisiadou, Dimitri Krainc.
      N-acetyl-l-leucine (NALL), a derivative of the branched-chain amino acid leucine, has shown therapeutic potential for neurodegenerative diseases, including in prodromal stages of Parkinson's disease (PD). However, the mechanism of its protective effects has been largely unknown. Using human induced pluripotent stem cell-derived dopaminergic neurons from patients carrying GBA1, LRRK2, or VPS35 mutations, as well as from sporadic PD cases, we found that NALL treatment markedly reduced Ser129 phosphorylated α-synuclein (pS129-syn). Discovery-based proteomic analysis revealed that NALL treatment upregulated lysosomal, mitochondrial, and synaptic proteins without inducing cytotoxicity. The reduction of pS129-syn was dependent on serine protease HTRA1, which was robustly induced by NALL. Moreover, NALL increased the expression of wild-type parkin in mutant dopaminergic neurons, leading to increased glycosylated dopamine transporter, elevated synaptic membrane-associated synaptojanin-1, and accelerated synaptic vesicle endocytosis, suggesting improved synaptic function. Furthermore, in LRRK2R1441C knockin mice, NALL administration decreased pS129-syn, elevated parkin levels, and ameliorated dopamine-dependent motor learning deficits. These findings highlight the therapeutic potential of NALL for PD by its protective effects on α-synuclein pathology and synaptic function in vulnerable dopaminergic neurons.
    Keywords:  Cell biology; Neurodegeneration; Neuroscience; Parkinson disease
    DOI:  https://doi.org/10.1172/JCI196137
  6. J Alzheimers Dis. 2026 Mar 04. 13872877261424284
    TDP-43 phosphorylation: Exploring kinases, phosphatases, and therapeutic potential in neurodegeneration.
    Liti Zhang, Yichen Huang, Wei Huang, Qianqian Huang, Yizhou Lin, Jianlan Gu.
      TAR DNA-binding protein 43 (TDP-43) is a multifunctional DNA/RNA-binding protein whose abnormal phosphorylation and aggregation are central to the pathogenesis of several neurodegenerative diseases. TDP-43 proteinopathy, characterized by hyperphosphorylation and cytoplasmic accumulation, is a defining pathological feature of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, and is frequently observed in Alzheimer's disease. The phosphorylation state of TDP-43 is dynamically regulated by a network of protein kinases-including CK1, GSK3β, CDC7, and PKA-and counterbalanced by phosphatases such as PP2A and PP1; however, the precise molecular mechanisms governing this equilibrium in disease remain incompletely understood. Notably, phosphorylated TDP-43 acquires prion-like properties, enabling self-templated aggregation and cell-to-cell propagation, which amplifies pathology and drives disease progression. These insights have catalyzed the development of therapeutic strategies aimed at modulating TDP-43 phosphorylation, with kinase inhibitors and phosphatase enhancers emerging as promising candidates for targeting TDP-43 proteinopathies. This review integrates current knowledge on the regulatory networks controlling TDP-43 phosphorylation, examines its role in prion-like spread, and evaluates emerging therapeutic approaches aimed at mitigating TDP-43-mediated neurodegeneration.
    Keywords:  Alzheimer's disease; TDP-43; neurodegenerative disease; phosphatase; phosphorylation; protein kinase
    DOI:  https://doi.org/10.1177/13872877261424284
  7. Chin Med J (Engl). 2026 Mar 05. 139(5): 653-671
    Role of LRRK2 in physiological activities, diseases, and therapy.
    Zhuoran Wang, Qingfang Li, Lingxi Yan, Mingyu Du, Xiawei Wei.
       ABSTRACT: Leucine-rich repeat kinase 2 (LRRK2) is a critical target for the treatment of Parkinson's disease (PD) and potentially other diseases. LRRK2 is involved in intracellular signaling, immune response, and inflammation, with key roles in both the central nervous system and peripheral tissues. LRRK2 mutations are linked to cellular dysfunction including mitochondrial and neuronal damage and can disrupt signaling pathway balance, thereby contributing to PD and other disorders. Inhibiting LRRK2 kinase activity shows potential for treating PD by correcting cellular imbalances and reducing neuronal damage. However, risks associated with regulating a multifunctional protein must be addressed. Further research on the molecular partners and tissue-specific functions of LRRK2 is essential for developing targeted therapies and improving treatment options for related diseases. This review offers a comprehensive analysis of LRRK2, with a focus on its physiological functions, disease involvement, and emerging therapeutic strategies.
    Keywords:  Immune response; Inflammation; Clinical trial; Inhibitors; Intracellular signaling; LRRK2; Novel targets; Parkinson’s disease; Targeted therapy
    DOI:  https://doi.org/10.1097/CM9.0000000000003989
  8. Front Cell Neurosci. 2026 ;20 1738415
    Dual targeting of the UPS and autophagy as a novel therapy for neurodegenerative proteinopathies.
    Georgie Lines, Martin Helley, Sébastien Gillotin, Janet Brownlees, James Duce, Phillip Smethurst.
      Neurodegenerative proteinopathies are characterized by impaired protein clearance and the accumulation of misfolded or aggregated proteins, ultimately leading to neuronal death. The two principal pathways responsible for protein degradation in cells are the ubiquitin proteasome system (UPS) and autophagy. Emerging evidence indicates that these pathways share regulatory components and engage in extensive crosstalk. In this review, we summarize the mechanisms of the UPS and autophagy, highlight their points of interaction, and discuss therapeutic opportunities to modulate both systems in parallel to enhance protein clearance in neurodegenerative disease.
    Keywords:  UPS—ubiquitin proteasome system; autophagy; neurodegenearation; neurodegenerative diseases; proteasome; therapeutics
    DOI:  https://doi.org/10.3389/fncel.2026.1738415
  9. Sci Adv. 2026 Mar 06. 12(10): eaed3579
    Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress.
    Kenneth Ehses, Jorge P López-Alonso, Odetta Antico, Yannik Lang, Till Rudack, Abdussalam Azem, Miratul M K Muqit, Iban Ubarretxena-Belandia, Rubén Fernández-Busnadiego.
      Cells have evolved organelle-specific responses to maintain protein homeostasis (proteostasis). During proteostatic stress, mitochondria down-regulate translation and enhance protein folding, yet the underlying mechanisms remain poorly defined. Here, we used cryo-electron tomography to observe the structural consequences of mitochondrial proteostatic stress within human cells. We detected protein aggregates within the mitochondrial matrix, accompanied by a marked remodeling of cristae architecture. Concomitantly, the number of mitochondrial ribosome complexes was significantly reduced. Mitochondrial Hsp60 (mHsp60), a key protein folding machine, underwent major conformational changes to favor complexes with its co-chaperone mHsp10. We visualized the interactions of mHsp60 with native substrate proteins and determined in vitro mHsp60 cryo-electron microscopy structures enabling nucleotide state assignment of the in situ structures. These data converge on a model of the mHsp60 functional cycle and its essential role in mitochondrial proteostasis. More broadly, our findings reveal structural mechanisms governing mitochondrial protein biosynthesis and their remodeling under proteostatic stress.
    DOI:  https://doi.org/10.1126/sciadv.aed3579
  10. Curr Opin Cell Biol. 2026 Mar 05. pii: S0955-0674(26)00015-3. [Epub ahead of print]100 102627
    Neighbors who talk: Mitochondria-lysosome crosstalk in homeostasis.
    Akriti Prashar, Rosa Puertollano.
      Mitochondria are highly dynamic and multifaceted organelles that perform essential cellular functions such as producing energy, regulating metabolism, and orchestrating immune responses. Lysosomes are crucial signaling hubs that are important for nutrient sensing, signal transduction, and regulation of cellular degradation and recycling processes including the removal of damaged mitochondrial components or entire mitochondria. Together, these two organelles perform critical cellular functions. Emerging evidence links defects in both organelles to multiple diseases, underscoring how their functions are intricately linked. To coordinate their activities, mitochondria and lysosomes engage in bidirectional crosstalk, enabling reciprocal regulation of their respective functions. These 'organelle conversations' can occur through direct interactions at membrane contact sites where both organelles physically interact via stabilization by molecular tethers, or at a distance through signaling pathways. Here we discuss recent progress in our understanding of the mechanisms underlying mitochondria-lysosome crosstalk and how this communication is altered in pathological conditions.
    DOI:  https://doi.org/10.1016/j.ceb.2026.102627
  11. Neurobiol Dis. 2026 Feb 27. pii: S0969-9961(26)00080-X. [Epub ahead of print] 107336
    Voltage-gating and neuronal signalling in neurodegeneration: From neuropathology to therapeutic opportunities in motor neuron disease.
    Charan Kotapati, Le Thuy Van Tran, Fernanda C Cardoso.
      Voltage-gated ion channels (VGICs) are central to motor neuron excitability, governing the initiation and propagation of action potentials and synaptic transmission. Disruption of their finely tuned gating properties contributes to pathology-associated hyperexcitability, a hallmark of several neurodegenerative conditions, including motor neuron disease (MND). In this review, we examine the physiological roles of voltage-gated sodium, calcium and potassium channels in motor neurons, and evaluate how mutations, altered expression, aberrant biophysics, and maladaptive signalling impair the voltage signalling processes that drive and underlie neuronal dysfunction and degeneration. We synthesise evidence linking ion channel dysfunction to altered excitability, excitotoxicity, impaired neurotransmission, motor system instability and progressive motor neuron loss in MND. We discuss current therapies that offer modest benefit and may act directly or indirectly on neuronal excitability but with limited target specificity. Motivated by the the urgent need for effective treatments for MND, we discuss emerging strategies that leverage highly selective VGIC modulators, particularly gating-modifier peptides inhibitors, to counteract hyperexcitability in MND. We further highlight that understanding how voltage-sensing and channel gating are altered in MND offers new avenues for selective targeted intervention. Together, the evidence supports VGICs as critical yet poorly explored therapeutic targets for halting motor neurodegeneration.
    Keywords:  Amyotrophic lateral sclerosis; Drug target; Hyperexcitability; Motor neuron disease; Neuropathogenesis; Voltage-gated ion channel
    DOI:  https://doi.org/10.1016/j.nbd.2026.107336
  12. Comput Methods Biomech Biomed Engin. 2026 Feb 28. 1-28
    Modeling the growth of cytosolic TDP-43 inclusion bodies and accumulated neurotoxicity of misfolded oligomers in neurons.
    Andrey V Kuznetsov.
      This paper introduces a mathematical model for the growth of transactive response DNA binding protein of 43 kDa (TDP-43) inclusion bodies in neuron soma. The parameter representing the accumulated neurotoxicity caused by misfolded TDP-43 oligomers is also introduced. The model's equations enable the numerical calculation of the concentrations of TDP-43 monomers, dimers, free oligomers, and oligomers deposited in inclusion bodies. By simulating the deposition of free oligomers into inclusion bodies, the model predicts the size of TDP-43 inclusion bodies. An approximate solution to the model equations is derived for the scenario where protein degradation machinery is dysfunctional, leading to infinite half-lives for TDP-43 dimers, monomers, and both free and deposited oligomers. This solution, valid at large times, predicts that the radius of the inclusion body increases proportionally to the cube root of time, whereas the accumulated neurotoxicity increases linearly with time. To the best of the author's knowledge, this study is the first to model the relationship between the size of TDP-43 inclusion bodies and time, and the first to introduce the concept of accumulated neurotoxicity caused by misfolded TDP-43 oligomers. Sensitivity analysis of the approximate solution indicates that the inclusion body radius and accumulated neurotoxicity become independent of the kinetic constants at large timescales. Unlike the case of infinite half-lives, the numerical solution for physiologically relevant (finite) half-lives demonstrates that the long-term behavior of the inclusion body radius and accumulated neurotoxicity remains dependent on the kinetic constants, converging to distinct curves over time.
    Keywords:  Finke-Watzky model; Neuron; amyotrophic lateral sclerosis; frontotemporal lobar degeneration; mathematical modeling
    DOI:  https://doi.org/10.1080/10255842.2026.2618583
  13. Ageing Res Rev. 2026 Feb 27. pii: S1568-1637(26)00065-6. [Epub ahead of print]118 103073
    Proteostasis, disease and the ageing neuron: Compartmental complexity in non-renewing cells.
    Rosemary A Coleman, Michaela E Johnson, Anna Konopka, Yee Lian Chew.
      Proteostasis, the maintenance of protein homeostasis, is a critical cellular process for neuronal health that declines with age, contributing to neurodegenerative disease. This review examines the molecular architecture of the proteostasis network, how this is disrupted in ageing neurons, and its impact on neuronal function. We discuss unique challenges posed by the complexity arising from distinct neuronal compartments with distinct functions, as well as neurons' high energy demands, and post-mitotic status. We next detail how proteostasis mechanisms differ across neuronal compartments and neural subtypes, and how these differences influence susceptibility to stress and disease. Finally, we explore how these differences shape selective vulnerability in neurodegenerative diseases. By integrating recent transcriptomic and proteomic insights, this review highlights the need for compartment- and cell-type-specific approaches to mitigate proteostasis collapse in the ageing brain.
    Keywords:  Ageing; Axon; Dendrite; Neurodegeneration; Proteostasis
    DOI:  https://doi.org/10.1016/j.arr.2026.103073
  14. Front Cell Dev Biol. 2025 ;13 1750142
    In Vitro retinal ganglion cell differentiation and enrichment under the scope: do subtypes matter?
    Tahani W Baakdhah, Jeremy M Sivak.
      Retinal ganglion cells (RGCs) play a pivotal part transmitting visual data to the brain. Yet, damaged RGCs are unable to maintain and regrow axons and connectivity, as in the common blinding disease glaucoma. Thus, the idea of rescuing and replacing damaged RGCs holds immense therapeutic potential. In recent years pluripotent stem cells cultured in both 2D and 3D (retinal organoid) environments have generated RGCs from healthy- and patient-derived cells. These models can be used to study normal retinal physiology and compare it to the diseased retina. Although the effects of glaucomatous injuries on RGCs have been well-studied in animal models, much less is known about similar mechanisms in the human retina. Further, using in vitro-derived RGCs as a tool for cell characterization and replacement is still in its infancy. In particular, many distinct RGC subtypes have been described, and it remains unclear how well this diversity is reflected in the various differentiation protocols, or their functional roles in human health and disease. In this review we summarize the currently described subtypes of human RGCs and their markers and discuss recent evidence for subtype-specific vulnerabilities to injury and disease. Finally, we synthesize the limited evidence for subtype differentiation in human stem cell culture approaches. Increased understanding of this human RGC diversity will provide new tools to enrich for selective subtypes and ultimately fill key translational gaps in human glaucoma research.
    Keywords:  glaucoma; pluripotent stem cells; retinal ganglion cells; retinal injury; retinal organoids; retinal regeneration
    DOI:  https://doi.org/10.3389/fcell.2025.1750142
  15. Methods Enzymol. 2026 ;pii: S0076-6879(25)00527-0. [Epub ahead of print]727 75-91
    Imaging and quantifying organelle contact sites using a reversible splitFAST complementation system.
    Jason A Weesner, Chi-Lun Chang.
      Organelle contact sites are crucial hubs for inter-organelle logistics; yet, visualizing these dynamic foci of sub-micro scale in living cells is challenging. In this chapter, we describe how to use the FABCON (Fluorogen-Activated Bimolecular complementation at CONtact sites) toolkit to detect and quantify contact sites. FABCON labels contact sites via a reversible, fluorogen-dependent complementation of the splitFAST system. This protocol first describes the engineering principle of FABCON, allowing customization to model systems of interest. Next, we provide detailed instructions for using FABCON to monitor mitochondria-lipid droplet interactions in mammalian cells and how to quantify levels of contact sites via intensity-based measurement and line scanning. FABCON can be broadly applied to visualize and quantify other contact sites. With proper validation and optimization, FABCON provides a robust platform to study the dynamic regulation of organelle contact sites.
    Keywords:  Bimolecular fluorescence complementation; Lipid droplets; Mitochondria; Organelle contact sites; SplitFAST
    DOI:  https://doi.org/10.1016/bs.mie.2025.11.023
  16. Einstein (Sao Paulo). 2026 ;pii: S1679-45082026000100609. [Epub ahead of print]24 eAO1716
    Guided and unguided neural organoids play complementary roles in studying neurodevelopment and neuroinflammation.
    Raphaella Josino, Bruno Yukio Yokota-Moreno, Isabella de Sousa Nóbrega, André Luíz Teles E Silva, Melissa Bernardini Bachir Moysés, Guilherme Grecco Ferreira, Mariana Silva Branquinho, Elisa Varella Branco, Maria Rita Passos-Bueno, Andrea Laurato Sertié.
       OBJECTIVE: This study aimed to compare guided dorsal forebrain neural organoids with unguided neural organoids, focusing on differences in structural organization, cellular composition, and functional properties.
    METHODS: Using the same human induced pluripotent stem cell line, we applied two established differentiation protocols in parallel to generate guided and unguided neural organoids.
    RESULTS: Guided neural organoids exhibited reproducible cytoarchitecture, relatively homogeneous morphology, and robust network activity, making them particularly well-suited for modeling specific aspects of cortical neurodevelopment and neurodevelopmental disorders. In contrast, unguided neural organoids displayed greater heterogeneity in morphology and cellular composition, including prominent development of astrocytes, microglia, and choroid plexus-like structures that respond to inflammatory stimuli, positioning them as valuable models for studying neuroinflammation during brain development.
    CONCLUSION: These findings emphasize the importance of selecting neural organoids protocols based on specific research questions, and suggest that the guided and unguided approaches can complement each other to provide insights into neurodevelopmental and neuroinflammatory processes.
    DOI:  https://doi.org/10.31744/einstein_journal/2026AO1716
  17. Brain. 2026 Feb 28. pii: awag083. [Epub ahead of print]
    Constitutive neuronal expression and disease-associated upregulation of chitinases in amyotrophic lateral sclerosis.
    Nayana Gaur, Christin Angerer, Zeynep I Gunes, Mihai Ancau, Mengzhe Wang, Henrick Riemenschneider, Charlene-Annett Hurler, Simon Mungwa, Patrick Lüningschrör, Anxhela Zhiti, Robert Steinbach, Michael Briese, Mugdha Srivastava, Mario Plaas, Andreas Hermann, Michael Sendtner, Sarah Jäkel, Dieter Edbauer, Jochen Herms, Sabine Liebscher, Julian Grosskreutz, Monika S Brill.
      Chitinases are hydrolytic enzymes responsible for degrading chitin and have been evolutionarily conserved across various species. Although their signaling pathways are not fully understood, the chitinases are considered active immunomodulators across several cell types. Specific isoforms, including Chitotriosidase-1 (CHIT1), Chitinase-3-like protein 1 (CHI3L1), and human-specific Chitinase-3-like protein 2 (CHI3L2), have emerged as markers of inflammation across the neurodegenerative spectrum, including amyotrophic lateral sclerosis (ALS). ALS is a fatal neuromuscular condition, and therapeutic development has been severely hindered by phenotypic heterogeneity and an incomplete understanding of etiology. Although several overlapping disease mechanisms can contribute to neuronal death, inflammation can exacerbate pathology. Prior studies have reported that CHIT1, CHI3L1, and CHI3L2 levels are elevated in the cerebrospinal fluid (CSF) of ALS patients and associated with disease aggressiveness. Nevertheless, several open questions critical to our understanding of the chitinases' role in ALS disease burden remain: namely, 1) which cell types in the central nervous system (CNS) are chitinase sources under physiological conditions, 2) which of these display chitinase upregulation in ALS, and 3) what is the diagnostic utility of the chitinases relative to established biomarkers. Here, we utilize pre-clinical models and post-mortem human tissue to demonstrate at both the transcriptomic and protein level that neurons are a primary source of chitinases; furthermore, neuronal chitinase expression is conserved across species. Under physiological conditions, CHI3L1 is more abundant and widely expressed across various cell types, whereas CHIT1 is predominantly expressed in neurons. Additionally, utilizing symptomatic mice from three familial ALS models, we demonstrate isoform-specific expression profiles, with astroglial and microglial upregulation of CHI3L1, and neuronal and microglial upregulation of CHIT1. Differing expression dynamics and diagnostic utility were also noted in our clinical cohort: CSF CHIT1 and CHI3L2 levels had more discriminatory power when distinguishing between ALS vs. non-ALS controls, while CHI3L1 was more closely associated with inflammation and aging across the neurodegenerative spectrum. Although the chitinases did not diagnostically outperform the neurofilament proteins as biomarkers, we propose that appreciating their expression patterns can aid in optimizing biomarker-guided trial design. Taken together, we demonstrate that chitinase upregulation in ALS is evident in various CNS cell types and that its neuronal expression may provide new insights into its role in disease activity.
    Keywords:  CHI3L1; CHI3L2; CHIT1; amyotrophic lateral sclerosis; chitinase; neuron
    DOI:  https://doi.org/10.1093/brain/awag083
  18. Autophagy. 2026 Mar 06.
    The TBCK-PPP1R21-FERRY3/C12orf4 complex: a RAB5-GAP brake essential for endo-lysosomal homeostasis.
    Yingji Chen, Xiayun Xu, Yi Zheng, Hongyan Wang, Chenji Wang.
      TBCK syndrome is a severe neurodevelopmental disorder characterized by hypotonia, intellectual disability, and progressive neurodegeneration. While the TBCK gene has been implicated in MTOR signaling, its primary molecular function has remained controversial. In a recent study, we identify TBCK as the catalytic core of a heterotrimeric complex comprising TBCK, PPP1R21, and FERRY3/C12orf4. This complex functions as a specific GTPase-activating protein (GAP) for RAB5. TBCK deficiency or missense mutations of its key residues in the RABGAP-TBC domain lead to constitutive RAB5 hyperactivation, which blocks the transition from early to late endosomes and results in the formation of massively enlarged RAB5-positive endosomes. Furthermore, this RAB5 hyperactivation drives the constitutive activation of the PIK3C3/VPS34 complex. These defects culminate in a failure of lysosomal enzyme delivery and a secondary collapse of macroautophagic/autophagic flux. These findings redefine TBCK syndrome as a primary disorder of endosomal dynamics and highlight the TBCK-PPP1R21-FERRY3 axis as a critical "brake" for maintaining neuronal homeostasis.
    Keywords:  Autophagic flux; CLN15; RAB5; TBCK syndrome; endosomal trafficking; lysosomal storage disease; neurodegeneration
    DOI:  https://doi.org/10.1080/15548627.2026.2642337
  19. Drug Metab Pharmacokinet. 2026 Feb 16. pii: S1347-4367(26)00014-5. [Epub ahead of print]67 101528
    Applications of in vitro transporter assays for mechanistic characterization and prediction of clinical drug-drug interactions.
    Krisztina Herédi-Szabó, Sumito Ito, Xiaomin Liang, Yeojin Park, Masud Parvez, Philip Sandoval, Hong Shen, Kelly M Staiger, Kazuhiro Tetsuka, Mark S Warren, Ling Zou, Yurong Lai.
      Drug transporters play essential roles in governing the absorption, distribution, metabolism, and excretion (ADME) of therapeutic drugs. Transporter modulation frequently contributes to clinically significant drug-drug interactions (DDIs). This review provides a comprehensive overview of in vitro transporter assay systems and their applications in mechanistic characterization and prediction of transporter-mediated DDIs. Current global regulatory guidelines, including ICH M12, highlight key transporters requiring evaluation and emphasize the need for mechanistic insight to support risk assessment. A broad range of in vitro platforms-membrane vesicles, transporter-overexpressing cell lines, polarized monolayers, primary human hepatocytes and kidney cells, induced pluripotent stem cell (iPSC)-derived systems, organoids, and organ-on-chip models-are described, with discussion of their advantages, limitations, and translational relevance. These systems enable the determination of kinetic parameters, the evaluation of vectorial transport, and the integration of transporter-enzyme interplay. Challenges in in vitro-to-in vivo extrapolation (IVIVE), including substrate-dependent inhibition, nonspecific binding, and variability in assay conditions, are addressed alongside emerging strategies such as biomarker-informed modeling, quantitative proteomics, and physiologically based pharmacokinetic (PBPK) modeling. Collectively, the review provides guidance on the effective application of transporter assays in drug discovery and development to improve DDI prediction, support regulatory decision-making, and advance precision medicine.
    Keywords:  Drug transporters; Drug-drug interactions; Endogenous biomarkers; In vitro to in vivo extrapolation. ADME; Microphysiological systems; PBPK; Pharmacokinetics
    DOI:  https://doi.org/10.1016/j.dmpk.2026.101528
  20. Nat Commun. 2026 Mar 03.
    Tubulin transforms Tau and α-synuclein condensates from pathological to physiological.
    Lathan Lucas, Phoebe S Tsoi, My Diem Quan, Kyoung-Jae Choi, Josephine C Ferreon, Allan Chris M Ferreon.
      Proteins undergo phase separation to form membraneless condensates that spatially organize biomolecular interactions. These condensates can support cellular physiology or instigate pathological protein aggregation. Tau and α-synuclein (αSyn) are neuronal proteins that form heterotypic Tau:αSyn condensates associated with physiological and pathological processes. Tau and αSyn regulate microtubules, but also misfold and co-deposit in aggregates linked to neurodegenerative disease, highlighting the ambivalent impact of Tau:αSyn condensation in health and disease. Here, we show that Tubulin modulates Tau:αSyn condensates by promoting microtubule interactions and inhibiting homotypic and heterotypic pathological oligomers. In the absence of Tubulin, Tau-driven condensation accelerates formation of pathogenic Tau:αSyn heterodimers and amyloid fibrils. Tubulin partitioning into condensates promotes microtubule polymerization and prevents Tau and αSyn oligomerization. We identify distinct Tau and αSyn structural states in pathological Tubulin-absent versus physiological Tubulin-rich condensates. In neuronal models, microtubule loss drives pathological oligomer formation and neurite loss, whereas inducible Tau condensation stabilizes microtubules.
    DOI:  https://doi.org/10.1038/s41467-026-69618-3
  21. F1000Res. 2026 ;15 74
    A guide to selecting high-performing antibodies for MMP7 (UniProt ID: P09237) for use in western blot and immunoprecipitation.
    Michael Biddle, Jemma Cooper, Carolyn Jones, Katie Dixon, Harvinder Virk.
      Matrix metallopeptidase 7 (MMP7, also known as matrilysin) is a secreted zinc-dependent endopeptidase implicated in extracellular matrix remodelling and fibrotic processes. Elevated MMP7 expression is a hallmark of idiopathic pulmonary fibrosis and other interstitial lung diseases, where it has emerged as a candidate biomarker for disease progression. Identifying high-quality research antibodies is therefore essential to enable robust investigation of MMP7 biology and its translational potential. In this study, we systematically evaluated ten commercial antibodies for western blot and immunoprecipitation using a standardized knockout validation approach in human A549 cells, comparing readouts in MMP7 knockout lines with isogenic parental controls. These experiments form part of a larger collaborative initiative to address antibody reproducibility by characterizing commercial antibodies for human proteins and making the results openly available to the community. While antibody use and protocol conditions will vary between laboratories, this report provides a resource to guide selection of the most suitable reagents for studies of MMP7 in health and disease.
    Keywords:  MMP7; Matrilysin; P09237; antibody validation; idiopathic pulmonary fibrosis; immunoprecipitation; interstitial lung disease; matrix metallopeptidase 7; western blot
    DOI:  https://doi.org/10.12688/f1000research.175973.1
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