bims-axbals 2026-09-13 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2026–09–13
sixteen papers selected by
TJ Krzystek

BetaII-spectrin gaps and patches emerge from the patterned assembly of the actin/spectrin membrane skeleton in human motor neuron axons.
Astrocyte-derived extracellular vesicle phosphorylated TDP-43 as a blood-based biomarker for amyotrophic lateral sclerosis.
Altered neuronal start codon stringency favors cap-independent repeat-associated non-AUG translation.
"S-Tau-Lled" Lysosomes Disrupt Autophagic Processes in Neurodegeneration.
Synaptobrevin-2 Containing Extracellular Vesicles Are Rapidly Incorporated Into Mammalian Neurons via a Dynamin-Dependent Pathway.
Cellular modifiers of TDP-43 phase transition and cytoplasmic aggregation.
Decoding Frontotemporal Dementia: Genes, Proteins and Prospects for Precision Medicine.
Avl9 defines a family of DENN domain GTPase-activating proteins.
Retromer-targeted therapy for neurodegenerative diseases.
Midbrain organoids as next-generation models for Parkinson's disease: From pathogenesis to therapeutic discovery.
Investigating Translocation Mechanisms of TDP-43 Into the Endoplasmic Reticulum Using Budding Yeast Models.
Reduced mechanical shear is associated with early cortical differentiation and GDNF-GFRA1/RET signalling in human brain organoids.
Neuronal polarity: Opposing actin networks drive transient polarization.
Spatiotemporal control of Atg9 vesicle fusion in autophagosome formation.
Culture media alter retinal organoid physiology promoting AAV transduction and retinal ganglion cell survival.
Brain organoids, high-density MEAs, and deep learning: A new paradigm for functional neurobiomarker discovery.

Elife. 2026 Sep 08. pii: RP108021. [Epub ahead of print]14

BetaII-spectrin gaps and patches emerge from the patterned assembly of the actin/spectrin membrane skeleton in human motor neuron axons.

Nahir Guadalupe Gazal, Maria Jose Castellanos-Montiel, Guillermina Bruno, Anna Kristina Franco-Flores, Sarah Lépine, Lale Gursu, Ghazal Haghi, Gilles Maussion, Wolfgang E Reintsch, Fernando D Stefani, Agustín Anastasía, Mariano Bisbal, Ezequiel Axel Gorostiza, Thomas M Durcan, Nicolás Unsain.

  The actin/spectrin membrane-associated periodic skeleton (MPS) is a cytoskeletal structure that supports axonal integrity and function. Lower spinal motor neurons (MNs) are characterized by exceptionally long axons and are particularly susceptible to degeneration in a wide range of hereditary neuromuscular disorders, including amyotrophic lateral sclerosis. Using confocal and super-resolution imaging, we characterized the spatial distribution of βII-spectrin and the assembly pattern of the MPS in human MN axons derived from induced pluripotent stem cells. We discovered a striking gap-and-patch pattern in the medial axon, where sharply demarcated βII-spectrin gaps alternate with patches containing a well-organized MPS. The pattern is acutely induced by the kinase inhibitor staurosporine and pharmacological inhibition of actin polymerization prevents patch formation, indicating a requirement for actin nucleation in MPS assembly. Our data supports a model in which spectrin incorporation into nascent MPS patches depletes neighboring regions, producing long-range gaps-and-patches patterns.

Keywords:  MPS; actin; axon; cell biology; cytoskeleton; human; iPSCs; motor neurons; mouse; neuroscience; spectrin; staurosporine

DOI:  https://doi.org/10.7554/eLife.108021
Neurobiol Dis. 2026 Sep 10. pii: S0969-9961(26)00346-3. [Epub ahead of print] 107601

Astrocyte-derived extracellular vesicle phosphorylated TDP-43 as a blood-based biomarker for amyotrophic lateral sclerosis.

Tanya H Butt, Madeleine Strait, Lina Marcinczyk, Grace Katz, Vrinda Kalia, Cherine Jaafar, Roheeni Saxena, Adnan Divjan, Brianna Saglimbeni, Marfred E Munoz Umanes, Eva Tipps, Moon Han, Paul Mehta, Ikjae Lee, Hiroshi Mitsumoto, Pam Factor-Litvak, Neil A Shneider, Marianthi-Anna Kioumourtzoglou, Diane B Re.

  Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by central nervous system (CNS) neuroglial TAR DNA-binding protein 43 (TDP-43) pathology in ~90-95% of cases. Non-invasive biomarkers are critically needed to reduce diagnostic delay, enable patient stratification, and assess treatment efficacy in clinical trials. Astrocyte-derived extracellular vesicles (ADEVs) represent promising CNS liquid biopsy biomarkers, given astrocyte involvement in ALS pathogenesis and the ability of ADEVs to cross the blood-brain barrier and carry TDP-43. Here, we assessed the diagnostic performance of TDP-43 and its hyperphosphorylated pathological form, phospho-Ser409 (pTDP-43), quantified in ADEVs, for distinguishing ALS cases from matched healthy controls. ADEVs were immunoisolated from whole blood (n = 76) and plasma (n = 86) across three ALS biorepositories/cohorts. ADEV quality and enrichment were validated in accordance with minimal information for studies of extracellular vesicles guidelines, and protein levels were normalized by ratio to tetraspanin cluster of differentiation 81 (CD81). Diagnostic accuracy was evaluated by logistic regression and random forest models with cross-validation, adjusting for age and sex across 100 random seeds. Plasma ADEV pTDP-43/CD81 ratio best predicted ALS case status, with a mean AUC of 0.89 (95% CI: 0.75-0.99) from logistic models, corresponding to a mean sensitivity and specificity of 87% and 89%, respectively, and a mean AUC of 0.86 (95% CI: 0.82-0.90) from random forest models. Although the specificity of ADEV pTDP-43 relative to disease mimics and associations with disease progression require further investigation, these findings support its potential as a biomarker candidate for ALS and for patient stratification in TDP-43-targeted clinical trials.

Keywords:  Amyotrophic lateral sclerosis; Astrocytes; Extracellular vesicles; TDP-43; pTDP-43

DOI:  https://doi.org/10.1016/j.nbd.2026.107601
Nucleic Acids Res. 2026 Sep 07. pii: gkag880. [Epub ahead of print]54(17):

Altered neuronal start codon stringency favors cap-independent repeat-associated non-AUG translation.

Clare M Wieland, Shannon E Wright, Sydney Willey, Ishita Purwar, Samantha J Grudzien, Amy Krans, Erinn L Laimon, Melissa J Asher, Adrian M Isaacs, Amanda L Garner, Peter K Todd.

Intronic GGGGCC repeat expansions in C9orf72 cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). This expansion supports a non-canonical form of translational initiation known as repeat-associated non-AUG (RAN) translation to produce toxic dipeptide repeat proteins that contribute to neurodegeneration. Here, we find that the efficiency of RAN translation and its dependency on the 5' 7-methylguanosine mRNA cap are variable across cell types, with both rodent neurons and human iNeurons favoring cap-independent RAN translation from two distinct repeats (CGG and GGGGCC) across multiple reading frames. Treatment with an eIF4E inhibitor that blocks cap-dependent translation enhances RAN translation specifically in neurons. Intriguingly, cap-independent RAN translation exhibits less reliance on near-cognate codons for initiation than cap-dependent RAN translation. This finding led us to identify a surprising global alteration in neuronal start codon stringency as a contributor to the relatively higher cap-independent RAN translation in this cell type. This effect correlates with cytoplasmic redistribution of eIF1 in neurons and is reversed with overexpression of the eukaryotic initiation factor eIF5, which relaxes start codon stringency and preferentially enhances cap-dependent RAN translation. Together, these findings reveal several neuron-specific features of translational regulation that favor cap-independent RAN translation with implications for nucleotide repeat expansion disorder pathogenesis.

DOI: https://doi.org/10.1093/nar/gkag880
Traffic. 2026 Sep;27(3): e70051

"S-Tau-Lled" Lysosomes Disrupt Autophagic Processes in Neurodegeneration.

Anaïs Bécot, Mehdi Kabani.

Tauopathies are a class of neurodegenerative diseases characterized by the accumulation of hyperphosphorylated, misfolded and aggregated Tau proteins and by dysfunctions in the autophagy-lysosome system. Whether the latter are a cause or a consequence of the former is unclear. The answer may come from a recent study by Mirfakhar et al. Using human iPSC-derived neurons harboring the MAPT p.R406W mutation in Tau, they were able to show that pathogenic Tau is able to broadly impair lysosomal function ahead of Tau accumulation. They also show that the degradative function of lysosomes, but not their motility, can be restored through pharmacological activation of autophagy, leading to reduced Tau levels. This work opens new therapeutic opportunities to eliminate early-on pathological misfolded Tau proteins before they can engage in a vicious cycle of aggregation, amplification and propagation.

DOI: https://doi.org/10.1111/tra.70051
J Neurochem. 2026 Sep;170(9): e70551

Synaptobrevin-2 Containing Extracellular Vesicles Are Rapidly Incorporated Into Mammalian Neurons via a Dynamin-Dependent Pathway.

Victoria Hannett, A Alejandro Vilcaes, Siewert Hugelier, Qing Tang, Melike Lakadamyali, Natali L Chanaday.

  Synaptobrevin-2 (Syb2) is a SNARE protein essential for neurotransmitter release and communication in the nervous system. We previously showed that Syb2 is also exchanged among neurons via extracellular vesicles (EVs). Host neurons rapidly integrate exogenous Syb2 into their synaptic vesicle cycle to support neurotransmitter release. However, the endocytic mechanism by which neurons incorporate Syb2-containing EVs is unknown. Here, we use a fusion of Syb2 with the pH-sensitive GFP (Syb2-pHluorin) to track the incorporation of Syb2-containing EVs into rat hippocampal and cortical neurons and the trafficking of exogenous Syb2 to synaptic vesicles at synapses. We determined that Syb2-containing EVs are endocytosed via a Dynamin-dependent pathway, largely independently of macropinocytosis. The same endocytic route is used in the somatodendritic and axonal compartment and it occurs very rapidly, with the majority of Syb2-pHluorin residing in internal acidic organelles at 30 min after EV addition, including synaptic vesicles at synapses. Leveraging this finding, we used EVs to sparsely deliver Syb2-pHluorin to synapses and track the fusion and endocytosis of single synaptic vesicles. The results indicate that Syb2-pHluorin-positive synaptic vesicles are endocytosed with either ultrafast (< 1 s) or fast (~1-3 s) kinetics during synaptic transmission, suggesting limited diffusion and high fidelity in the fast retrieval of synaptic vesicle molecules immediately after fusion. Our findings expand our understanding of the mechanisms EVs use to enter neurons and open the door for future applications of EVs as vehicles to deliver fluorescent molecules in a neuron-specific, targeted manner.

Keywords:  dynamin; endocytosis; extracellular vesicle; neuron; synaptic vesicle recycling; synaptobrevin‐2

DOI:  https://doi.org/10.1111/jnc.70551
Elife. 2026 Sep 08. pii: RP110172. [Epub ahead of print]15

Cellular modifiers of TDP-43 phase transition and cytoplasmic aggregation.

Natalie Chin, Qi Zhang, Jizhong Zou, Ken Chih-Chien Cheng, Wei Zheng, Yihong Ye.

  RNA-binding protein TAR DNA-binding protein 43 (TDP-43) can form liquid-like nuclear assemblies whose phase behavior is thought to influence its aggregation propensity and neurotoxic activity. The mechanisms that govern the liquid-to-solid phase transition of TDP-43 remain poorly defined. Here, we combined chemical and genome-wide genetic screens to identify cellular factors that modulate the phase behavior of an RNA-binding-defective TDP-43 mutant. Our screens uncovered multiple cellular processes, including RNA splicing, protein translation, proteostasis imbalance, and nuclear export as TDP-43 phase regulators. We also developed a semi-permeabilized cell system that partially recapitulates the TDP-43 phase transition in vitro, and showed that nuclear export inhibition reshapes the nuclear environment to favor RNA-dependent liquid-liquid phase separation (LLPS) of TDP-43, which mitigates its aggregation. Nuclear export inhibition in a brain organoid model bearing an ALS-associated mutation reduces pathogenic phospho-TDP-43 accumulation. These findings identify multiple modulators of TDP-43 phase transitions in a sensitized model system and establish a framework for further dissecting the link between nuclear transport and TDP-43 phase dynamics.

Keywords:  TDP-43; XPO1; cell biology; human; liquid-liquid phase separation; protein aggregation

DOI:  https://doi.org/10.7554/eLife.110172
Curr Alzheimer Res. 2026 Aug 30.

Decoding Frontotemporal Dementia: Genes, Proteins and Prospects for Precision Medicine.

Kaushik Raj, Nandani Kumari, Pragya Bharti, Ranjeet Kumar, Dharmendra Kumar.

  Frontotemporal Dementia is an umbrella term for several neurodegenerative disorders that have a similar presentation pattern, which is accompanied by neural damage and brain tissue loss in the frontal and temporal regions. Recent studies have observed that the heterogeneity of Frontotemporal Dementia (FTD) is reflected in clinical features, genetics, and molecular perspectives. Specifically, the major forms of pathology in FTD are linked to abnormal protein accumulation, which includes tau, TAR DNA-binding protein 43 (TDP-43), and fused in sarcoma (FUS). Moreover, genetic research on FTD has identified vital mutations in MAPT (Microtubule-associated protein Tau), GRN (Progranulin Gene), and C9ORF72 genes (Chromosome 9 open reading frame genes). Recent developments in neuroimaging, biomarker levels in body fluids, and molecular profiling have increased diagnostic precision, enabling earlier detection of disease subtypes. Neurofilament light chain (NfL), progranulin, and several other biomarkers, together with novel neuroimaging approaches, are currently being applied for disease classification, prognosis, and disease treatment monitoring. These developments have accelerated the application of precision medicine for FTD, including antisense oligonucleotides, progranulin-restorative drugs, tau-specific therapies, and gene therapy. Despite advances in elucidating the biology of FTD, no disease-modifying therapies have yet been developed, and treatments remain symptomatic until now. Undoubtedly, there are many challenges when taking into account variable presentation, overlapping pathologies, and the lack of robust biomarkers. The aim of this paper is to provide an in-depth analysis of the epidemiology, clinical features, molecular pathologies, biomarkers, and potential therapeutic approaches concerning FTD, with a particular emphasis on the growing role of precision medicine. Omics technologies, biomarker- based patient stratification, and hypothesis-driven clinical trials are undoubtedly essential steps towards personalized therapy for FTD.

Keywords:  Frontotemporal dementia; neurodegeneration; precision medicine; biomarkers; gene therapy; primary progressive aphasia; neurofilament light chain

DOI:  https://doi.org/10.2174/0115672050478591260821105132
J Cell Biol. 2026 Nov 02. pii: e202601003. [Epub ahead of print]225(11):

Avl9 defines a family of DENN domain GTPase-activating proteins.

Ryan C Vignogna, J Christopher Fromme.

Ras-related GTPases are molecular switches regulating hundreds of signaling and trafficking pathways in cells. Many GTPase regulators remain to be identified despite extensive genetic and biochemical screens. Here we present the results of computational protein-protein interaction screens and functional experiments identifying the DENN domain protein Avl9 as a GTPase-activating protein for Arf1. Avl9 is involved in secretion and cell migration, but its molecular function has not been characterized. We determined that Avl9 possesses robust Arf-GAP activity and is recruited to secretory vesicles by Rab8. We find that Avl9 GAP function is conserved in humans and enhances cell migration. We propose that several other DENN domain proteins are also candidate GAPs, and we demonstrate that one candidate previously characterized as a Rab-GEF, DENND6A, exhibits strong Arf-GAP activity toward ARL8B, explaining its role in lysosome positioning. Collectively, this work uncovers a family of monomeric "DENN GAP" proteins that regulate diverse cell biological pathways.

DOI: https://doi.org/10.1083/jcb.202601003
Mol Neurodegener. 2026 Sep 10. pii: 55. [Epub ahead of print]21(1):

Retromer-targeted therapy for neurodegenerative diseases.

Michele Persico, Sophronea Tuithung, Alejandra Lorenzo, Darynaisha Crawford, Simona Eleuteri, David K Simon.

  Alzheimer's disease (AD), Parkinson's disease (PD), and Amyotrophic Lateral Sclerosis (ALS) are neurodegenerative diseases characterized by dysfunction of the endosomal-lysosomal system (ELS). Four shared neurodegenerative mechanisms across ALS, PD and AD are regulated by the ELS, namely proteostasis and related protein misfolding, mitochondrial function, neurotransmission and neuroinflammation. These mechanisms are interconnected, contributing to neurodegeneration in a "snowball" manner. The retromer, a multimeric, evolutionarily conserved protein complex involved in intracellular protein trafficking, is at the crossroad of these neurodegenerative processes. This narrative review focuses on exploring the retromer structure, function as a master regulator of the ELS, and how this impacts proteostasis, mitochondrial biogenesis and homeostasis, neurotransmission and neuroinflammation across neurodegenerative diseases. We explore how alterations in retromer function can play an important role in neurodegeneration and discuss the impact of genetic and pharmacological manipulations of VPS35, one of the main retromer subunits. In vitro and in vivo studies have identified that the retromer enhances the activity of protein degradation pathways via the ELS, namely macroautophagy, chaperone-mediated autophagy, and the ELS itself, with concomitant reduction in misfolded protein levels. Also, in some model systems, when the retromer role is enhanced or restored, mitochondrial function is rescued, dysfunctional neurotransmission is restored, and the damaging effects of neuroinflammation are dampened. Lastly, we highlight the role of a novel pharmacological class of agents that enhance retromer function as a strategy for potentially slowing the progression of these neurodegenerative diseases in in vivo models of PD and ALS. We discuss the challenges in targeting the retromer, current limitations and potential off-target effects of retromer enhancement. Overall, the retromer regulates shared mechanisms across neurodegenerative diseases and retromer enhancers could represent a novel disease-modifying strategy in AD, PD and ALS.

Keywords:  Alzheimer’s disease; Amyotrophic lateral sclerosis; Neurodegeneration; Parkinson’s disease; Retromer; Therapy

DOI:  https://doi.org/10.1186/s13024-026-00971-z
Exp Neurol. 2026 Sep 11. pii: S0014-4886(26)00389-4. [Epub ahead of print] 116022

Midbrain organoids as next-generation models for Parkinson's disease: From pathogenesis to therapeutic discovery.

Dai-Yi Jiang, Shun-Yu Yao, Miao-Qiao Du, Lan-Xin Lin, Xu-Hui Kang, Yong Peng.

  Parkinson's disease (PD) is characterized by selective degeneration of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc) and pathological aggregation of α-synuclein. Traditional two-dimensional (2D) cell cultures and animal models have provided valuable insights but fail to recapitulate the cellular architecture and pathophysiology of the human midbrain. Three-dimensional (3D) midbrain organoids self-organize into neural structures that mimic key aspects of human midbrain development and disease pathology. This review examines midbrain organoid-based PD modeling through a concept-driven lens, addressing five questions: (i) Which aspects of PD can organoids model? (ii) How are technological advances reshaping the field? (iii) How do organoids complement existing model systems? (iv) What are the current limitations, and how can they be addressed? (v) What is the path toward clinical translation? Organoids reliably reproduce mitochondrial and lysosomal dysfunction and, in SNCA triplication models, α-synuclein accumulation, but seldom progressive neurodegeneration or mature Lewy pathology. By distinguishing established findings from emerging technologies and providing a realistic assessment of current limitations, this review offers a framework for prioritizing organoid applications in PD research and translation.

Keywords:  Cell therapy; Disease modeling; Dopaminergic neurons; Drug discovery; Induced pluripotent stem cells; Midbrain organoids; Parkinson's disease

DOI:  https://doi.org/10.1016/j.expneurol.2026.116022
Traffic. 2026 Sep;27(3): e70054

Investigating Translocation Mechanisms of TDP-43 Into the Endoplasmic Reticulum Using Budding Yeast Models.

Miku Saito, Hana Tsuzuki, Akira Hosomi.

  Signal peptides direct secretory and membrane proteins to the endoplasmic reticulum (ER), but proteins lacking classical signal peptides can occasionally engage the ER translocation machinery. TDP-43 is a nuclear RNA-binding protein implicated in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 pathology has been linked to extracellular TDP-43 species, association with the ER luminal oxidoreductase PDI, and ER stress-related phenotypes, yet whether TDP-43 fragments can directly access the ER lumen remains unclear. Here, we used budding yeast to examine signal peptide-independent ER entry of TDP-43. C-terminal fragments of TDP-43 acquired N-glycans in ste24Δ cells, whereas full-length TDP-43 showed little detectable ER entry. Endo H digestion confirmed N-glycosylation of the fragments, and a protease protection assay supported ER luminal localization of TDP-43(Δ2-89). ER entry was reduced by sec61-41 and sec66Δ, indicating engagement of a Sec61/Sec66-dependent translocation pathway. Deletion analyses identified opposing sequence elements: residues 320-343 facilitated ER entry, whereas an N-terminal region upstream of the nuclear localization signal suppressed it. TDP-43(Δ2-89) also accessed the secretory pathway, and selected disease-associated variants caused Ire1-dependent growth vulnerability without increasing detectable ER translocation. These findings reveal a Ste24-suppressed route for noncanonical ER entry of TDP-43 fragments.

Keywords:  Ste24; TDP‐43; endoplasmic reticulum; signal peptide; translocon; yeast

DOI:  https://doi.org/10.1111/tra.70054
Stem Cells Transl Med. 2026 Aug 18. pii: szag070. [Epub ahead of print]15(9):

Reduced mechanical shear is associated with early cortical differentiation and GDNF-GFRA1/RET signalling in human brain organoids.

Zizhen Zhao, Jingran Du, Shan Zhang, Haowen Shi, Hui Chen, Hong Cheng, Lihua Zhou, Chenju Yi, Jiachuan Wang.

  Early cortical differentiation in human brain organoids is a critical step of corticogenesis, but remains poorly coordinated under conventional culture conditions. In a standard orbital shaker system, mechanical shear and variability in extracellular matrix support, can disrupt neuroepithelial organisation, leading to inconsistent early cortical differentiation. Here, we investigated how ClinoStar-associated low-shear culture conditions affect early corticogenic marker expression in brain organoids and examined GFRA1/RET-related signaling as a candidate pathway associated with these culture-related effects. Using a low-shear ClinoStar bioreactor, we observed improved neuroepithelial-like expansion, enhanced tissue organisation, and promoted early cortical differentiation during the neuroepithelial expansion stage. Compared with conventional conditions, low-mechanical shear in ClinoStar was associated with increased proliferation capacity and supported the number of TBR2+ intermediate progenitors and TBR1+ early cortical neurons. Transcriptomic analysis revealed enrichment of neuronal differentiation and neuroactive ligand-receptor interaction pathways, with increased upregulation of GDNF signalling components under reduced mechanical shear. Functional experiments showed that GDNF supplementation increased TBR2+ intermediate progenitor-associated and TBR1+ early neuronal marker-related populations in brain organoids, suggesting a positive effect on early corticogenic marker expression. Consistent with this, GFRA1/RET levels were elevated in organoids in the ClinoStar culture with low-mechanical shear stress, and manipulation of GFRA1 affected early cortical differentiation outcomes. These findings suggest that ClinoStar low-shear culture promoted early corticogenic marker expression, potentially associated with GDNF-GFRA1/RET signalling. Collectively, this study provides a refined culture framework for improving the reproducibility and structural organisation of human brain organoid models of early cortical differentiation.

Keywords:  GDNF receptor; brain organoid; early cortical differentiation; low-shear culture; neuroepithelial expansion

DOI:  https://doi.org/10.1093/stcltm/szag070
Curr Biol. 2026 Sep 07. pii: S0960-9822(26)00936-X. [Epub ahead of print]36(17): R953-R955

Neuronal polarity: Opposing actin networks drive transient polarization.

Maria S J Braem, Lukas C Kapitein.

How does a neuron develop only one axon? A recent study shows that axon specification is preceded by an oscillatory programme in which actin waves periodically discharge from the cell body into individual neurites, transiently overcoming contractility. This local-activation, global-inhibition mechanism ensures only one neurite at a time can grow.

DOI: https://doi.org/10.1016/j.cub.2026.07.037
Autophagy. 2026 Sep 09.

Spatiotemporal control of Atg9 vesicle fusion in autophagosome formation.

Takumi Kimura, Tetsuya Kotani, Hitoshi Nakatogawa.

  Atg9 vesicles serve as membrane seeds for autophagosome formation. These vesicles are derived from the Golgi/endosomes and localized to the pre-autophagosomal structure or phagophore assembly site (PAS) upon autophagy induction. How these vesicles are maintained as discrete membrane carriers while diffusing through the cytoplasm and subsequently become competent for downstream events at the PAS has remained unknown. Here, we show that the Atg9-interacting protein Atg23 remains associated with Atg9 vesicles following their formation and protects them from inappropriate fusion with endomembranes during their movement through the cytoplasm. Upon arrival at the PAS, Atg1-mediated phosphorylation of Atg9 triggers the dissociation of Atg23, thereby enabling efficient recruitment of the lipid-transfer protein Atg2. Collectively, these findings define a spatiotemporally regulated mechanism in which Atg23 preserves Atg9 vesicles during cytoplasmic transport, whereas its dissociation enables their productive utilization in autophagosome formation.

Keywords:  Atg9; Phosphorylation-dependent regulation; autophagosome; membrane trafficking; vesicle coating; yeast

DOI:  https://doi.org/10.1080/15548627.2026.2730073
Gene Ther. 2026 Sep 05.

Culture media alter retinal organoid physiology promoting AAV transduction and retinal ganglion cell survival.

Michelle O'Hara-Wright, Benjamin Y Lim, Melissa M Mangala, Vivienne Kaiser, Emilie Wong, Deborah Aubin, Victoria Nemeruck, Hallur Reynisson, Fatemeh Doroudian, Otilia P Y Chan, Nader Aryamanesh, Joao A Paulo, Stefano Palomba, Mehdi Mirzaei, Samantha L Ginn, Anai Gonzalez-Cordero.

Human iPSC-derived retinal organoids offer a human-relevant platform for inherited retinal disease (IRD) gene therapy, yet robust AAV transduction in vitro remains challenging. Here we show that culture in BrainPhys™ (BP) medium markedly enhances AAV-mediated gene delivery. Brief BP exposure during the transduction window improves uptake, whereas continuous BP culture yields the strongest effects, indicating contributions from acute entry processes and longer-term cellular remodelling. Quantitative proteomics reveal coordinated upregulation of viral entry and trafficking mediators, including integrins that form αVβ5, and the trans-Golgi entry factor GPR108, together with enrichment of endosomal/ER-Golgi transport proteins, providing a mechanistic basis for enhanced vector processing. BP concurrently promotes neuronal maturation and metabolism, with pronounced increases in neurotrophic and synaptic proteins and broad enhancement of oxidative phosphorylation components. Functional calcium imaging demonstrates comparable neuronal dynamics across conditions but reveals robust, recurrent network-level bursts under BP, consistent with strengthened connectivity. BP also preserves retinal ganglion cells and maintains expression of canonical markers, aligning with a BDNF-centred interactome and improved circuit integration. Collectively, these findings identify the culture environment as a critical determinant of AAV efficacy in human retinal tissue models and position BP as a simple, scalable strategy to reduce vector requirements, enhance retinal cells targeting, and increase the fidelity of organoid-based non-animal testing for IRD gene therapy development.

DOI: https://doi.org/10.1038/s41434-026-00642-0
Comput Biol Med. 2026 Sep 05. pii: S0010-4825(26)00486-5. [Epub ahead of print]215 111921

Brain organoids, high-density MEAs, and deep learning: A new paradigm for functional neurobiomarker discovery.

Meesala Krishna Murthy.

  Biomarker discovery, essential in neuroscience research, has traditionally been based on static molecular omics, which frequently reveal established pathogenesis at the network level when irreversible structural damage occurs. In this review, the paradigm shift of functional "digital phenotyping" is discussed, along with its implementation by combining human induced pluripotent stem cell (hiPSC)-derived brain organoids with high-density multielectrode arrays (HD-MEAs). Researchers can use advanced architecture deep learning (DL) algorithms, such as Convolutional and Graph Neural Networks, to identify predictive signatures of diseases at the network level by separating complex spatiotemporal dynamics in firing patterns. These digital functional biomarkers can their ability to detect abnormal burst kinetics, abnormal oscillatory coupling, and abnormal functional connectomes before the onset of structural cell loss. Moreover, we discuss the underlying methods of artificial intelligence (AI) analysis and advances in phenotypic drug discovery using organoid electrophysiology, changing the paradigm of therapeutic targeting from the clearance of molecular aggregates to the functional recuperation of neural circuit health. In conclusion, a combination of powerful 3D culture technology, state-of-the-art microelectronics, and machine learning offers an extensive novel translational platform for dissecting early neurodevelopmental and neurodegenerative diseases, ultimately driving precision therapeutic approaches for the brain and other organs.

Keywords:  Brain organoids; Deep learning; Digital phenotyping; High-density MEA; Network electrophysiology

DOI:  https://doi.org/10.1016/j.compbiomed.2026.111921