bioRxiv Subject Collection: Neuroscience's Journal
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Sunday, September 14th, 2025
| Time |
Event |
| 7:31a |
Interpreting convolutional neural networks to study wide-field amacrine cell inhibition in the retina
Wide-field amacrine cells (ACs) play a unique role in retinal processing by integrating visual information across a large spatial area. Their inhibitory influence has been implicated in multiple retinal functions such as differential motion detection and the suppression of retinal activity during eye movements. However, a coherent understanding of their general function is lacking due to difficulties in directly recording from these cells and identifying effective visual stimuli to activate them. In this study, we used convolutional neural networks (CNNs) to investigate wide-field inhibition mediated by wide-field ACs in the marmoset retina. We trained CNNs to mimic the function of the retina by predicting retinal ganglion cell (RGC) population responses to naturalistic movie stimuli and optimising the most exciting inputs (MEIs) to visualise RGCs' receptive field (RF) structures. We then optimized suppressive surrounds beyond classical RGC RF boundaries, intended to capture the inhibitory effect of wide-field ACs on RGC activity. These optimized surrounds reduced MEI-elicited activity by 10% to 30%, demonstrating that CNNs not only mimic retinal responses but can also reveal hidden computational aspects of wide-field inhibition. However, suppression strength and generalization varied across architectures and datasets, indicating potential model-specific effects, highlighting the importance of cautious interpretation. Overall, our approach illustrates how interpretability methods applied to artificial neural networks can offer new hypotheses regarding biological retinal computation, paving the way for targeted experimental validation. | | 9:30a |
In vivo single-cell gene editing using RNA electroporation reveals sequential adaptation of cortical neurons to excitatory-inhibitory imbalance
The balance between excitatory and inhibitory neurotransmission is fundamental for normal brain function, yet the adaptation of individual neurons to disrupted excitatory-inhibitory balance is not well understood. We developed highly efficient, in vivo RNA electroporation-based single-cell gene editing to investigate neuronal responses to loss of fast inhibition. Using CRISPR-Cas9 components delivered as RNA, we knocked out GABA-A receptor {beta} subunits in individual layer 2/3 cortical neurons in mouse visual cortex, eliminating fast inhibition. In vivo patch-clamp recordings revealed that cortical neurons adapted to inhibition loss through two sequential mechanisms: a transient reduction of excitatory synaptic input, followed by intrinsic membrane property changes that decreased input resistance. This sequential adaptation program ultimately prevented target neurons from contributing spikes to the cortical network. Our RNA-based single-cell gene editing approach enables investigation of cellular responses independent of network effects, providing new insights into neuronal homeostasis and gene function in individual cells in vivo. | | 9:30a |
Dual role of GABAB receptor in oligodendrocyte function and immune modulation in experimental multiple sclerosis
GABAB receptors (GABABR) mediate the actions of the inhibitory neurotransmitter GABA in the central nervous system, regulating key processes such as synaptic activity, interneuron communication and excitation-inhibition balance in the brain. Recent studies using the GABABR agonist baclofen have revealed a critical role for these receptors in promoting oligodendroglial differentiation in both health and disease, highlighting their potential as therapeutic targets in demyelinating diseases such as multiple sclerosis (MS). In this study, we identify a dual role for oligodendroglial GABABR in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. Conditional deletion of the GABAB1 subunit in NG2+ cells ameliorates acute disease symptoms while inducing an immune-like phenotype in oligodendrocytes. This immunomodulatory role is further supported by pharmacological activation of GABABR in oligodendrocytes, which reduces the expression of MHC class II in these cells. Notably, baclofen treatment after EAE symptom onset attenuates the course of the disease while enhancing oligodendrocyte progenitor cell differentiation and suppressing T cell infiltration into demyelinating lesions. Moreover, prophylactic baclofen administration delays disease onset and further decreases immune cell recruitment into the spinal cord, underscoring its potent immunomodulatory effect. These data demonstrate that GABABR signaling exerts context-dependent effects on both oligodendrocyte lineage progression and neuroinflammatory responses. Importantly, these compelling findings validate baclofen, a drug already approved for MS-associated spasticity, as a promising candidate for therapies targeting both inflammation and remyelination, advancing our understanding of glial-immune interactions in demyelinating diseases and supporting the translational potential of GABABR modulation in MS. | | 9:30a |
Lysosomal multi-omics reveals altered sphingolipid catabolism as driver of lysosomal dysfunction in the aging brain.
Recent data indicate that lipid composition has profound influence on the brain function and that changes in lipid homeostasis affect brain aging and predisposition to neurodegenerative diseases. Lipids dynamically reside in multiple intracellular locations and their organellar distribution is important for specific interactions and biological function. During brain aging lipid changes have been specifically noted in lysosomes, but the identity of the accumulated lipids, their interactions with other biomolecules such as proteins, and their functional relevance have not been characterized. We used mass spectrometry (MS) to assess longitudinal changes in the lipidome and proteome of lysosomes isolated from the mouse cortex, from the age of 3- to 24-months. Our statistical and machine learning analyses identified two factors demonstrating predictive power for age and differences in both lipids and proteins. Of these, factor 1 was the best predictor of sample age. Factor 1 lipids with the highest feature importance included multiple species of hexosylceramides (HexCer) and their sulfonated derivatives, sulfatides (SHexCer), all of which increased with age. Increased factor 1 proteins included myelin proteins, select sphingolipid catabolism enzymes and proteins associated with lysosomal storage diseases. Our analyses suggested that mechanisms underlying factor 1 encompass the combination of an age-dependent increase in lysosomal delivery of myelin components and alterations in lysosomal sphingolipid catabolism favoring degradation of sphingomyelin over HexCer. The overall age-related lysosomal changes resembled those observed in lysosomal storage diseases, particularly Gaucher disease, where accumulation of HexCer species is associated with lysosomal dysfunction. To corroborate factor 1 predictions, we employed a combination of biochemical, imaging and flow cytometry approaches, which confirmed alterations in sphingolipid catabolism and lysosomal accumulation of myelin components. These changes were associated with age-related alteration in lysosomal morphology, lysosomal dysfunction and inhibition of autophagy in both neurons and microglia. Our findings indicate that factors contributing to lysosomal aging resemble those observed in lysosomal storage diseases and underscore the significance of organelle-specific analyses for dissecting mechanisms contributing to brain aging. | | 9:30a |
Beyond Locomotion: How Specialized Motor Rhythms Enable Vertebrate Escape from Capture
Escape behaviors following capture are crucial for survival, yet their underlying neurobiological mechanisms remain poorly understood. We investigated how Xenopus laevis tadpoles use struggling movements to escape head restraint. High-speed video tracking revealed a stereotyped sequence of body flexions with distinct kinematics during capture and release. We further recorded motoneuron and motor nerve activity along the body axis during fictive struggling to reconstruct biologically realistic struggling commands, to drive the movement of a biomechanically detailed tadpole model. Simulations showed that struggling - characterized by long-duration, low-frequency, caudorostral muscle activation -was optimized to generate escape forces. Notably, hydrodynamic thrust alone proved insufficient for release. However, direct mechanical interactions between the tadpole body and the restraining object generated additional reactive forces that facilitated escape. These findings demonstrate how animals use coordinated motor outputs and body mechanics to interact with environment to generate maximal freeing forces as the fundamental escape strategy. | | 5:33p |
Dysregulation of energy metabolism and calcium homeostasis in iPSC-derived neurons carrying Presenilin-1 M146L gene mutation
Impaired cellular activities, particularly in highly active cells such as neurons, are primarily supported by metabolic abnormalities and failures in Ca2+; homeostasis. Here, we provide an integrative analysis of human iPSC-derived neurons (iNs) carrying the Presenilin-1 M146L gene mutation (PS1M146L) and control cells (PS1control). PS1M146L iNs exhibited abnormal Ca2+; dynamics, a significant increase in key parameters of mitochondrial respiration, and higher intracellular ROS levels. KCl-evoked depolarisation was significantly lower in PS1M146L, suggesting a failure in maintaining the electrochemical gradient across the plasma membrane. Following thapsigargin stimulation, mitochondrial Ca2+ levels ([Ca2+]m) were significantly reduced in PS1M146L, while [Ca2+]m did not differ significantly between genotypes after treatment with bradykinin, suggesting that impairments in the [Ca2+]m homeostasis are particularly evident under stress conditions and do not impact the 1,4,5-triphosphate (IP3) pathway. Since iNs of both genotypes were sensitive to the MCU-1 inhibitor, the deficits observed in PS1M146L could be the consequence of impairments in the ER-mitochondria contacts. Our results illustrate the utility of iNs carrying PS1 mutations in understanding how human neurons alter relevant pathways before neurodegeneration. | | 5:33p |
Maximized field-of-view deep-brain calcium imaging through gradient-index lenses
Advances in genetically encoded fluorescent indicators have enabled increasingly sensitive optical recordings of neural activity. However, light scattering in the mammalian brain tissue restricts optical access to deeper regions. To address this limitation, researchers often employ implanted gradient-index (GRIN) lenses to reach deep brain areas. Nevertheless, the severe optical aberrations of GRIN lenses significantly reduce the effective field of view (FOV). In this work, we present a simple and robust imaging approach that combines low-NA telecentric scanning (LNTS) of laser excitation with high-NA fluorescence collection to increase the FOV. This configuration effectively eliminates common aberrations such as astigmatism and field curvature, resulting in a FOV ~100% as large as the GRIN lens facet area ?corresponding to a ~400% increase in imaging area compared with conventional approaches. We validate this method through both structural and functional in vivo imaging. The highly consistent imaging performance, fully maximized imaging FOV, and the very simple optical design make this method well-suited for broad dissemination in neuroscience research. | | 5:33p |
Granularity of thalamic head direction cells
Head direction signaling is fundamental for spatial orientation and navigation. The anterodorsal nucleus of the thalamus (ADn) contains a high density of head direction (HD) cells that process sensorimotor inputs for subsequent synaptic integration in postsynaptic cortical areas. We tested the hypothesis that individual HD cells show differences in their firing patterns and connectivity by recording and juxtacellularly labeling single HD cells in subregions of the ADn in awake mice during passive rotation. We identified HD cells that exhibited different response profiles to light, sound, and movement. We also identified a mediolateral gradient of calretinin-expressing (CR+) ADn cells, with CR+ HD cells having narrower tuning widths, lower maximal firing rates, and different intrinsic properties compared to CR- cells. Axons of labeled HD cells could be followed to the retrosplenial cortex, with collaterals innervating the thalamic reticular nucleus (type I cells); others additionally innervated the dorsomedial striatum (type II cells). Most medial CR+ cells preferentially projected to ventral retrohippocampal regions. Surprisingly, we also identified a subpopulation of medial CR+ cells with twisted dendrites and descending axons that avoided the thalamic reticular nucleus, termed tortuosa HD cells (type III cells). We conclude that HD cells of the mouse ADn comprise distinct cell types, providing parallel head-direction-modulated sensorimotor messages to synaptic target neurons within the head direction network. | | 5:33p |
Stage-specific extracellular vesicle cargo from Schwann cells orchestrates peripheral nerve regeneration
Schwann cells (SCs) play a critical role in peripheral nerve regeneration, undergoing dynamic phenotype transitioning from myelinating to repair stages following injury. While SC-derived extracellular vesicles (SC-EVs) have emerged as key mediators of intercellular communication during nerve repair, their stage-specific molecular cargo and functional roles remained incomplete understood. Here, we delineate protein, microRNA and lncRNA landscapes of SC-EVs across distinct differentiation stages, including immature, myelinating, and repair phenotypes, using an in vitro model of primary rat SCs. We show that myelinating SC-EVs are enriched with reprogramming factor SOX2 and neurotrophin receptor p75NTR, while repair SC-EVs carry distinct microRNAs predicted to modulate genes involved in myelin ensheathment, neuronal differentiation and neurogenesis. Moreover, repair SC-EVs contain long non-coding RNAs (lncRNAs) that may regulate miRNA activity. These findings reveal a novel mechanism by which SC-EVs orchestrate neuronal regeneration through stage-specific molecular cargo, and establishes a foundational model for investigating SC plasticity in peripheral nerve repair. |
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