bioRxiv Subject Collection: Neuroscience's Journal

In vitro 2 In vivo : Bidirectional and High-Precision Generation of In Vitro and In Vivo Neuronal Spike Data
Neurons encode information in a binary manner and process complex signals. However, predicting or generating diverse neural activity patterns remains challenging. In vitro and in vivo studies provide distinct advantages, yet no robust computational framework seamlessly integrates both data types. We address this by applying the Transformer model, widely used in large-scale language models, to neural data. To handle binary data, we introduced Dice loss, enabling accurate cross-domain neural activity generation. Structural analysis revealed how Dice loss enhances learning and identified key brain regions facilitating high-precision data generation. Our findings support the 3Rs principle in animal research, particularly Replacement, and establish a mathematical framework bridging animal experiments and human clinical studies. This work advances data-driven neuroscience and neural activity modeling, paving the way for more ethical and effective experimental methodologies.

Single-dose administration of therapeutic divalent siRNA targeting MECP2 prevents lethality for one year in an MECP2 duplication mouse model
MECP2 duplication syndrome (MDS) is a rare X-linked neurodevelopmental disorder caused by duplications of the dosage-sensitive methyl-CpG-binding protein 2 (MECP2) gene. Developing effective therapies for MDS is particularly challenging due to the variability in MECP2 expression among patients and the potential risk of inducing Rett syndrome through excessive pharmacological intervention. Reducing dosage to optimize silencing levels often compromises durability and necessitates increased dosing frequency. We present here a series of fully chemically modified small interfering RNAs (siRNAs) designed for both isoform-selective and total MECP2 silencing. Among these, we identify six lead siRNA candidates across two distinct chemical scaffolds, achieving targeted total MECP2 expression reductions ranging from 25% to 75%, sustained for at least four months following a single administration. The efficacy and safety of human ortholog silencing were evaluated using two mouse models with distinct levels of human MECP2 transgene expression. In the severe duplication model, a single dose of the total isoform-silencing siRNA fully rescued early mortality and behavioral impairments. Additionally, we show that the isoform-selective targeting strategy may be safer in mild cases of MDS where exaggerated pharmacology may lead to Rett Syndrome. Overall, this study introduces a series of preclinical candidates with the capacity to address the varying levels of MECP2 duplication encountered in clinical settings. Furthermore, it establishes a target selection strategy that may be applied to other dosage-sensitive gene imbalances.

Familial ALS/FTD-associated RNA-Binding deficient TDP-43 mutants cause neuronal and synaptic dysregulation in vitro
TDP-43 is an RNA-binding protein constituting the pathological inclusions observed in ~95% of ALS and ~50% of FTD patients. In ALS and FTD, TDP-43 mislocalises to the cytoplasm and forms insoluble, hyperphosphorylated and ubiquitinated aggregates that enhance cytotoxicity and contribute to neurodegeneration. Despite its primary role as an RNA/DNA-binding protein, how RNA-binding deficiencies contribute to disease onset and progression is little understood. Among many identified familial mutations in TDP-43 causing ALS/FTD, only two mutations cause an RNA-binding deficiency, K181E and K263E. In this study, we used CRISPR/Cas9 to knock-in the two disease-linked RNA-binding deficient mutations in SH-SY5Y cells, generating both homozygous and heterozygous versions of the mutant TDP-43 to investigate TDP-43-mediated neuronal disruption. Significant changes were identified in the transcriptomic profiles of these cells, in particular, between K181E homozygous and heterozygous cells, with the most affected genes involved in neuronal differentiation and synaptic pathways. This result was validated in cell studies where the neuronal differentiation efficiency and neurite morphology were compromised in TDP-43 cells compared to unmodified control. Interestingly, divergent neuronal regulation was observed in K181E-TDP-43 homozygous and heterozygous cells, suggesting a more complex signalling network associated with TDP-43 genotypes and expression level which warrants further study. Overall, our data using cell models expressing the ALS/FTD disease-causing RNA-binding deficient TDP-43 mutations at endogenous levels show a robust impact on transcriptomic profiles at the whole gene and transcript isoform level that compromise neuronal differentiation and processing, providing further insights on TDP-43-mediated neurodegeneration.

Computational Mechanisms of Temporal Anticipation in Perception and Action
To interact effectively with our surroundings, we rely on strategies to reduce uncertainty. One important source of information is temporal regularities, which enable us to form predictions about when events will occur, and through this, prepare for them in advance. Such preparation was shown to facilitate motor planning, yet the impact of temporal anticipation on perceptual acuity is unknown, and the cognitive computations underlying this process remain debated. To answer these questions, we administered a new difficult change discrimination task with variable anticipatory periods (N=142). We show that both perceptual sensitivity and motor responses are influenced by temporal structure. Using computational modelling, we show that the cognitive operation underlying this behavior is based on a logarithmic transformation of the event hazard rate (HR) and reveal a crucial role of temporal-estimation noise in shaping this computation, both when temporal information is encoded, and when it is decoded. Together, our results highlight the fundamental contribution of anticipation in directing behavior and advance our understanding of temporal processing in the brain.

Temporal and Spatial Scales of Resting-state Human Cortical Activity Throughout Lifespan
Sensorimotor and cognitive abilities undergo substantial changes throughout the human lifespan, but the corresponding changes in the functional properties of cortical networks remain poorly understood. This can be studied using temporal and spatial scales of functional magnetic resonance imaging (fMRI) signals, which provide a robust description of the topological structure and temporal dynamics of neural activity. For example, timescales of resting-state fMRI signals can parsimoniously predict a significant amount of the individual variability in functional connectivity networks identified in adult human brains. In the present study, we quantified and compared temporal and spatial scales in resting-state fMRI data collected from 2,352 subjects between the ages of 5 and 100 in Developmental, Young Adult, and Aging datasets from Human Connectome Project. For most cortical regions, we found that both temporal and spatial scales largely decreased with age across most cortical areas throughout the lifespan, with the visual cortex and the limbic network consistently showing the largest and smallest scales, respectively. For some prefrontal regions, however, these two scales displayed non-monotonic trajectories during adolescence and peaked around the same time during adolescence and decreased throughout the rest of the lifespan. We also found that cortical myelination increased monotonically throughout the lifespan, and its rate of change was significantly correlated with the changes in both temporal and spatial scales across different cortical regions in adulthood. These findings suggest that temporal and spatial scales in fMRI signals, as well as cortical myelination, are closely coordinated during both development and aging.

Dissecting the cortical stages of invariant word recognition
Fluent reading requires the brain to precisely encode the positions of letters within words, distinguishing for instance FORM and FROM across variations in size, position, and font. While early visual areas are known to encode retinotopic positions, how these representations transform into invariant neural codes remains unclear. Building on a computational model of reading, we used 7T fMRI and MEG to reveal a cortical hierarchy in which early visual areas (V1-V4) predominantly encode retinotopic information, whereas higher-level regions, including the Visual Word Form Area (VWFA), transition to an ordinal letter-position code. MEG analyses confirm that retinotopic encoding emerges early (60-200 ms), followed by a shift toward ordinal representations in later time windows (220-450 ms). Despite this transition, word position remained a dominant factor across all time points, suggesting a concurrent coding of both retinotopic and abstract positional information. These findings uncover the spatiotemporal dynamics by which the human brain transforms visual input into structured linguistic representations, shedding light on the cortical stages of reading and their developmental and clinical implications.

Polygenic Associations between Motor Behaviour, Neuromotor Traits, and Active Music Engagement in Four Cohorts
Phenotypic investigations have shown that actively engaging with music, i.e., playing a musical instrument or singing may be protective of motor decline in aging. For example, music training associated with enhanced sensorimotor skills accompanied by changes in brain structure and function. Although it is possible that the benefits of active music engagement "transfer" to benefits in the motor domain, it is also possible that the genetic architecture of motor behaviour and the motor system structure may influence active music engagement. This study investigated whether polygenic scores (PGS) for five behavioural motor traits, 12 neuromotor structural brain traits, and seven rates of change in brain structure traits trained from existing discovery genomewide association studies (GWAS) predict active music engagement outcomes in four independent cohorts of unrelated individuals of European ancestry: the Canadian Longitudinal Study on Aging (CLSA; N=22,198), Wisconsin Longitudinal Study (WLS; N=4,605), Vanderbilts BioVU Repository (BioVU; N=6,150), and Vanderbilts Online Musicality study (OM; N=1,559). Results were meta-analyzed for each PGS main effect across outcomes and cohorts, revealing that PGS for a faster walking pace was associated with higher amounts of active music engagement. Within CLSA, a higher PGS for walking pace was associated with greater odds of engaging with music. Findings suggest a shared genetic architecture between motor function and active music engagement. Future intervention-based research should consider the genetic underpinnings of motor behavior when evaluating the effects of music engagement on motor function across the lifespan.

Characterizing Complex Upper Limb Movements with and without Visual Feedback in Typically Developing Children
The development of upper limb movements has been primarily described through reaching movements, which may not have the complex motor planning and execution demands of many daily tasks. In this study, we introduced a complex task in which individuals had to navigate their hand from a start target through two openings in a simple maze to reach an end target. In half the trials, participants received visual feedback of their hand position, and in half of the trials they did not. Thirty-one participants ages 8 to 17 years completed the study. We found that with visual feedback, reaction time, number of speed peaks, movement time, and hand path length all decreased with age. Number of speed peaks, movement time, and hand path length were all increased without visual feedback, however, the impact of removing visual feedback was greatest on the younger children and decreased with age. Our results demonstrate that complex upper limb movements are refined across childhood and adolescence, with a decreasing reliance on visual feedback likely due to increasing feedforward control and improved ability to use proprioceptive feedback. This task can be applied to clinical populations such as cerebral palsy to assess impairments in motor planning and execution as well as determine how proprioceptive impairments contribute to complex movements.

Progressive remote memory decline coincides with parvalbumin interneuron hyperexcitability and enhanced inhibition of cortical engram cells in a mouse model of Alzheimers disease
Patients with Alzheimers disease (AD) initially show temporally-graded retrograde amnesia, which gradually progresses into more severe retrograde amnesia. Although mouse models of AD have provided insight into neurobiological mechanisms contributing to impaired formation and retrieval of new memories, the process underlying the progressive loss of remote memories in AD has remained elusive. Here, we demonstrate age-dependent remote memory decline in APP/PS1 mice, which coincides with progressive hyperexcitability of parvalbumin (PV) interneurons in the medial prefrontal cortex (mPFC). Analysis of Fos expression showed that the remote memory deficit is not mirrored by changes in reactivation of memory-encoding neurons, so-called engram cells, nor PV interneuron (re)activation, in the mPFC. However, inhibitory input is enhanced onto engram cells compared to non-engram cells specifically in APP/PS1 mice. Our data indicate that age-dependent remote memory impairment in APP/PS1 mice is due to increased innervation of cortical engram cells by hyperexcitable PV interneurons, suggesting that dysfunctional inhibitory microcircuits in the neocortex mediate progressive retrograde amnesia in AD.

Goal-directed visual information processing with GABAergic inhibition in parietal cortex
Goal-directed visual information processing involves tracking relevant visual signals (targets) over space and time. However, goal-irrelevant visual signals (distractors) can interfere with the tracking of targets. The neuronal mechanisms, which promote the tracking of targets in the challenge of interference from distractors remain elusive. Here, we used time-resolved functional magnetic resonance spectroscopy (fMRS) to measure dynamic changes of {gamma}-aminobutyric acid (GABA), a chief inhibitory neurotransmitter, and glutamate, a chief excitatory neurotransmitter, in the parietal and visual cortices while participants performed a visual tracking task for targets among distractors. We found that the more targets had to be tracked, the greater the concentrations of GABA and glutamate in parietal cortex. In visual cortex only the concentration of glutamate increased with the number of tracking targets. Concentration changes of GABA and glutamate in parietal cortex only were differentially associated with performance: Better target tracking was associated with greater increase in GABA concentration and smaller increase in glutamate concentration. These results suggest that GABAergic inhibition in parietal cortex plays a crucial role in minimizing interference during target tracking over space and time, thereby promoting goal-directed visual information processing.

Circadian Variation in Salivary Oxytocin in pre-menopausal women
This brief report presents circadian variation in salivary oxytocin levels in a sample of 58 female participants, including 35 healthy controls and 23 patients with borderline personality disorder (BPD). A significant increase in salivary oxytocin levels was observed between awakening and early afternoon (between 1 and 2 PM) (F = 20.54, p < 0.001, partial eta squared = 0.27, 99% achieved power). There were no significant group differences and no Group by Time interaction. These findings have implication for research in the field and suggest the need to control for time of assessment, as done in studies assessing cortisol.

A Sensitive Period for the Development of Temporally Coherent Visual Cortical Processing in Humans: Evidence from Sight Recovery Following Congenital Cataracts
Typical cortical development requires early sensory experience. In humans who had suffered from a transient period of blindness due to dense bilateral congenital cataracts (CC), multiple investigations of cortical activation strength have suggested that extrastriate visual regions are especially vulnerable to aberrant early postnatal visual input. Yet, to date, how early experience might sculpt the temporal stability of human visual cortical processing has not been investigated. In CC individuals, we previously found a persistent and replicable reduction of the earliest event-related marker of extrastriate processing, the P1 wave. Here, we report that this robust reduction of the P1 in CC individuals results from an attenuated temporal coherence of cortical oscillations across trials, rather than from a generally reduced extrastriate cortical activation strength. In two experiments, compared to matched normally sighted controls, CC individuals (n = 12 and 13, respectively) exhibited diminished oscillatory phase coherence (i.e., higher temporal variability), rather than lower oscillatory amplitudes during visual processing. Furthermore, phase coherence information, but not activation strength, allowed classifying sight recovery individuals with congenital vs. developmental etiologies. Finally, exchanging the signal phase and activation strength information between CC and matched control individuals confirmed that group differences in P1 amplitude were largely driven by oscillatory timing. These group differences, specific to the CC group, were not found in groups of sight-recovery individuals who had suffered from developmental cataracts. Our results indicate that the intricate temporal orchestration of visual processing in human extrastriate cortex requires visual experience in an early postnatal sensitive period.

Material Damage to Multielectrode Arrays after Electrolytic Lesioning is in the Noise
The quality of stable long-term recordings from chronically implanted electrode arrays is essential for experimental neuroscience and brain-computer interfaces. This work uses scanning electron microscopy (SEM) to image and analyze eight 96-channel Utah arrays previously implanted in motor cortical regions of four subjects (subject H = 2242 days implanted, F = 1875, U = 2680, C = 594), providing important contributions to a growing body of long-term implant research leveraging this imaging technology. Four of these arrays have been used in electrolytic lesioning experiments (H = 10 lesions, F = 1, U = 4, C = 1), a novel electrolytic perturbation technique using small direct currents. In addition to surveying physical damage, such as biological debris and material deterioration, this work also analyzes whether electrolytic lesioning created damage beyond what is typical for these arrays. Each electrode was scored in six damage categories, identified from the literature: abnormal debris, metal coating cracks, silicon tip breakage, parylene C delamination, parylene C cracks, and shank fracture. This analysis confirms previous results that observed damage on explanted arrays is more severe on the outer-edge electrodes versus inner electrodes. These findings also indicate that are no statistically significant differences between the damage observed on normal electrodes versus electrodes used for electrolytic lesioning. This work provides evidence that electrolytic lesioning does not significantly affect the quality of chronically implanted electrode arrays and can be a useful tool in understanding perturbations to neural systems. Finally, this work also includes the largest collection of single-electrode SEM images for previously implanted multielectrode Utah arrays, spanning eleven different intact arrays and one broken array. As the clinical relevance of chronically implanted electrodes with single-neuron resolution continues to grow, these images may be used to provide the foundation for a larger public database and inform further electrode design and analyses.

Single-cell characterization of the human C2 dorsal root ganglion recovered from C1-2 arthrodesis surgery: implications for neck pain
Neurons in the dorsal root ganglion (DRG) receive and transmit sensory information from the tissues they innervate and from the external environment. Upper cervical (C1-C2) DRGs are functionally unique as they receive input from the neck, head, and occipital cranial dura, the latter two of which are also innervated by the trigeminal ganglion (TG). The C2 DRG also plays an important role in neck pain, a common and disabling disorder that is poorly understood. Advanced transcriptomic approaches have significantly improved our ability to characterize RNA expression patterns at single-cell resolution in the DRG and TG, but no previous studies have characterized the C2 DRG. Our aim was to use single-nucleus and spatial transcriptomic approaches to create a molecular map of C2 DRGs from patients undergoing arthrodesis surgery with ganglionectomy. Patients with acute (<3 months) or chronic ([≥]3 months) neck pain were enrolled and completed patient-reported outcomes and quantitative sensory testing prior to surgery. C2 DRGs were characterized with bulk, single nucleus, and spatial RNA sequencing technologies from 22 patients. Through a comparative analysis to published datasets of the lumbar DRG and TG, neuronal clusters identified in both TG and DRG were identified in the C2 DRG. Therefore, our study definitively characterizes the molecular composition of human C2 neurons and establishes their similarity with unique characteristics of subsets of TG neurons. We identified differentially expressed genes in endothelial, fibroblast and myelinating Schwann cells associated with chronic pain, including FGFBP2, C8orf34 and EFNA1 which have been identified in previous genome and transcriptome wide association studies (GWAS/TWAS). Our work establishes an atlas of the human C2 DRG and identifies altered gene expression patterns associated with chronic neck pain. This work establishes a foundation for the exploration of painful disorders in humans affecting the cervical spine.