bioRxiv Subject Collection: Neuroscience's Journal

Reduction of right-hemispheric auditory cortex activity in response to speech in more experienced paediatric cochlear implant users
In case of severe hearing loss early in life or congenital deafness, cochlear implants (CIs) represent the method of choice to restore hearing and enable language acquisition. While speech intelligibility has been shown to improve during the first year after implantation to then reach a plateau, the underlying neuroplastic changes are poorly understood. Here, we longitudinally compared the cortical processing of speech stimuli in a case-control design with two groups of pre-lingually deafened CI users (4.4 vs. 25.8 months of CI experience) and an age-matched control group with normal hearing (NH; mean group ages ~9 years). In two experiments, participants were presented with running speech and vowel sequences while fNIRS and EEG data were obtained simultaneously. Despite trends in this direction, cortical activity did not increase significantly with more CI experience and did not approach the higher levels observed in the NH controls. However, in the speech experiment, the less experienced CI group showed an abnormal shift of activity to the right hemisphere not observed in the other two groups. These results hence imply that adaptation to CI-based hearing is not characterised by a gradual increase of activity in left-hemispheric language network, but a reduction of abnormal activity elsewhere.

Microstructural Brain Correlates of Inter-individual Differences in Respiratory Interoception
Interoception, the perception and integration of physiological signals, is a fundamental aspect of self-awareness and homeostasis. While previous work has explored interoceptive processing in relation to the cardiac system, research in the respiratory domain, particularly in relation to brain structure and function, is limited. To address this gap, we utilised a Bayesian psychophysical model to quantify perceptual, metacognitive, and affective dimensions of respiratory interoception in a sample of 207 healthy participants. We also measured individual whole-brain microstructural indices of myelination, myeloarchitecture, and cortical iron using quantitative brain imaging. Voxel-based quantification analyses revealed distinct patterns of cortical microstructure in the insular, cingulate, and primary sensory cortices, which underpin interoceptive perceptual sensitivity and precision. In addition, metacognitive bias was associated with increased myelination of the cingulate cortex and periaqueductal grey, while metacognitive sensitivity correlated with myelination of the midline prefrontal cortex. At an affective level, sensitivity to respiratory resistance was related to the myelination of the primary somatosensory cortex. By revealing specific histological brain patterns tied to individual differences in respiratory interoception, our results uncover the neural pathways that govern perceptual, metacognitive, and emotional facets of interoceptive processing.

DNA aptamers that modulate biological activity of model neurons
There is an urgent need for agents that promote health and regeneration of cells and tissues, specifically to treat diseases of the aging nervous system. Age-associated nervous system degeneration and various diseases are driven by many different biochemical stresses, often making it difficult to target any one disease cause. Our laboratory has previously identified DNA aptamers with apparent regenerative properties in murine models of multiple sclerosis by selecting aptamers that bind oligodendrocyte membrane preparations. Here, we screened vast libraries of molecules(~10^14 unique DNAs) for the ability to bind cultured human SH-SY5Y neuroblastoma cells asmodel neurons to demonstrate the feasibility of identifying biologically active aptamers by cyclesof cell selection. Many of these DNA aptamers bind undifferentiated and differentiated culturedSH-SY5Y cells. Several of these aptamers modulate the biological activity of SH-SY5Y cells upontreatment in culture.

Spatially Enhanced Processing for Valuable Objects in Prefrontal Cortex Neurons During Efficient Search
It is recently shown that objects with long-term reward associations can be efficiently located during visual search. The neural mechanism for valuable object pop-out is unknown. In this work, we recorded neuronal responses in the ventrolateral prefrontal cortex (vlPFC) with known roles in visual search and reward processing in macaques while monkeys engaged in efficient vs inefficient visual search for high-value fractal objects (targets). Behavioral results and modeling using multi-alternative attention-modulated drift-diffusion (MADD) indicated that efficient search was concurrent with enhanced processing for peripheral objects. Notably, neural results showed response amplification and receptive field widening to peripherally presented targets in vlPFC during visual search. Both neural effects predict higher target detection and were found to be correlated with it. Our results suggest that value-driven efficient search independent of low-level visual features arises from reward-induced spatial processing enhancement of peripheral valuable objects.

Abnormal morphology and synaptogenic signaling in astrocytes following prenatal opioid exposure
In recent decades, there has been a dramatic rise in the rates of children being born after in utero exposure to drugs of abuse, particularly opioids. Opioids have been shown to have detrimental effects on neurons and glia in the central nervous system (CNS), but the impact of prenatal opioid exposure (POE) on still-developing synaptic circuitry is largely unknown. Astrocytes exert a strong influence on synaptic development, secreting factors that both promote and inhibit synapse formation and neuronal maturation in the developing CNS. Here, we investigated the effects of the partial mu-opioid receptor agonist, buprenorphine, on astrocyte synaptogenic signaling and morphological development in cortical cell culture. Acute buprenorphine treatment had no effect on excitatory synapse number in astrocyte-free neuron cultures. In conditions where neurons shared culture media with astrocytes, buprenorphine attenuated the synaptogenic capabilities of astrocyte-secreted factors. Neurons cultured from drug-naive mice showed no change in synapses when treated with factors secreted by astrocytes from POE mice. However, this same treatment was synaptogenic when applied to neurons from POE mice, suggestive of a complex neuroadaptive response that maintains synaptogenic pathways in the face of impaired astrocyte signaling. In addition to promoting morphological and connectivity changes in neurons, POE exerted a strong influence on astrocyte development, disrupting their structural maturation and promoting the accumulation of lipid droplets (LD), suggestive of a maladaptive stress response in the developing nervous system.

Connectome caricatures: removing large-amplitude co-activation patterns in resting-state fMRI emphasizes individual differences
High-amplitude co-activation patterns are sparsely present during resting-state fMRI but drive functional connectivity1-5. Further, they resemble task activation patterns and are well-studied3,5-10. However, little research has characterized the remaining majority of the resting-state signal. In this work, we introduced caricaturing--a method to project resting-state data to a subspace orthogonal to a manifold of co-activation patterns estimated from the task fMRI data. Projecting to this subspace removes linear combinations of these co-activation patterns from the resting-state data to create Caricatured connectomes. We used rich task data from the Human Connectome Project (HCP)11 and the UCLA Consortium for Neuropsychiatric Phenomics12 to construct a manifold of task co-activation patterns. Caricatured connectomes were created by projecting resting-state data from the HCP and the Yale Test-Retest13 datasets away from this manifold. Like caricatures, these connectomes emphasized individual differences by reducing between-individual similarity and increasing individual identification14. They also improved predictive modeling of brain-phenotype associations. As caricaturing removes group-relevant task variance, it is an initial attempt to remove task-like co-activations from rest. Therefore, our results suggest that there is a useful signal beyond the dominating co-activations that drive resting-state functional connectivity, which may better characterize the brain's intrinsic functional architecture.

Drosulfakinin signaling encodes early-life memory for adaptive social plasticity
Drosophila establishes social clusters in groups, yet the underlying principles remain poorly understood. Here we performed a systemic analysis of social network behavior (SNB) that quantifies individual social distance (SD) in a group over time. The SNB assessment in 175 inbred strains from the Drosophila Genetics Reference Panel revealed a tight association of short SD with long developmental time, low food intake, and hypoactivity. The developmental inferiority in short-SD individuals was compensated by their group culturing. By contrast, developmental isolation silenced the beneficial effects of social interactions in adults and blunted the plasticity of SNB under physiological challenges. Transcriptome analyses showed genetic diversity for SD traits, whereas social isolation reprogrammed select genetic pathways, regardless of SD phenotypes. In particular, social deprivation suppressed the expression of the neuropeptide Drosulfakinin (Dsk) in three pairs of adult brain neurons. Male-specific DSK signaling to Cholecystokinin-like receptor 17D1 mediated the SNB plasticity. In fact, transgenic manipulations of the DSK signaling were sufficient to imitate the state of social experience. Given the functional conservation of mammalian Dsk homologs, we propose that animals have evolved a dedicated neural mechanism to encode early-life experience and transform group properties adaptively.

Sex differences in oxycodone-taking behaviors are linked to disruptions in reward-guided, decision-making functions
Problematic opioid use that emerges in a subset of individuals may be due to pre-existing disruptions in the biobehavioral mechanisms that regulate drug use. The identity of these mechanisms is not known, but emerging evidence suggests that suboptimal decision-making that is observable prior to drug use may contribute to the pathology of addiction and, notably, serve as a powerful phenotype for interrogating biologically based differences in opiate-taking behaviors. The current study investigated the relationship between decision-making phenotypes and opioid-taking behaviors in male and female Long Evans rats. Adaptive decision-making processes were assessed using a probabilistic reversal-learning task and oxycodone- (or vehicle, as a control) taking behaviors assessed for 32 days using a saccharin fading procedure that promoted dynamic intake of oxycodone. Tests of motivation, extinction, and reinstatement were also performed. Computational analyses of decision-making and opioid-taking behaviors revealed that attenuated reward-guided decision-making was associated with greater self-administration of oxycodone and addiction-relevant behaviors. Moreover, pre-existing impairments in reward-guided decision-making observed in female rats was associated with greater oxycodone use and addiction-relevant behaviors when compared to males. These results provide new insights into the biobehavioral mechanisms that regulate opiate-taking behaviors and offer a novel phenotypic approach for interrogating sex differences in addiction susceptibility and opioid use disorders.

Microgliosis, astrogliosis and loss of aquaporin-4 polarity in frontal cortex of COVID-19 patients
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), causing human coronavirus disease 2019 (COVID-19), not only affects the respiratory tract, but also impacts other organs including the brain. A considerable number of COVID-19 patients develop neuropsychiatric symptoms that may linger for weeks and months and contribute to "long-COVID". While the neurological symptoms of COVID-19 are well described, the cellular mechanisms of neurologic disorders attributed to the infection are still enigmatic. Here, we studied the effect of an infection with SARS-CoV-2 on the structure and expression of marker proteins of astrocytes and microglial cells in the frontal cortex of patients who died from COVID-19 in comparison to non-COVID-19 controls. Most of COVID-19 patients had microglial cells with retracted processes and rounded and enlarged cell bodies in both gray and white matter, as visualized by anti-Iba1 staining and confocal fluorescence microscopy. In addition, gray matter astrocytes in COVID-19 patients were frequently labeled by intense anti-GFAP staining, whereas in non-COVID-19 controls, most gray matter astrocytes expressed little GFAP. The most striking difference between astrocytes in COVID-19 patients and controls was found by anti-aquaporin-4 (AQP4) staining. In COVID-19 patients, a large number of gray matter astrocytes showed an increase in AQP4. In addition, AQP4 polarity was lost and AQP4 covered the entire cell, including the cell body and all cell processes, while in controls, AQP4 immunostaining was mainly detected in endfeet around blood vessels and did not visualize the cell body. In summary, our data suggest neuroinflammation upon SARS-CoV-2 infection including microgliosis and astrogliosis, including loss of AQP4 polarity.

An integrative single-cell atlas to explore the cellular and temporal specificity of neurological disorder genes during human brain development
Single-cell technologies have enhanced comprehensive knowledge regarding the human brain by facilitating an extensive transcriptomic census across diverse brain regions. Nevertheless, understanding the cellular and temporal specificity of neurological disorders remains ambiguous due to the developmental variations. To address this gap, we illustrated the dynamics of disorder risk gene expressions under development by integrating multiple single-cell RNA sequencing datasets. We constructed a comprehensive single-cell atlas of developing human brains, encompassing 393,060 single cells across diverse developmental stages. Temporal analysis revealed the distinct expression patterns of disorder risk genes, including autism, highlighting their temporal regulation in different neuronal and glial lineages. We identified distinct neuronal lineages diverged across developmental stages, each exhibiting temporal-specific expression patterns of disorder genes. Lineages of non-neuronal cells determined by molecular profiles also showed temporal-specific expressions, indicating a link between cellular maturation and the risk of disorder. Furthermore, we explored the regulatory mechanisms involved in early brain development, revealing enriched patterns of fetal cell types for neuronal disorders, indicative of the prenatal stage's influence on disease determination. Our findings facilitate unbiased comparisons of cell type-disorder associations and provide insight into dynamic alterations in risk genes during development, paving the way for a deeper understanding of neurological disorders.

Verbal semantic expertise is associated with reduced functional connectivity between left and right anterior temporal lobes
The left and right anterior temporal lobes (ATLs) encode semantic representations. They show graded hemispheric specialisation in function, with the left ATL contributing preferentially to verbal semantic processing. We investigated the underlying causes of this organisation, using resting-state functional connectivity as a measure of functional segregation between ATLs. We analysed two independent resting-state fMRI datasets (N=86 and N=642) in which participants' verbal semantic expertise was measured using vocabulary tests. In both datasets, people with more advanced verbal semantic knowledge showed weaker functional connectivity between left and right ventral ATLs. This effect was highly specific. It was not observed for within-hemisphere connections between semantic regions (ventral ATL and inferior frontal gyrus; IFG, though it was found for left-right IFG connectivity in one dataset). Effects were not found for tasks probing semantic control, non-semantic cognition or face recognition. Our results suggest that hemispheric specialisation in the ATLs is not an innate property but rather emerges as people develop highly detailed verbal semantic representations. We propose that this effect is a consequence of the left ATL's greater connectivity with left-lateralised written word recognition regions, which causes it to preferentially represent meaning for advanced vocabulary acquired primarily through reading.

Adjacent Neuronal Fascicle Guides Motoneuron 24 Dendritic Branching and Axonal Routing Decisions through Dscam1 Signaling
The formation and precise positioning of axons and dendrites are crucial for the development of neural circuits. Although juxtracrine signaling via cell-cell contact is known to influence these processes, the specific structures and mechanisms regulating neuronal process positioning within the central nervous system (CNS) remain to be fully identified. Our study investigates motoneuron 24 (MN24) in the Drosophila embryonic CNS, which is characterized by a complex yet stereotyped axon projection pattern, known as axonal routing. In this motoneuron, the primary dendritic branches project laterally toward the midline, specifically emerging at the sites where axons turn. We observed that Scp2-positive neurons contribute to the lateral fascicle structure in the ventral nerve cord (VNC) near MN24 dendrites. Notably, the knockout of the Down syndrome cell adhesion molecule (dscam1) results in the loss of dendrites and disruption of proper axonal routing in MN24, while not affecting the formation of the fascicle structure. Through cell-type specific knockdown and rescue experiments of dscam1, we have determined that the interaction between MN24 and Scp2-positive fascicle, mediated by Dscam1, promotes the development of both dendrites and axonal routing. Our findings demonstrate that the holistic configuration of neuronal structures, such as axons and dendrites, within single motoneurons can be governed by local contact with the adjacent neuron fascicle, a novel reference structure for neural circuitry wiring.

Dopamine D2R and opioid MOR availability in autism spectrum disorder
Opioid and dopamine receptor systems are implicated in the pathoetiology of autism, but in vivo human brain imaging evidence for their role remains elusive. Here, we investigated regional type 2 dopamine and mu-opioid receptor (D2R and MOR, respectively) availabilities and regional interactions between the two neuromodulatory systems associated with autism spectrum disorder (ASD). In vivo positron emission tomography (PET) with radioligands [11C]raclopride (D2R) and [11C]carfentanil (MOR) was carried out in 16 adult males with high functioning ASD and 19 age and sex matched controls. Regional group differences in D2R and MOR receptor availabilities were tested with linear mixed models and associations between regional receptor availabilities were examined with correlations. There were no group differences in whole-brain voxel-wise analysis of DR2 but ROI analysis presented a lower overall mean D2R availability in striatum of the ASD versus control group. Post hoc regional analysis revealed reduced D2R availability in nucleus accumbens of the ASD group. The whole-brain voxel-wise analysis of MOR revealed precuneal up-regulation in the ASD group, but there was no overall group difference in the ROI analysis for MOR. MOR down-regulation was observed in the hippocampi of the ASD group in a post hoc analysis. Regional correlations between D2R and MOR availabilities were weaker in the ASD group versus control group in the amygdala and nucleus accumbens. These alterations may translate to disrupted modulation of social motivation and reward in ASD.

A deep learning-based approach for unbiased kinematic analysis in CNS injury
Traumatic spinal cord injury (SCI) is a devastating condition that impacts over 300,000 individuals in the US alone. Depending on the severity of the injury, SCI can lead to varying degrees of sensorimotor deficits and paralysis. Despite advances in our understanding of the underlying pathological mechanisms of SCI and the identification of promising molecular targets for repair and functional restoration, few therapies have made it into clinical use. To improve the success rate of clinical translation, more robust, sensitive, and reproducible means of functional assessment are required. The gold standards for the evaluation of locomotion in rodents with SCI are the Basso Beattie Bresnahan (BBB) and Basso Mouse Scale (BMS) tests. To overcome the shortcomings of current methods, we developed two separate marker-less kinematic analysis paradigms in mice, MotorBox and MotoRater, based on deep-learning algorithms generated with the DeepLabCut open-source toolbox. The MotorBox system uses an originally designed, custom-made chamber, and the MotoRater system was implemented on a commercially available MotoRater device. We validated the MotorBox and MotoRater systems by comparing them with the traditional BMS test and extracted metrics of movement and gait that can provide an accurate and sensitive representation of mouse locomotor function post-injury, while eliminating investigator bias and variability. The integration of MotorBox and/or MotoRater assessments with BMS scoring will provide a much wider range of information on specific aspects of locomotion, ensuring the accuracy, rigor, and reproducibility of behavioral outcomes after SCI.

Repeated LPS induces training and tolerance of microglial responses across brain regions
Background: Neuroinflammation is involved in the pathogenesis of almost every central nervous system disorder. As the brain's innate immune cells, microglia fine tune their activity to a dynamic brain environment. Previous studies have shown that repeated bouts of peripheral inflammation can trigger long-term changes in microglial gene expression and function, a form of innate immune memory. Methods and Results: In this study, we used multiple low-dose lipopolysaccharide (LPS) injections in adult mice to study the acute cytokine, transcriptomic, and microglia morphological changes that contribute to the formation of immune memory in the frontal cortex, hippocampus, and striatum, as well as the long-term effects of these changes on behavior. Training and tolerance of gene expression was shared across regions, and we identified 3 unique clusters of DEGs (2xLPS-sensitive, 4xLPS-sensitive, LPS-decreased) with different biological functions. 2xLPS-sensitive DEG promoters were enriched for binding sites for IRF and NFkB family transcription factors, two key regulators of innate immune memory. We quantified shifts in microglia morphological populations and found that while the proportion of ramified and rod-like microglia mostly remained consistent within brain regions and sexes with LPS treatment, there was a shift from ameboid towards hypertrophic morphological states across immune memory states and a dynamic emergence and resolution of trains of rod-like microglia with repeated LPS. Conclusions: Together, findings support the dynamic regulation of microglia during the formation of immune memories in the brain and support future work to exploit this model in brain disease contexts.

ACSS2 contributes to transcriptional regulation in Cajal-Retzius cells in a mouse model of Alzheimer's disease
Dysregulation of histone acetylation in the brain has emerged as a major contributor to human Alzheimer's disease (AD). The mechanisms by which these protective or risk-conferring epigenetic marks are established and maintained are under intense investigation. ACSS2 (Acetyl-CoA Synthetase 2) is a key metabolic enzyme that is chromatin-associated in neurons. ACSS2 is recruited to specific promoters and generates a local pool of acetyl-CoA from acetate, thereby fueling histone acetylation and driving the expression of neuronal genes that regulate learning and memory. Here, we examine the contribution of ACSS2-mediated histone acetylation to AD-related molecular and behavioral outcomes. Using a mouse model of human pathological AD-Tau injection, we show that loss of ACSS2 exacerbates Tau-related memory impairments, while dietary supplementation of acetate rescues learning in an ACSS2-dependent manner. Combining state-of-the-art proteomic and genomic approaches, we demonstrate that this effect is accompanied by ACSS2-dependent incorporation of acetate into hippocampal histone acetylation, which facilitates gene expression programs related to learning. Further, we identify Cajal-Retzius neurons as a critical hippocampal neuronal population affected, exhibiting the largest epigenetic and transcriptional dysregulation. Overall, these results reveal ACSS2 as a key neuroprotective metabolic enzyme, dysregulation of which might play an important role in the etiology of human AD, and guide the development of future therapies for AD and related dementia.

RT-Sort: an action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies
With the use of high density multi electrode recording devices, electrophysiological signals resulting from action potentials of individual neurons can now be reliably detected on multiple adjacent recording electrodes both in vivo and in vitro. Spike sorting assigns these signals to putative neural sources. However, until now, spike sorting can only be performed after completion of the recording, preventing true real time usage of spike sorting algorithms. Utilizing the unique propagation patterns of action potentials along axons detected as high fidelity sequential activations on adjacent electrodes, together with a convolutional neural network based spike detection algorithm, we introduce RT-Sort (Real Time Sorting), a spike sorting algorithm that enables the sorted detection of action potentials within 7.5ms{+/-}1.5ms (mean{+/-}STD) after the waveform trough while the recording remains ongoing. RT-Sort's true real-time spike sorting capabilities enable closed loop experiments with latencies comparable to synaptic delay times. We show RT-Sort's performance on both Multi-Electrode Arrays as well as Neuropixels probes to exemplify RT-Sort's functionality on different types of recording hardware and electrode configurations.

Integrated number sense tutoring remediates aberrant neural representations in children with mathematical disabilities
Number sense is essential for early mathematical development but it is compromised in children with mathematical disabilities (MD). Here we investigate the impact of a personalized 4-week Integrated Number Sense (INS) tutoring program aimed at improving the connection between nonsymbolic (sets of objects) and symbolic (Arabic numerals) representations in children with MD. Utilizing neural pattern analysis, we found that INS tutoring not only improved cross-format mapping but also significantly boosted arithmetic fluency in children with MD. Critically, the tutoring normalized previously low levels of cross-format neural representations in these children to pre-tutoring levels observed in typically developing, especially in key brain regions associated with numerical cognition. Moreover, we identified distinct, 'inverted U-shaped' neurodevelopmental changes in the MD group, suggesting unique neural plasticity during mathematical skill development. Our findings highlight the effectiveness of targeted INS tutoring for remediating numerical deficits in MD, and offer a foundation for developing evidence-based educational interventions.