Biology subjects

Grasso, C.

Publications and source records attributed to Grasso, C..

15 recordsLinked to original sources

bioRxiv2026

Increased activity without changes in coupling between somata and apical dendrites during visual mismatches

Leading theories of cortical function posit that sensory processing involves a comparison between top-down predictions and bottom-up sensory data. Tests of these theories have been hampered by experimental challenges related to simultaneously recording top-down and bottom-up signals in response to sensory stimuli that either do or do not match internally-generated predictions. Here, we conduct dual-plane 2-photon calcium imaging near-simultaneously from distal apical dendrites and somata of pyramidal neurons in each of 4 different regions of mouse visual cortex while the mice are presented with visual sequences that can either match or mismatch previously habituated visual stimuli. Specifically, we examine the responses in the distal apical dendrites and cell bodies of pyramidal neurons while mice view either movie clips that reverse unexpectedly or Gabor patch sequences that have orientations that do not match habituated patterns. We find that in response to unexpected reversals in natural movies, both the apical dendrites and somata show increased activity that decreases over repeated exposures, consistent with a prediction error response. However, we do not find any clear evidence for increased activity in response to mismatches in Gabor sequences, beyond possible release from adaptation effects. We additionally use volumetric images to connect dendritic and somatic compartments and examine the coupling between connected dendrites and cell bodies in layer 5 pyramidal neurons. We do not find evidence for changes in coupling in response to mismatch stimuli, either for natural movies or Gabor sequences. Our results are consistent across four regions of visual cortex. We also observe that increased responses to reversals in natural movies are stronger in layer 2/3 than layer 5 pyramidal neurons. Altogether, these data suggest that visual cortex is sensitive to deviations from previously-experienced naturalistic inputs. Our data do not suggest that this mismatch sensitivity extends to artificial stimuli, nor do they support theories of prediction error causing changes in the coupling between apical dendrites and somata.

neuroscience↗

bioRxiv2026

Goal directed closed-loop training of network bursts in cortical cultures produces improved performance and error correction over days

Dissociated neural cultures are living systems with no evolutionary history in their current form, which makes them a testbed for asking what goals neural tissue can learn to pursue once it is removed from its evolved body. It remains unclear which features of network activity such a culture can be trained to control, and whether that training is retained from one day to the next. We built an open-source closed-loop platform, the Holistic Agential Learning platform (HAL), that detects a network burst on a high-density microelectrode array, estimates its spatial origin in real time, and applies a minimal reinforcement rule. Here, a burst that originates off the goal side triggers global random stimulation that persists until the next burst. Over days of training, rat cortical cultures (n=10) increased the fraction of bursts that initiated on the goal side. This gain accrued between sessions, with little change within a session, a consolidation-like pattern that we interpret as a statement about timescale while the mechanism remains untested. The burst origin moved toward the goal side, while the burst peak and the repertoire of propagation directions were preserved. Trained cultures also recovered from incorrect states more reliably over days, while the rate at which they entered those states was unchanged, and this recovery effect was the most robust difference from unstimulated controls (n=6). Cultures that began on either side of chance converged to a similar level of performance. Damaged cultures (n=6) with comparable burst statistics showed neither the across-day gain nor the consolidation-like pattern. Training reweighted the activity patterns each culture already had, and we saw no new ones, which we read as a simple form of niche construction in which the tissue keeps a trace of its history that biases what it does next. These results identify burst initiation and error recovery as trainable variables in a novel living system, and they support training the tissue rather than engineering the machine.

bioengineering↗

bioRxiv2026

Psilocybin collapses visual change detection and drives cortical dynamics toward a state of surprise

Psilocybin profoundly alters visual perception, yet the neuronal mechanisms underlying these effects remain unclear. Here we combined large-scale Neuropixels recordings with cell-type specific optogenetics in head-fixed mice performing a visual change-detection task. Psilocybin severely impaired task performance without overt motor deficits. In cortex, the drug modestly suppressed activity of layer 5 neurons while preserving representations of image identity. By contrast, psilocybin imposed a 4-Hz oscillation on visually evoked activity that preferentially affected neurons encoding image change rather than image identity. Under psilocybin, expected image repetitions aberrantly recruited change-encoding ensembles and shifted cortical population dynamics towards trajectories normally evoked by genuine stimulus changes. These effects were strongest in somatostatin-expressing (SST) interneurons in visual cortex. The strength of this modulation depended on image structure and was greatest for images with clear, continuous contours, which preferentially recruited change-encoding ensembles. These findings demonstrate that psilocybin drives internally generated cortical surprise signals, providing a circuit mechanism for altered perception in the acute psychedelic state.

neuroscience↗

bioRxiv2026

Large oncosomes reprogram bone marrow mesenchymal stem cells to establish a pre-metastatic niche

Metastatic progression depends on the systemic remodeling of distant tissues before tumor cell arrival, yet the cancer-derived signals that orchestrate this process remain poorly understood. Large oncosomes (LOs) are atypically large (>1 um), tumor-derived extracellular vesicles shed by invasive cancer cells. Here, we demonstrate that LOs function as systemic mediators of pre-metastatic niche formation by activating innate immune sensing in bone marrow mesenchymal stem cells (BM-MSCs). Systemic administration of prostate- and breast cancer-derived LOs to immunocompetent tumor-bearing mice did not affect primary tumor growth but increased metastatic burden. LOs induced a robust, dose-dependent interferon-driven inflammatory program, characterized by interferon-stimulated genes and neutrophil chemokines. Mechanistically, this response was driven by LO-associated nucleic acids activating convergent cytosolic DNA- and RNA-sensing pathways in recipient stromal cells. LO-conditioned BM-MSCs promoted the accumulation and polarization of neutrophils toward an immunosuppressive, polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) phenotype. In vivo, genetic suppression of LO shedding in tumor cells reduced PMN-MDSC accumulation in the bone marrow, which was reverted by systemic LO administration. Together, these findings establish LOs as specialized carriers of immunomodulatory signals that reprogram the bone marrow microenvironment to support metastatic colonization, identifying a previously unrecognized mechanism linking tumor vesiculation to immune remodeling at distant sites.

cancer biology↗

bioRxiv2026

Nested Contextual change and the temporal compression of episodic memory

How does the structure of events influence the when and the where of life experiences in comparison to the what? We developed a novel virtual reality (VR) environment to understand how the quantity of information within nested structures influence participants memory for events. Participants moved through a series of virtual rooms (events) where images (items) appeared in randomised locations on a 3 by 3 grid located on a wall. Participants were asked to remember the what (old/new), when (timeline location), and where (grid location), of the images they experienced. Two types of nested events were tested (6 rooms, each containing 4 images; 3 rooms, each containing 8 images), all lasting an equivalent number of seconds. We found a strong temporal compression effect at nested levels in which participants remembered early items and events happening later, and later items and events happening earlier, than the original experience. Crucially, presenting four-item events resulted in a greater compression rate than eight-item events. We also found greater temporal distances between pairs of items occurring within eight-item events than pairs of items which occurred on either side of a boundary. Memory for when depends on the nested compression of information within events.

neuroscience↗

bioRxiv2026

A Cross-Species Enhancer-AAV Toolkit for Cell Type-Specific Targeting Across the Basal Ganglia

The mammalian basal ganglia (BG) orchestrate motor, cognitive, and affective functions, yet cell type-specific genetic access remains limited, especially beyond rodents. Key structures implicated in movement and psychiatric disorders, including pallidum, subthalamic nucleus, and dopaminergic midbrain, lack scalable tools for cross-species targeting. Here, we present a comprehensive enhancer-AAV library enabling selective labeling and manipulation of major BG neuronal populations: striatal projection neuron subtypes, pallidal and subthalamic neurons, and midbrain dopaminergic and GABAergic populations. Using an evolutionarily informed discovery pipeline, we identified enhancers targeting canonical, non-canonical, and disease-relevant cell types, with validation demonstrating robust cross-species conservation of specificity between mouse and macaque. Computational modeling revealed sequence features predictive of in vivo performance, including motif grammar, chromatin accessibility, and evolutionary conservation, and identified distinct regulatory architectures across glial, projection, and interneuron lineages. This work establishes a comprehensive cross-species viral toolkit for the BG, unlocking previously inaccessible cell types for circuit dissection.

neuroscience↗

bioRxiv2025

Map of spiking activity underlying change detection in the mouse visual system

Visual behavior requires coordinated activity across hierarchically organized brain circuits. Understanding this complexity demands datasets that are both large-scale (sampling many areas) and dense (recording many neurons in each area). Here we present a database of spiking activity across the mouse visual system--including thalamus, cortex, and midbrain--while mice perform an image change detection task. Using Neuropixels probes, we record from >75,000 high-quality units in 54 mice, mapping area-, cortical layer-, and cell type-specific coding of sensory and motor information. Modulation by task-engagement increased across the thalamocortical hierarchy but was strongest in the midbrain. Novel images modulated cortical (but not thalamic) responses through delayed recurrent activity. Population decoding and optogenetics identified a critical decision window for change detection and revealed that mice use an adaptation-based rather than image-comparison strategy. This comprehensive resource provides a valuable substrate for understanding sensorimotor computations in neural networks.

neuroscience↗

bioRxiv2024

Identification of brain-like functional information architectures in embryonic tissue of Xenopus laevis.

Understanding how populations of cells collectively coordinate activity to produce the complex structures and behaviors that characterize multicellular organisms, and which coordinated activities, if any, survive processes that reshape cells and tissues into organoids, are fundamental issues in modern biology. Here we show how techniques from complex systems and multivariate information theory provide a framework for inferring the structure of collective organization in non-neural tissue. Many of these techniques were developed in the context of theoretical neuroscience, where these statistics have been found to be altered during different cognitive, clinical, or behavioral states, and are generally thought to be informative about the underlying dynamics linking biology to cognition. Here we show that these same patterns of coordinated activity are also present in the aneural tissues of evolutionarily distant biological systems: preparations of embryonic Xeno-pus laevis tissue (known as "basal Xenobots"). These similarities suggest that such patterns of activity either arose independently in these two systems (epithelial constructs and brains); are epiphenomenological byproducts of other dynamics conserved across vastly different configurations of life; or somehow directly support adaptive behavior across diverse living systems. Finally, these results provide unambiguous support for the hypothesis that, despite their apparent simplicity as collections of non-neural epithelial cells, Xenobots are in fact integrated, complex systems in their own right, with sophisticated internal information structures.

systems biology↗

bioRxiv2024

Stimulus history, not expectation, drives sensory prediction errors in mammalian cortex

Hierarchical predictive coding (HPC) models have recently flourished in neuroscience1-9. Feedforward and feedback processing are at the heart of HPC models. Previous experimental studies using fMRI, EEG/MEG, and LFP9-11 do not reliably resolve feedback modulation from local computations and feedforward outputs. Here, using open-science8, multi-species, multi-area, high-density12, laminar neurophysiology13, we empirically test whether hierarchical predictive coding is a key component shaping cortical processing of visual stimuli. To isolate visual information processing and eliminate motor/reward confounders9-11, we use a no-report task. Our task leveraged so-called global oddballs (GO) as unpredictable, deviant stimuli that circumvent low-level adaptation. We examined their responses relative to local oddballs (LO) that we habituated into highly predictable priors. Four surprising findings in this dataset challenge many existing hierarchical predictive coding models. First, GO responses were exclusive to higher-order, more cognitive areas rather than early-to-mid visual cortex. Second, inhibitory interneuron-targeted optogenetics in primates and mice and waveform shape analysis in primates revealed no evidence that predictive suppression was implemented via these interneurons. Third, highly predictable LO responses dominated in over 50% of all neurons, including in higher-order cortex, which should have anticipated them, indicating limited evidence for predictive suppression. Lastly, prediction error responses evoked by GOs did not evoke feedforward processing. These results reveal circuit dynamics that govern how prediction shapes visual processing, motivating more neurally constrained predictive processing models.

neuroscience↗

bioRxiv2024

Revealing non-trivial information structures in aneural biological tissues via functional connectivity

A central challenge in the progression of a variety of open questions in biology, such as morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Information-theoretic approaches provide a quantitative framework for extracting patterns from data, but so far have been predominantly applied to neuronal systems at the tissue-level. Here, we demonstrate how time series of Ca2+ dynamics can be used to identify the structure and information dynamics of other biological tissues. To this end, we expressed the calcium reporter GCaMP6s in an organoid system of explanted amphibian epidermis derived from the African clawed frog Xenopus laevis, and imaged calcium activity pre- and post- a puncture injury, for six replicate organoids. We constructed functional connectivity networks by computing mutual information between cells from time series derived using medical imaging techniques to track intracellular Ca2+. We analyzed network properties including degree distribution, spatial embedding, and modular structure. We find organoid networks exhibit more connectivity than null models, with high degree hubs and mesoscale community structure with spatial clustering. Utilizing functional connectivity networks, we show the tissue retains non-random features after injury, displays long range correlations and structure, and non-trivial clustering that is not necessarily spatially dependent. Our results suggest increased integration after injury, possible cellular coordination in response to injury, and some type of generative structure of the anatomy. While we study Ca2+ in Xenopus epidermal cells, our computational approach and analyses highlight how methods developed to analyze functional connectivity in neuronal tissues can be generalized to any tissue and fluorescent signal type. Our framework therefore provides a bridge between neuroscience and more basal modes of information processing. Author summaryA central challenge in understanding several diverse processes in biology, including morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Significant progress in understanding information integration has occurred in neuroscience via the use of observable live calcium reporters throughout neural tissues. However, these same techniques have seen limited use in the non-neural tissues of multicellular organisms despite similarities in tissue communication. Here we utilize methods designed for neural tissues and modify them to work on any tissue type, demonstrating how non-neural tissues also contain non-random and potentially meaningful structures to be gleaned from information theoretic approaches. In the case of epidermal tissue derived from developing amphibians, we find non-trivial informational structure over greater spatial and temporal scales than those found in neural tissue. This hints at how more exploration into information structures within these tissue types could provide a deeper understanding into information processing within living systems beyond the nervous system.

systems biology↗

bioRxiv2023

Senescence phenotype of lymph node stromal cells from patients with rheumatoid arthritis is partly restored by dasatinib treatment

ObjectiveCellular senescence is a state of proliferation arrest of cells occurring during aging. The persistence and accumulation of senescent cells has been implicated in the pathogenesis of age-related diseases like rheumatoid arthritis (RA). RA is a chronic autoimmune disease in which loss of immune tolerance and systemic autoimmunity precedes clinical onset of disease. Lymph node stromal cells (LNSCs) are important regulators of immune tolerance. Accordingly, accumulating senescent LNSCs may potentially lead to defective immune tolerance and the development of systemic autoimmune disease. MethodsHuman LNSCs were isolated and cultured from inguinal lymph node needle biopsies from individuals at risk of developing RA (RA-risk individuals), RA patients and seronegative healthy volunteers. Senescence hallmarks and the effect of dasatinib treatment were assessed using quantitative PCR, flow cytometry, microscopy and live-cell imaging. ResultsCell size, granularity and autofluorescence were significantly higher in RA LNSCs compared with control LNSCs. Stainings indicate more senescence associated {beta}-galactosidase activity, more lipofuscin positive granules and increased DNA damage in RA-risk and RA LNSCs compared with control LNSCs. Moreover, we found altered gene expression levels of senescence associated genes in LNSCs from RA patients. Strikingly, the capacity to repair irradiation induced DNA damage was significantly lower in RA-risk and RA LNSCs compared with control LNSCs. Treating LNSCs with dasatinib significantly improved cell size and DNA repair capacity of cultured LNSCs. ConclusionWe observed multiple senescent hallmarks in RA LNSCs and to lesser extent already in RA-risk LNSCs, which could partly be restored by dasatinib treatment. KEY MESSAGES What is already known on this topic?- Synovial fibroblasts from RA patients display a senescent phenotype and accumulate in inflamed synovial tissue. What does this study add?- Lymph node stromal cells (LNSCs) from RA patients, and to a lesser extent from RA-risk, display key hallmarks of senescence. - Both ex vivo and in vitro LNSCs from RA patients have an increased cell size compared with control LNSCs. - RA and RA-risk LNSCs have an impaired ability to repair DNA damage - Treating LNSCs with dasatinib significantly improved cell size and DNA repair capacity of LNSCs. How might this study impact on clinical practice or future developments?- These hallmarks of senescence in LNSCs may indicate premature aging and loss of function of the immunomodulatory lymph node stromal compartment during RA development. Dasatinib treatment of LNSCs shows that senolytics may be an effective preclinical drug to restore cell function early in disease.

cell biology↗

bioRxiv2023

SHIELD: Skull-shaped hemispheric implants enabling large-scale-electrophysiology datasets in the mouse brain

To understand the neural basis of behavior, it is essential to measure spiking dynamics across many interacting brain regions. While new technologies, such as Neuropixels probes, facilitate multi-regional recordings, significant surgical and procedural hurdles remain for these experiments to achieve their full potential. Here, we describe a novel 3D-printed cranial-replacement implant (SHIELD) enabling electrophysiological recordings from distributed areas of the mouse brain. This skull-shaped implant is designed with customizable insertion holes, allowing dozens of cortical and subcortical structures to be recorded in a single mouse using repeated multi-probe insertions over many days. We demonstrate the procedures high success rate, biocompatibility, lack of adverse effects on behavior, and compatibility with imaging and optogenetics. To showcase the scientific utility of the SHIELD implant, we use multi-probe recordings to reveal novel insights into how alpha rhythms organize spiking activity across visual and sensorimotor networks. Overall, this method enables powerful large-scale electrophysiological measurements for the study of distributed brain computation.

neuroscience↗

bioRxiv2023

Identification and mapping of human lymph node stromal cell subsets by combining single-cell RNA sequencing with spatial transcriptomics.

Lymph node stromal cells (LNSCs) have a crucial immunomodulatory function, but their heterogeneity in human is incompletely understood. Here, we report the single cell RNA sequencing (scRNA-seq) of 12000 LNSCs isolated from a human lymph node (LN). This study comprehensively defines the gene signatures of 10 fibroblast subtypes: CCL21+SC, CCL19+SC, CD34+CXCL14+SC, pericytes, DES+SC, LAMP5+SC, NR4A1+BCAM+ SC, HLA-DR+SC, SEPT4+SC and GLDN+SC. To explore the heterogeneous stromal compartment within the complex LN tissue architecture, we integrated the scRNA-seq profiles of the identified LNSC subsets with a publicly available human spatial transcriptomic LN dataset and predicted their location within the complex LN tissue architecture. Each LNSC subtype was spatially restricted to specific LN regions, indicating different LNSC-lymphocyte interactions which was further investigated using NicheNet. The positioning of distinct LNSC subtypes in different LN regions sets the stage for future research on the relationship between LNSC-specific niches and immunomodulatory function during health and disease.

cell biology↗

bioRxiv2023

Recurrent pattern completion drives the neocortical representation of sensory inference

When sensory information is incomplete or ambiguous, the brain relies on prior expectations to infer perceptual objects. Despite the centrality of this process to perception, the neural mechanism of sensory inference is not known. Illusory contours (ICs) are key tools to study sensory inference because they contain edges or objects that are implied only by their spatial context. Using cellular resolution, mesoscale two-photon calcium imaging and multi-Neuropixels recordings in the mouse visual cortex, we identified a sparse subset of neurons in the primary visual cortex (V1) and higher visual areas that respond emergently to ICs. We found that these highly selective IC-encoders mediate the neural representation of IC inference. Strikingly, selective activation of these neurons using two-photon holographic optogenetics was sufficient to recreate IC representation in the rest of the V1 network, in the absence of any visual stimulus. This outlines a model in which primary sensory cortex facilitates sensory inference by selectively strengthening input patterns that match prior expectations through local, recurrent circuitry. Our data thus suggest a clear computational purpose for recurrence in the generation of holistic percepts under sensory ambiguity. More generally, selective reinforcement of top-down predictions by pattern-completing recurrent circuits in lower sensory cortices may constitute a key step in sensory inference.

neuroscience↗

bioRxiv2023

Stimulus novelty uncovers coding diversity in visual cortical circuits

Detecting novel stimuli in the environment is critical for learning and survival, yet the neural basis of novelty processing is not understood. To characterize cell type-specific novelty processing, we surveyed the activity of [~]15,000 excitatory and inhibitory neurons in mice performing a visual task with novel and familiar stimuli. Clustering revealed a dozen functional neuron types defined by experience-dependent encoding. Vasoactive-intestinal-peptide (Vip) expressing inhibitory neurons were diverse, encoding novel stimuli, omissions of familiar stimuli, or behavioral features. Distinct Somatostatin (Sst) expressing inhibitory neurons encoded either familiar or novel stimuli. Subsets of excitatory neurons co-clustered with specific Vip or Sst subpopulations, while Sst and Vip inhibitory clusters were non-overlapping. This study establishes that novelty processing is mediated by diverse functional neuron types in the visual cortex.

neuroscience↗