Neuron

A prevailing view in affective neuroscience holds that innate and learned behaviors are processed through distinct neuroanatomical pathways, one pre-wired, the other running on synaptic plasticity. However, here we show that processing innate and learned threats in the lateral amygdala deviates fundamentally from this view. We tracked the three core elements of circuit function (excitatory neurons, inhibitory neurons, and neuromodulators) in mice, as they were exposed to an innately aversive looming stimulus and as they learned a cued threat. Tracking the same neurons across sessions, revealed a subpopulation of excitatory neurons recruited by the innate threat that was preferentially potentiated following auditory threat learning. Furthermore, both forms of threat converged on the same modulatory mechanisms: the disinhibitory VIP/SST motif and norepinephrine release, but with a critical difference. While the innately aversive stimulus possessed privileged access to these pathways, the learned cue acquired access through synaptic plasticity. In this instance, learning about a new threat apparently recruits a circuit that protects animals from natural threats.

Flexible behavior requires generalizable memory and learning. For example, we rapidly learn to commute in new cities by reusing our knowledge of Euclidean two-dimensional space and structures like roundabouts and subway systems without forgetting how to get to a favorite restaurant back home. Yet we lack a detailed understanding of how the brain uses existing knowledge to generalize while retaining the memory of specific past experiences. To address this gap, we combine behavioral measurements, neural recordings, and computational modeling in an abstract sequential image navigation task to study three forms of generalization: mnemonic generalization, from visual to mental navigation; transitive generalization, from trained to novel routes; and structural generalization, from familiar to new environments. In contrast to monkeys and humans, recurrent neural networks failed at all generalizations. We found that a structured entorhinal-hippocampal memory model, which provides a content-independent metric scaffold based on grid cells for storing experience, coupled to a policy recurrent network, succeeds at all three. The content-independent scaffold enables mnemonic and transitive generalization through path integration and facilitates structural generalization by allowing reuse of a previously learned action policy network. Moreover, the scaffold's high combinatorial capacity permits continual learning without catastrophic forgetting. We recorded neural activity from the entorhinal cortex and posterior parietal cortex of two monkeys performing the task and found two distinct computations across the neural population. Modularizing an entorhinal and parietal action policy network to separately track distance and initiate actions captured the distinct population dynamics and improved model performance. Finally, we added a reinforcement learning module to the network that enabled it to learn an appropriate scale factor to align the grid periodicity with the environmental temporal structure. Our findings reveal that an architecture which factorizes invariant metric representations from rapid sensory associations and a transferable policy learns, generalizes, and remembers like the brain.

All physical interactions between an organism and its environment occur within the space immediately adjacent to and surrounding its body, its peripersonal space (PPS). This space has been extensively studied behaviorally in humans, and through sparse single-neuron recordings in primates. However, how PPS is represented and organized at cellular and circuit scales remains poorly understood. Here, using dense extracellular recordings in the mouse rostro-lateral visual cortex (VISrl; >19,000 single units), we reveal the cellular and circuit organization of PPS in mice. Visuo-tactile neurons prioritize near-body space while also representing farther space in a direction-selective manner, tracking approaching but not receding objects across the environment. VISrl PPS neurons integrate vision and touch nonlinearly, and their tactile responses are progressively facilitated as visual objects near the body. PPS neurons are embedded in structured networks characterized by "like-to-like" functional connectivity and remap according to recent visuo-tactile statistics. Together, these findings establish VISrl as a circuit-accessible substrate for PPS, and reveal how near-body space is represented by a dynamic, plastic, multisensory cortical network.

Microglia are the predominant immune cells in multiple sclerosis (MS) demyelinating lesions, where they phagocytose myelin, but whether they destroy myelin or merely scavenge its debris is unknown. Here, we explore whether pathogenic autoantibodies found in MS may induce the phagocytic destruction of myelin by microglia. Applying patient-derived, myelin-targeting antibodies to the mouse cortex, we developed an in vivo model of MS with focal demyelination that depended on epitope specificity and Fc gamma receptor and complement binding. Longitudinal monitoring of microglia-myelin interactions using in vivo two-photon microscopy revealed rapid microglial envelopment of intact myelin driving myelin loss, while single-cell RNA sequencing identified a demyelination-associated microglial signature. Parallel changes were observed in human MS lesions, where microglia enveloped intact myelin and similar genes were upregulated. Inhibition of Brutons tyrosine kinase (BTK) limited microglial transcriptional changes and prevented myelin loss following microglial envelopment. These findings directly implicate microglia in pathological myelin loss and support BTK inhibition as a therapeutic strategy to prevent demyelination by modulating microglia behavior.

The hippocampus (HPC) and medial entorhinal cortex (MEC) are essential for learning, memory, and spatial cognition, and both exhibit dorsoventral (longitudinal) organization across mammalian species. While prior studies have highlighted functional differences along this axis, the molecular basis and cross-species conservation of these differences remain poorly understood. Here, we employed spatial transcriptomics to generate a comprehensive molecular atlas of HPC and MEC in five species-human, tree shrew, mouse, canine, and pig-standardizing the dorsoventral axis for cross-species comparison. Using support vector machine (SVM) models, we identified high-weight genes predictive of dorsoventral identity and revealed conserved functional patterns: dorsal HPC was enriched for cytoskeletal and synaptic pathways, while ventral HPC favored nucleotide and energy metabolism. In the MEC, dorsal regions were enriched for calcium transport and lipid metabolism, whereas ventral regions were associated with calcium homeostasis and amyloid regulation. Species-specific SVM models uncovered dramatic divergence, leading us to propose the ancestral confinement theory, suggesting that conserved dorsoventral features are maintained within an evolutionary framework that permits species-specific adaptations. To link molecular patterns with cell types, we conducted single-nucleus RNA sequencing of tree shrew HPC and MEC and integrated data from other species. Deconvolution analysis showed species-specific GABAergic neuron distributions along the axis, with notable dorsal enrichment in human and ventral enrichment in other species. Together, our findings provide a cross-species molecular framework of HPC and MEC organization, revealing both conserved and species-specific dorsoventral programs underlying brain function and evolution.

Tauopathies are characterized by the accumulation and spread of pathogenic tau aggregates throughout the brain, a process that is increasingly recognized to involve not only neurons but also microglia. However, whether pathogenic MAPT directly alters microglial degradative capacity remains poorly understood. Here, using isogenic human induced pluripotent stem cell-derived microglia carrying the pathogenic MAPT IVS10+16 mutation, we identify tau as a regulator of microglial lysosomal function. MAPT IVS10+16 microglia exhibited coordinated suppression of lysosomal and autophagic pathways, reduced lysosomal protease abundance and activity, and impaired autophagosome-lysosome fusion. Mutant microglia also showed reduced uptake of extracellular tau aggregates, reduced tau accumulation in acidic compartments, and a blunted lysosomal response to proteopathic stress. Conversely, genetic loss of MAPT increased lysosomal degradative capacity and accumulation of extracellular tau aggregates within acidic compartments, supporting a cell-intrinsic role for endogenous tau in regulating microglial degradative function. Pharmacologic enhancement of the autophagy lysosome pathway in MAPT IVS10+16 microglia increased proteolytic activity and improved tau handling. Together, these findings reveal a reciprocal relationship between tau and microglial lysosome function and identify degradative capacity as a modifiable component of the microglial response to tau pathology.

Adaptive behavior requires updating responses when contingencies change while preserving prior associations and the capacity to learn a new. How this trade-off is resolved remains unknown. Here, we combined in vivo imaging of apical tuft spines in the secondary motor cortex (M2) with biologically constrained network modeling in mice performing a cross-modal rule-switch task. M2 inactivation impaired rule-switching but not learning or maintenance, identifying it as a conflict resolution substrate. Adaptation was accompanied by elevated spine turnover concentrated within stable dendritic hotspots, in which the formation, elimination and clustering of new spines were coupled and pre-existing spines were lost early. A network model reproduces these dynamics and predicts that dendritic hotspots are critical for resource-efficient adaptation. Within these reusable domains, spines encoding the prior rule are replaced by newly-relevant ones via sharing of plasticity-related resources. Preventing reuse increases both the plasticity and the engram size requirements to encode the two rules. We propose that dendritic hotspots provide a mechanistic substrate for efficient adaptive learning.

Experimental models that preserve native mammalian CNS circuitry while enabling longitudinal analysis of circuit assembly at single-cell resolution remain scarce, limiting mechanistic studies and therapeutic discovery. Here, we establish embryonic mouse hindbrain explants as a scalable in vitro model that maintains the long-range olivo-cerebellar circuit while providing direct experimental access to both pre- and postsynaptic neurons. The preparation supports repeated live imaging, targeted single-cell manipulation and labelling, electrophysiology, ultrastructural analysis, and single-cell RNA sequencing during circuit assembly. Hindbrain explants faithfully recapitulate key features of olivo-cerebellar organization and development, including cytoarchitecture, synaptic organization and maturation, neuronal differentiation, and spontaneous network activity while preserving developmental glial features. By combining developmental and physiological fidelity with longitudinal multimodal accessibility, this resource bridges the gap between reductionist cultures and technically demanding in vivo approaches, providing a versatile and ethical model for investigating the molecular and cellular mechanisms of cerebellar circuit assembly and disease.

Damage to the primary visual cortex causes loss of conscious vision, yet some patients retain the ability to respond to stimuli despite reporting no visual experience. Why similar lesions produce such different behavioral phenotypes remains unclear. While research to date has focused primarily on spared pathways that bypass V1, here we asked whether these divergent outcomes are also linked to the brain's intrinsic functional architecture. In the largest resting-state fMRI cohort of patients with unilateral V1 damage reported to date, we quantified information sharing between regions across cortical and subcortical parcels in blindsight-positive and blindsight-negative patients, as well as in age-matched healthy controls. Despite comparable lesions, the two patient groups displayed distinct hierarchical patterns on the cortex: B+ patients preserved a sensory-to-association organization as in healthy controls, whereas B- patients exhibited a marked flattening of this hierarchy. The effect was driven by abnormally low shared-information coupling within unimodal cortices and scaled continuously with single-subject behavioral blind-field detection performance. A thalamic region consistent with the pulvinar, linking the contralesional visual cortex and the frontal eye field, discriminated B+ from B- patients. These findings highlight the system-level consequences of V1 damage supporting blindsight, suggesting that the unimodal-transmodal axis might track not only global states of consciousness, but also whether sensory information can guide behavior without awareness.

Understanding which genes are reproducibly dysregulated in which cell types is foundational knowledge for efforts to slow or reverse pathologies. For neuropathologies, such efforts rely primarily on differential expression analysis of single-nucleus RNA-seq (snRNA-seq) data. However, this strategy suffers from experimental and statistical challenges that limit marker gene reproducibility. We describe a novel strategy called Covariation Projection Analysis (CoPA) that combines the power of bulk sampling with the precision of single-cell methods. By projecting bulk gene coexpression modules onto pseudobulked snRNA-seq cell types, CoPA reveals the cellular origins of highly reproducible genomic programs and their relative importance among cell types. By comparing CoPA projection patterns between normal and pathological human brain samples using differential CoPA (dCoPA), we identify gene coexpression modules that are uniformly and reproducibly dysregulated in specific neocortical cell types in Alzheimers disease or schizophrenia. We share our findings through a novel web application called CoPA Cabana (https://oldhamlab.shinyapps.io/copacabana/).

Pain is a conscious perceptual experience characterized by its aversive quality and consequent motivation to quench pain perception. The anterior cingulate cortex (ACC) critically contributes to the emotional dimension of pain. In both humans and rodents, ACC neural activity increases during acute and chronic pain, whereas ACC lesioning or excitability reduction decreases emotional reactivity during pain. However, the ACC is connected to many brain regions and is engaged during experiences beyond pain. Thus, it remains unclear through which circuit mechanisms the ACC shapes pain experience, and how specific those circuits are to nociception. Here, we show that excitatory input from the ACC to the dorsolateral periaqueductal gray (dlPAG) facilitates the affective-motivational dimension of pain. We first examined ACC[->]dlPAG connectivity using histology, optogenetics, and electrophysiology. We found that the axons of layer 5 ACC neurons terminate in the dlPAG and monosynaptically excite Slc17a6+ (VGLUT2-expressing) dlPAG neurons. Second, we genetically targeted ACC[->]dlPAG neurons with viral vectors to express the inhibitory DREADD hM4Di and then exposed the animals to an array of pain tests. We found that, across acute and chronic pain states, inhibition of the ACC[->]dlPAG pathway reduced affective-motivational but not reflexive pain behaviors. Third, we used fiber photometry to record neural calcium activity in the ACC in behaving mice and found that ACC[->]dlPAG neurons are engaged during a broad array of aversive experiences, rather than exclusively during pain, and exhibit task-specific activity patterns. Collectively, these results uncover the direct contribution of ACC[->]dlPAG neural activity to pain unpleasantness and the necessity of this pathway for generating aversive behavioral responses in general, rather than specifically for encoding the unpleasant quality of noxious stimuli.

Chronic pain mechanisms are complex, spanning multiple brain regions and networks. We ask whether resting brain activity carries a readout of that state. From a few minutes of resting-state electroencephalography (EEG), we generate a spectrogram to represent how each region of the cortex oscillates across frequency and time and pass it through CREST (Cortical Resting-state EEG Spatial Transformer): a frozen image-recognition network that reads each region as an image--here, a spectrogram--paired with a graph model that weighs the 56 cortical regions together to classify chronic-pain status. Across 125 people (74 with chronic pain, 51 healthy controls), evaluated through a leave-one-subject-out cross-validation, CREST separates the two groups with an area under the receiver operating characteristic curve (AUROC) = 0.782 (permutation p < 0.005). Control experiments implicate each persons individual alpha rhythm. Clinical relevanceA resting-state EEG readout of chronic MSK pain could clarify pathophysiology and inform treatment.

Spinal presynaptic inhibitory interneurons are thought to regulate proprioceptive sensory feedback to shape motor output, however, their specific contribution to motor behavior has been difficult to assess, partially due to the lack of a specific genetic handle. Here, we identify Sall3 as the transcription factor required for the establishment and maintenance of GABApre axo-axonic synapses on proprioceptive Ia afferent terminals. Loss of Sall3 in mice selectively eliminates GABApre boutons on Ia afferent terminals, resulting in altered sensory-evoked motor responses and impaired skilled locomotor behaviors. Together, these findings establish Sall3 as a key regulator of GABApre circuit development and provide a genetic framework for understanding how presynaptic inhibition shapes sensorimotor integration.

Investigating the neural mechanisms of social group interactions and other naturalistic behaviors in small animals remains limited by current technology. Tethered neural recording systems are incompatible with many of these behaviors, while existing wireless devices for small animals are constrained by weight, bandwidth, recording duration, and the lack of closed-loop modulation capabilities. To overcome these limitations, we developed a Wireless, Interactive, Lightweight Datalogger (WILD) with integrated flexible neural probes, optogenetics, an inertial measurement unit, an ultrasonic microphone, and a head-mounted camera. This platform enables simultaneous, long-term recording of neural activity, locomotor variables, vocalizations, and eye movements from groups of freely moving mice in both laboratory and outdoor settings. Model-based real-time signal processing detects specific neural events and behavioral motifs to trigger closed-loop neural interventions. By combining multimodal recordings with advanced onboard signal-processing capabilities in a compact device, WILD enables the investigation of neural mechanisms underlying a broad range of natural behaviors in small animals.

Microglia are central mediators of Alzheimers disease (AD) pathogenesis, yet the mechanisms driving disease-associated microglial states and their therapeutic modulation remain poorly understood. Here, we integrated single-nucleus transcriptomic datasets across the AD spectrum and identified disease- and lipid-associated microglia (DLaM) as a major AD-enriched population linked to genetic risk, neuropathology and cognitive decline. To model this state experimentally, we screened AD-relevant perturbations in human induced pluripotent stem cell (hiPSC)-derived microglia and found that ferric ammonium citrate (FAC) reproducibly induced a DLaM-like state characterized by lipid accumulation, lysosomal dysfunction and impaired A{beta} phagocytosis. Using a transcriptomics-based state-reversion screen, we identified LY2090314 as a potent modulator that restored microglial function and induced a distinct lysosomal-metabolic state. These findings establish a framework for transcriptomic disease-state-guided therapeutic discovery in AD.

The extent to which conserved neural circuit architectures depend on shared molecular specification programs remains unclear. Here, we address this question by examining the somatosensory system of the little skate, Leucoraja erinacea, an early-diverging vertebrate that retains ancestral features of both finned and limb-based body plans. We show that core features of somatosensory circuit organization, including laminar organization of the spinal cord and dorsally restricted targeting of sensory afferents, are deeply conserved. Unexpectedly, the molecular programs specifying dorsal root ganglion (DRG) sensory subtypes diverge extensively from those of mammals. Although DRG neuron subtype specification and spinal connectivity rely on target-derived cues, skates employ distinct neurotrophin receptor and transcription factor identity codes. These findings support a model in which conserved spinal circuit architectures provide a stable scaffold that leverages flexible sensory neuron specification programs, enabling the evolutionary diversification of vertebrate somatosensory systems. HighlightsO_LIIntegrated analysis of spinal cord and DRG neuronal diversity in Leucoraja erinacea C_LIO_LILaminar organization of the dorsal spinal cord is an ancestral vertebrate feature C_LIO_LIDivergent neurotrophin receptor and transcription factor codes in sensory neurons C_LIO_LIConserved target-dependent regulation of sensory identity and connectivity C_LI

The precise formation of synapses ensures the proper wiring and function of nervous systems. Specific synapse formation is controlled by synaptic adhesion molecules, which link pre- and post-synaptic cells. Despite this central role, details of how adhesion molecules organize and signal intracellularly to build core synaptic structures are limited. Here, we identify multiple tyrosine phosphorylation sites on the cytoplasmic tail of the C. elegans SYG-1 synaptic adhesion molecule that are critical to initiate presynapse formation. We determine that SRC-1 and SRC-2 tyrosine kinases are redundantly responsible for SYG-1 phosphorylation and are consequently critical for presynapse assembly. The phosphorylated population of SYG-1 localizes in clusters within a larger SYG-1 pool and these clusters mark sites of presynaptic active zone assembly. Reconstitution of SYG-1 clusters in vitro with SH2-domain adapters and WSP-1 reveals a dynamic biomolecular condensate-forming system. Blocking phosphotyrosine adapters and condensate formation in vivo results in the loss of SYG-1 clusters, defective presynapse formation, and compromised neurotransmission. We conclude that phosphorylation of a subpopulation of synaptic adhesion molecules activates and organizes them into condensate-based clusters to initiate presynapse formation.

Meso2EM is a correlative light and electron microscopy workflow that transfers neurons selected from mesoscale functional images to targeted electron microscopy. We recorded Ca{superscript 2} signals from layer 2/3 neurons across a contiguous 3 x 3 mm cortical field in awake mice and reidentified a selected neuron after fixation and tangential sectioning. Lectin-labeled vascular architecture served as a shared landmark across in vivo two-photon imaging, confocal microscopy, laboratory micro-CT of resin-embedded tissue, and block-surface scanning electron microscopy, guiding focused-ion-beam scanning electron microscopy to the target cell body. The same progressive-targeting principle also supported serial ATUM-SEM reconstruction of an in vivo-tracked dendrite and serial transmission electron microscopy of optically selected dendrites from a patch-clamp-recorded Martinotti cell. Meso2EM therefore provides a practical route for preserving target identity across large changes in scale and specimen state while restricting electron-microscopy acquisition to a selected region.

The brain is essential for animal survival and based on its conserved Bauplan, an impressive adaptive diversity has evolved. However, the genetic mechanisms regulating brain development and diversification remain enigmatic. The insect neural stem cells (neuroblasts, NBs) acquire different identities through the combinatorial expression of transcription factors (TFs), but this code is unknown for the brain. Here, we define the conserved core of TFs expressed in insect brain NBs by a combined analysis of single-cell expression from NBs derived from two holometabolous insects, the fly Drosophila melanogaster and the beetle Tribolium castaneum. In Tribolium, we established a Gal4 enhancer trap system to identify a line that marks NBs. From 37,137 sequenced NBs, we identified 10,425 brain NBs. In Drosophila, we sequenced 32,112 NB nuclei, identifying 12,389 brain NBs. Analysing the combined dataset strongly increased the sensitivity in specifying the core of 188 brain-specific TFs. We found two atypical clusters with some similarity to Type II NBs and identified seven transcription factors not previously associated with or confirmed in NBs (Hmx, CG15696, CG32532, dmrt99B, fD59A, TfAP-2, and Fer1). Our data reveals fundamental differences between brain and ventral nerve cord specification and paves the way to study the development and evolution of brain specific structures.

Astrocyte border formation is a conserved neuroprotective response to neural tissue disruption, yet astrocyte border states at implanted biomaterials remain less well characterized than injury responses. Here, we developed the Astrocyte Border Characterization (ABC) Tool, which leverages a shear-thinning, injectable biomaterial to locally deliver astrocyte-specific RiboTag AAVs and small molecule regulators in the mouse striatum, enabling molecular profiling and phenotypic modulation of astrocyte border (AB) cells. Spatially precise delivery of AAV using the ABC Tool yielded enhanced specificity and robust RiboTag expression in AB cells from 7-70 days post injection. Temporal transcriptomic profiling of AB cells revealed predominantly acute, transient changes in genes governing dedifferentiation, proliferation, metabolic reprogramming, and inflammation regulation. Persistent changes accounted for only 14% of regulated genes but involved critical gain of functions in immune regulation and host defense that mirrored astrocyte border responses at chronic CNS injuries. Local delivery of indiscriminate or astrocyte-selective ablation molecules delayed, rather than prevented, border formation, ultimately yielding thicker astrocytes borders with increased inflammation and fibrosis at the biomaterial-tissue interface. Conversely, local delivery of {beta}-hydroxybutyrate (BHB) from the ABC Tool altered key aspects of the transcriptional reprogramming to attenuate chronic astrocyte reactivity and prevent biomaterial contraction without exacerbating inflammation or fibrosis. Our findings establish the ABC Tool as a bioassay for studying and manipulating astrocyte borders at implanted biomaterials and identify focal metabolic regulation as a strategy to modulate AB cell phenotypes and enhance the CNS biocompatibility of biomaterials.