Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses

Integrating physiological and transcriptomic analyses at the single-neuron level

Neurons generate various spike patterns to execute different functions. Understanding how these physiological neuronal spike patterns are related to their molecular characteristics is a long-standing issue in neuroscience. Herein, we review the results of recent studies that have addressed this issue by integrating physiological and transcriptomic techniques. A sequence of experiments, including in vivo recording and/or labeling, brain tissue slicing, cell collection, and transcriptomic analysis, have identified the gene expression profiles of brain neurons at the single-cell level, with activity patterns recorded in living animals. Although these techniques are still in the early stages, this methodological idea is principally applicable to various brain regions and neuronal activity patterns. Accumulating evidence will contribute to a deeper understanding of neuronal characteristics by integrating insights from molecules to cells, circuits, and behaviors.

Cell-type-specific manifold analysis discloses independent geometric transformations in the hippocampal spatial code

Integrating analyses of genetically defined cell types with population-level approaches remains poorly explored. We investigated this question by focusing on hippocampal spatial maps and the contribution of two genetically defined pyramidal cell types in the deep and superficial CA1 sublayers. Using single- and dual-color miniscope imaging in mice running along a linear track, we found that population activity from these cells exhibited three-dimensional ring manifolds that encoded the animal position and running direction. Despite shared topology, sublayer-specific manifolds displayed distinct geometric features. Manipulating track orientation revealed rotational and translational changes in manifolds from deep cells, contrasting with more stable representations by superficial cells. These transformations were not observed in manifolds derived from the entire CA1 population. Instead, cell-type-specific chemogenetic silencing of either sublayer revealed independent geometric codes. Our results show how genetically specified subpopulations may underpin parallel spatial maps that can be manipulated independently.

Integrating multimodal data to understand cortical circuit architecture and function

In recent years there has been a tremendous growth in new technologies that allow large-scale investigation of different characteristics of the nervous system at an unprecedented level of detail. There is a growing trend to use combinations of these new techniques to determine direct links between different modalities. In this Perspective, we focus on the mouse visual cortex, as this is one of the model systems in which much progress has been made in the integration of multimodal data to advance understanding. We review several approaches that allow integration of data regarding various properties of cortical cell types, connectivity at the level of brain areas, cell types and individual cells, and functional neural activity in vivo. The increasingly crucial contributions of computation and theory in analyzing and systematically modeling data are also highlighted. Together with open sharing of data, tools and models, integrative approaches are essential tools in modern neuroscience for improving our understanding of the brain architecture, mechanisms and function.

Inhibitory specificity from a connectomic census of mouse visual cortex

Mammalian cortex features a vast diversity of neuronal cell types, each with characteristic anatomical, molecular and functional properties1. Synaptic connectivity shapes how each cell type participates in the cortical circuit, but mapping connectivity rules at the resolution of distinct cell types remains difficult. Here we used millimetre-scale volumetric electron microscopy2 to investigate the connectivity of all inhibitory neurons across a densely segmented neuronal population of 1,352 cells spanning all layers of mouse visual cortex, producing a wiring diagram of inhibition with more than 70,000 synapses. Inspired by classical neuroanatomy, we classified inhibitory neurons based on targeting of dendritic compartments and developed an excitatory neuron classification based on dendritic reconstructions with whole-cell maps of synaptic input. Single-cell connectivity showed a class of disinhibitory specialist that targets basket cells. Analysis of inhibitory connectivity onto excitatory neurons found widespread specificity, with many interneurons exhibiting differential targeting of spatially intermingled subpopulations. Inhibitory targeting was organized into 'motif groups', diverse sets of cells that collectively target both perisomatic and dendritic compartments of the same excitatory targets. Collectively, our analysis identified new organizing principles for cortical inhibition and will serve as a foundation for linking contemporary multimodal neuronal atlases with the cortical wiring diagram.

Multimodal mismatch responses in mouse auditory cortex

Our movements result in predictable sensory feedback that is often multimodal. Based on deviations between predictions and actual sensory input, primary sensory areas of cortex have been shown to compute sensorimotor prediction errors. How prediction errors in one sensory modality influence the computation of prediction errors in another modality is still unclear. To investigate multimodal prediction errors in mouse auditory cortex, we used a virtual environment to experimentally couple running to both self-generated auditory and visual feedback. Using two-photon microscopy, we first characterized responses of layer 2/3 (L2/3) neurons to sounds, visual stimuli, and running onsets and found responses to all three stimuli. Probing responses evoked by audiomotor (AM) mismatches, we found that they closely resemble visuomotor (VM) mismatch responses in visual cortex (V1). Finally, testing for cross modal influence on AM mismatch responses by coupling both sound amplitude and visual flow speed to the speed of running, we found that AM mismatch responses were amplified when paired with concurrent VM mismatches. Our results demonstrate that multimodal and non-hierarchical interactions shape prediction error responses in cortical L2/3.

Modulation by serotonin reveals preferred recurrent excitatory connectivity in layer II of rat neocortex

We reported that in layer II pyramidal cells of rat somatosensory cortex, 10 μM serotonin (5-HT) alters miniature excitatory postsynaptic current frequency in a subset of cells (47%, "responders", RC; "non-responders", NC otherwise) via 5-HT2 receptors (5-HT2R) but in all pairs reduced evoked excitatory postsynaptic current amplitude by ~50% (Agahari FA, Stricker C. 2021. Serotonergic modulation of spontaneous and evoked transmitter release in layer II pyramidal cells of rat somatosensory cortex. Cereb Cortex. 31:1182-1200. https://doi.org/10.1093/cercor/bhaa285.) suggestive of preferential connectivity. We provide different lines of evidence that distinguish these subsets. First, after 5-HT exposure, changes in miniature excitatory postsynaptic current, spontaneous EPSC frequency, or whole-cell noise (σw) were restricted to postsynaptic cells in pairs (PO) and RC but absent in presynaptic (PR) and NC. Second, exposure caused a large change in holding current with a small variability in NC, but a small one with a large variability in PO/RC. In addition, ΔRin in PO/RC was larger than in PR/NC, with a negative correlation between ΔIhold and ΔRin in NC, a positive in PO, but none in RC. Third, an unbiased classifier identified most PO as RC and all PR as NC. Our data establish two distinct sets of pyramidal cells having a preferred connectivity from NC → RC. 5-HT2R-mediated modulation of transmitter release may likely reduce the signal-to-noise ratio in the ipsilateral but leave the output to the contralateral side unaffected.

Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex

The brain predicts regularities in sensory inputs at multiple complexity levels, with neuronal mechanisms that remain elusive. Here, we monitored auditory cortex activity during the local-global paradigm, a protocol nesting different regularity levels in sound sequences. We observed that mice encode local predictions based on stimulus occurrence and stimulus transition probabilities, because auditory responses are boosted upon prediction violation. This boosting was due to both short-term adaptation and an adaptation-independent surprise mechanism resisting anesthesia. In parallel, and only in wakefulness, VIP interneurons responded to the omission of the locally expected sound repeat at the sequence ending, thus providing a chunking signal potentially useful for establishing global sequence structure. When this global structure was violated, by either shortening the sequence or ending it with a locally expected but globally unexpected sound transition, activity slightly increased in VIP and PV neurons, respectively. Hence, distinct cellular mechanisms predict different regularity levels in sound sequences.

RDoC Framework Through the Lens of Predictive Processing: Focusing on Cognitive Systems Domain

In response to shortcomings of the current classification system in translating discoveries from basic science to clinical applications, NIMH offers a new framework for studying mental health disorders called Research Domain Criteria (RDoC). This framework holds a multidimensional outlook on psychopathologies focusing on functional domains of behavior and their implementing neural circuits. In parallel, the Predictive Processing (PP) framework stands as a leading theory of human brain function, offering a unified explanation for various types of information processing in the brain. While both frameworks share an interest in studying psychopathologies based on pathophysiology, their integration still needs to be explored. Here, we argued in favor of the explanatory power of PP to be a groundwork for the RDoC matrix in validating its constructs and creating testable hypotheses about mechanistic interactions between molecular biomarkers and clinical traits. Together, predictive processing may serve as a foundation for achieving the goals of the RDoC framework.

Brain-body physiology: Local, reflex, and central communication

Behavior is tightly synchronized with bodily physiology. Internal needs from the body drive behavior selection, while optimal behavior performance requires a coordinated physiological response. Internal state is dynamically represented by the nervous system to influence mood and emotion, and body-brain signals also direct responses to external sensory cues, enabling the organism to adapt and pursue its goals within an ever-changing environment. In this review, we examine the anatomy and function of the brain-body connection, manifested across local, reflex, and central regulation levels. We explore these hierarchical loops in the context of the immune system, specifically through the lens of immunoception, and discuss the impact of its dysregulation on human health.

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We used transcriptomic and epigenomic cortical cell type taxonomies from mouse and human to define marker genes and putative enhancers and created a large toolkit of transgenic lines and enhancer AAVs for selective targeting of cortical cell populations. We report evaluation of fifteen new transgenic driver lines, two new reporter lines, and >800 different enhancer AAVs covering most subclasses of cortical cells. The tools reported here as well as the scaled process of tool creation and modification enable diverse experimental strategies towards understanding mammalian cortex and brain function.

2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons

Neural circuits are characterized by genetically and functionally diverse cell types. A mechanistic understanding of circuit function is predicated on linking the genetic and physiological properties of individual neurons. However, it remains highly challenging to map the transcriptional properties to functionally heterogeneous neuronal subtypes in mammalian cortical circuits in vivo. Here, we introduce a high-throughput two-photon nuclear phototagging (2P-NucTag) approach optimized for on-demand and indelible labeling of single neurons via a photoactivatable red fluorescent protein following in vivo functional characterization in behaving mice. We demonstrate the utility of this function-forward pipeline by selectively labeling and transcriptionally profiling previously inaccessible 'place' and 'silent' cells in the mouse hippocampus. Our results reveal unexpected differences in gene expression between these hippocampal pyramidal neurons with distinct spatial coding properties. Thus, 2P-NucTag opens a new way to uncover the molecular principles that govern the functional organization of neural circuits.

Confidence and second-order errors in cortical circuits

Minimization of cortical prediction errors has been considered a key computational goal of the cerebral cortex underlying perception, action, and learning. However, it is still unclear how the cortex should form and use information about uncertainty in this process. Here, we formally derive neural dynamics that minimize prediction errors under the assumption that cortical areas must not only predict the activity in other areas and sensory streams but also jointly project their confidence (inverse expected uncertainty) in their predictions. In the resulting neuronal dynamics, the integration of bottom-up and top-down cortical streams is dynamically modulated based on confidence in accordance with the Bayesian principle. Moreover, the theory predicts the existence of cortical second-order errors, comparing confidence and actual performance. These errors are propagated through the cortical hierarchy alongside classical prediction errors and are used to learn the weights of synapses responsible for formulating confidence. We propose a detailed mapping of the theory to cortical circuitry, discuss entailed functional interpretations, and provide potential directions for experimental work.

Desegregation of neuronal predictive processing

Neural circuits construct internal 'world-models' to guide behavior. The predictive processing framework posits that neural activity signaling sensory predictions and concurrently computing prediction-errors is a signature of those internal models. Here, to understand how the brain generates predictions for complex sensorimotor signals, we investigate the emergence of high-dimensional, multi-modal predictive representations in recurrent networks. We find that robust predictive processing arises in a network with loose excitatory/inhibitory balance. Contrary to previous proposals of functionally specialized cell-types, the network exhibits desegregation of stimulus and prediction-error representations. We confirmed these model predictions by experimentally probing predictive-coding circuits using a rich stimulus-set to violate learned expectations. When constrained by data, our model further reveals and makes concrete testable experimental predictions for the distinct functional roles of excitatory and inhibitory neurons, and of neurons in different layers along a laminar hierarchy, in computing multi-modal predictions. These results together imply that in natural conditions, neural representations of internal models are highly distributed, yet structured to allow flexible readout of behaviorally-relevant information. The generality of our model advances the understanding of computation of internal models across species, by incorporating different types of predictive computations into a unified framework.

Predictive Processing: A Circuit Approach to Psychosis

Predictive processing is a computational framework that aims to explain how the brain processes sensory information by making predictions about the environment and minimizing prediction errors. It can also be used to explain some of the key symptoms of psychotic disorders such as schizophrenia. In recent years, substantial advances have been made in our understanding of the neuronal circuitry that underlies predictive processing in cortex. In this review, we summarize these findings and how they might relate to psychosis and to observed cell type-specific effects of antipsychotic drugs. We argue that quantifying the effects of antipsychotic drugs on specific neuronal circuit elements is a promising approach to understanding not only the mechanism of action of antipsychotic drugs but also psychosis. Finally, we outline some of the key experiments that should be done. The aims of this review are to provide an overview of the current circuit-based approaches to psychosis and to encourage further research in this direction.

Sample collection protocol for single-cell RNA sequencing of functionally identified neuronal populations in vivo

Here, we present a sample collection protocol for single-cell RNA sequencing of functionally identified neuronal populations in vivo with a virally delivered activity-dependent labeling tool (CaMPARI2). We describe steps for photoconversion in mice during the onset of computationally relevant events in a virtual reality environment, followed by removal and dissociation of the photo-labeled tissue, and separation of differentially labeled groups with fluorescence-activated cell sorting (FACS). We then detail procedures for characterizing and examining functionally relevant groups using standard bioinformatic techniques. For complete details on the use and execution of this protocol, please refer to O'Toole et al.1.

How can neuromorphic hardware attain brain-like functional capabilities?

The author provides 4 design principles of how to make cortical microcircuits into neuromorphic hardwares, shedding light for the next generation neuromorphic hardware design.

A method to analyze gene expression profiles from hippocampal neurons electrophysiologically recorded in vivo

Hippocampal pyramidal neurons exhibit diverse spike patterns and gene expression profiles. However, their relationships with single neurons are not fully understood. In this study, we designed an electrophysiology-based experimental procedure to identify gene expression profiles using RNA sequencing of single hippocampal pyramidal neurons whose spike patterns were recorded in living mice. This technique involves a sequence of experiments consisting of in vivo juxtacellular recording and labeling, brain slicing, cell collection, and transcriptome analysis. We demonstrated that the expression levels of a subset of genes in individual hippocampal pyramidal neurons were significantly correlated with their spike burstiness, submillisecond-level spike rise times or spike rates, directly measured by in vivo electrophysiological recordings. Because this methodological approach can be applied across a wide range of brain regions, it is expected to contribute to studies on various neuronal heterogeneities to understand how physiological spike patterns are associated with gene expression profiles.

Predictive coding with spiking neurons and feedforward gist signaling

Predictive coding (PC) is an influential theory in neuroscience, which suggests the existence of a cortical architecture that is constantly generating and updating predictive representations of sensory inputs. Owing to its hierarchical and generative nature, PC has inspired many computational models of perception in the literature. However, the biological plausibility of existing models has not been sufficiently explored due to their use of artificial neurons that approximate neural activity with firing rates in the continuous time domain and propagate signals synchronously. Therefore, we developed a spiking neural network for predictive coding (SNN-PC), in which neurons communicate using event-driven and asynchronous spikes. Adopting the hierarchical structure and Hebbian learning algorithms from previous PC neural network models, SNN-PC introduces two novel features: (1) a fast feedforward sweep from the input to higher areas, which generates a spatially reduced and abstract representation of input (i.e., a neural code for the gist of a scene) and provides a neurobiological alternative to an arbitrary choice of priors; and (2) a separation of positive and negative error-computing neurons, which counters the biological implausibility of a bi-directional error neuron with a very high baseline firing rate. After training with the MNIST handwritten digit dataset, SNN-PC developed hierarchical internal representations and was able to reconstruct samples it had not seen during training. SNN-PC suggests biologically plausible mechanisms by which the brain may perform perceptual inference and learning in an unsupervised manner. In addition, it may be used in neuromorphic applications that can utilize its energy-efficient, event-driven, local learning, and parallel information processing nature.

Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations

In an ever-changing visual world, animals' survival depends on their ability to perceive and respond to rapidly changing motion cues. The primary visual cortex (V1) is at the forefront of this sensory processing, orchestrating neural responses to perturbations in visual flow. However, the underlying neural mechanisms that lead to distinct cortical responses to such perturbations remain enigmatic. In this study, our objective was to uncover the neural dynamics that govern V1 neurons' responses to visual flow perturbations using a biologically realistic computational model. By subjecting the model to sudden changes in visual input, we observed opposing cortical responses in excitatory layer 2/3 (L2/3) neurons, namely, depolarizing and hyperpolarizing responses. We found that this segregation was primarily driven by the competition between external visual input and recurrent inhibition, particularly within L2/3 and L4. This division was not observed in excitatory L5/6 neurons, suggesting a more prominent role for inhibitory mechanisms in the visual processing of the upper cortical layers. Our findings share similarities with recent experimental studies focusing on the opposing influence of top-down and bottom-up inputs in the mouse primary visual cortex during visual flow perturbations.

Experience shapes chandelier cell function and structure in the visual cortex

Detailed characterization of interneuron types in primary visual cortex (V1) has greatly contributed to understanding visual perception, yet the role of chandelier cells (ChCs) in visual processing remains poorly characterized. Using viral tracing we found that V1 ChCs predominantly receive monosynaptic input from local layer 5 pyramidal cells and higher-order cortical regions. Two-photon calcium imaging and convolutional neural network modeling revealed that ChCs are visually responsive but weakly selective for stimulus content. In mice running in a virtual tunnel, ChCs respond strongly to events known to elicit arousal, including locomotion and visuomotor mismatch. Repeated exposure of the mice to the virtual tunnel was accompanied by reduced visual responses of ChCs and structural plasticity of ChC boutons and axon initial segment length. Finally, ChCs only weakly inhibited pyramidal cells. These findings suggest that ChCs provide an arousal-related signal to layer 2/3 pyramidal cells that may modulate their activity and/or gate plasticity of their axon initial segments during behaviorally relevant events.

Computational components of visual predictive coding circuitry

If a full visual percept can be said to be a 'hypothesis', so too can a neural 'prediction' - although the latter addresses one particular component of image content (such as 3-dimensional organisation, the interplay between lighting and surface colour, the future trajectory of moving objects, and so on). And, because processing is hierarchical, predictions generated at one level are conveyed in a backward direction to a lower level, seeking to predict, in fact, the neural activity at that prior stage of processing, and learning from errors signalled in the opposite direction. This is the essence of 'predictive coding', at once an algorithm for information processing and a theoretical basis for the nature of operations performed by the cerebral cortex. Neural models for the implementation of predictive coding invoke specific functional classes of neuron for generating, transmitting and receiving predictions, and for producing reciprocal error signals. Also a third general class, 'precision' neurons, tasked with regulating the magnitude of error signals contingent upon the confidence placed upon the prediction, i.e., the reliability and behavioural utility of the sensory data that it predicts. So, what is the ultimate source of a 'prediction'? The answer is multifactorial: knowledge of the current environmental context and the immediate past, allied to memory and lifetime experience of the way of the world, doubtless fine-tuned by evolutionary history too. There are, in consequence, numerous potential avenues for experimenters seeking to manipulate subjects' expectation, and examine the neural signals elicited by surprising, and less surprising visual stimuli. This review focuses upon the predictive physiology of mouse and monkey visual cortex, summarising and commenting on evidence to date, and placing it in the context of the broader field. It is concluded that predictive coding has a firm grounding in basic neuroscience and that, unsurprisingly, there remains much to learn.

Approaches and considerations of studying neuronal ensembles: a brief review

First theorized by Hebb, neuronal ensembles have provided a framework for understanding how the mammalian brain operates, especially regarding learning and memory. Neuronal ensembles are discrete, sparsely distributed groups of neurons that become activated in response to a specific stimulus and are thought to provide an internal representation of the world. Beyond the study of region-wide or projection-wide activation, the study of ensembles offers increased specificity and resolution to identify and target specific memories or associations. Neuroscientists interested in the neurobiology of learning, memory, and motivated behavior have used electrophysiological-, calcium-, and protein-based proxies of neuronal activity in preclinical models to better understand the neurobiology of learned and motivated behaviors. Although these three approaches may be used to pursue the same general goal of studying neuronal ensembles, technical differences lead to inconsistencies in the output and interpretation of data. This mini-review highlights some of the methodologies used in electrophysiological-, calcium-, and protein-based studies of neuronal ensembles and discusses their strengths and weaknesses.

Connecting single-cell transcriptomes to projectomes in mouse visual cortex

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.