Mapping visual functions onto molecular cell types in the mouse superior colliculus

Behavioral Modulation and Molecular Definition of Wide-Field Vertical Cells in the Mouse Superior Colliculus

Visual information can have different meanings across species, and the same visual stimulus can drive appetitive or aversive behavior. The superior colliculus (SC), a visual center located in the midbrain has been involved in driving such behaviors. Within this structure, the wide-field vertical cells (WFV) are a conserved morphological cell type that is present in species ranging from reptiles to cats (Basso et al., 2021). Here, we report our investigation of the connectivity of the WFV, their visual responses, and how these responses are modulated by locomotion in male and female laboratory mice. We also address the molecular definition of these cells and attempt to reconcile recent findings acquired by RNA sequencing of single cells in the SC with the Ntsr1-Cre GN209 transgenic mouse line which was previously used to investigate WFV. We use viral strategies to reveal WFV inputs and outputs and confirm their unique response properties using in vivo two-photon imaging. Among the stimuli tested, WFV prefer looming stimuli, a small moving spot, and upward-moving visual stimuli. We find that only visual responses driven by a looming stimulus show a significant modulation by locomotion. We identify several inputs to the WFV as potential candidates for this modulation. These results suggest that WFV integrate information across multiple brain regions and are subject to behavioral modulation. Taken together, our results pave the way to elucidate the role of these neurons in visual behavior and allow us to interrogate the definition of cell types in the light of new molecular definitions.

Preference-independent saliency map in the mouse superior colliculus

Detecting salient stimuli in a visual scene is crucial for animal survival, yet how the brain encodes visual saliency remains unclear. Here, using two-photon calcium imaging, we reveal a preference-independent saliency map in the superficial superior colliculus of awake mice. Salient stimuli evoke stronger responses than uniform stimuli in both excitatory and inhibitory neurons, with similar encoding patterns across both cell types. The strongest response occurs when a salient stimulus is centered within the receptive field, with contextual effects extending approximately 40°. Response amplitude scales with saliency strength but remains independent of neurons' orientation or motion direction preferences. Notably, saliency-encoding neurons exhibit weak orientation and direction selectivity, indicating a complementary relationship between saliency and feature maps. Importantly, this preference-independent saliency encoding does not require cortical inputs. These findings provide insights into the neural mechanisms underlying visual saliency detection.

Characterize neuronal responses to natural movies in the mouse superior colliculus

While artificial stimuli have been widely used in visual neuroscience and have significantly advanced our understanding of visual processing, they differ dramatically from the natural scenes that animals encounter in the wild. How natural stimuli are encoded in the superior colliculus (SC) and how neuronal responses to artificial and natural stimuli are related remain poorly understood. Here I applied two-photon calcium imaging to record neuronal activity in the mouse superficial SC in response to natural movies. An unsupervised learning algorithm grouped recorded neurons into 16 clusters based on their response patterns. Each cluster exhibited distinct temporal profiles, which arose from differences in both receptive field coverage and how neurons encode local visual features. Interestingly, I found a strong correlation between neuronal responses to natural movies and functional properties previously characterized using artificial stimuli. This suggests that the SC maintains a stable neural representation of visual information that is largely independent of the types of visual stimuli. Furthermore, neuronal responses to natural movies varied with depth within the superficial SC and across genetically defined neuronal types. These findings bridge the gap between our understanding of responses to artificial and natural stimuli, providing new insights into visual processing in the SC.

Transcriptomic neuron types vary topographically in function and morphology

Neuronal phenotypic traits such as morphology, connectivity and function are dictated, to a large extent, by a specific combination of differentially expressed genes. Clusters of neurons in transcriptomic space correspond to distinct cell types and in some cases-for example, Caenorhabditis elegans neurons1 and retinal ganglion cells2-4-have been shown to share morphology and function. The zebrafish optic tectum is composed of a spatial array of neurons that transforms visual inputs into motor outputs. Although the visuotopic map is continuous, subregions of the tectum are functionally specialized5,6. Here, to uncover the cell-type architecture of the tectum, we transcriptionally profiled its neurons, revealing more than 60 cell types that are organized in distinct anatomical layers. We measured the visual responses of thousands of tectal neurons by two-photon calcium imaging and matched them with their transcriptional profiles. Furthermore, we characterized the morphologies of transcriptionally identified neurons using specific transgenic lines. Notably, we found that neurons that are transcriptionally similar can diverge in shape, connectivity and visual responses. Incorporating the spatial coordinates of neurons within the tectal volume revealed functionally and morphologically defined anatomical subclusters within individual transcriptomic clusters. Our findings demonstrate that extrinsic, position-dependent factors expand the phenotypic repertoire of genetically similar neurons.

Co-Conservation of Synaptic Gene Expression and Circuitry in Collicular Neurons

The superior colliculus (SC), a midbrain sensorimotor hub, is anatomically and functionally similar across vertebrates, but how its cell types have evolved is unclear. Using single-nucleus transcriptomics, we compared the SC's molecular and cellular organization in mice, tree shrews, and humans. Despite over 96 million years of evolutionary divergence, we identified ~30 consensus neuronal subtypes, including Cbln2+ neurons that form the SC-pulvinar circuit in mice and tree shrews. Synapse-related genes were among the most conserved, unlike neocortex, suggesting co-conservation of synaptic genes and circuitry. In contrast, cilia-related genes diverged significantly across species, highlighting the potential importance of the neuronal primary cilium in SC evolution. Additionally, we identified a novel inhibitory SC neuron in tree shrews and humans but not mice. Our findings reveal that the SC has evolved by conserving neuron subtypes, synaptic genes, and circuitry, while diversifying ciliary gene expression and an inhibitory neuron subtype.

Coordination of distinct sources of excitatory inputs enhances motion selectivity in the mouse visual thalamus

Multiple sources innervate the visual thalamus to influence image-forming vision prior to the cortex, yet it remains unclear how non-retinal and retinal input coordinate to shape thalamic visual selectivity. Using dual-color two-photon calcium imaging in the thalamus of awake mice, we observed similar coarse-scale retinotopic organization between axons of superior colliculus neurons and retinal ganglion cells, both providing strong converging excitatory input to thalamic neurons. At a fine scale of ∼10 µm, collicular boutons often shared visual feature preferences with nearby retinal boutons. Inhibiting collicular input significantly suppressed visual responses in thalamic neurons and specifically reduced motion selectivity in neurons preferring nasal-to-temporal motion. The reduction in motion selectivity could be the result of silencing sharply tuned direction-selective colliculogeniculate input. These findings suggest that the thalamus is not merely a relay but selectively integrates inputs from multiple regions to build stimulus selectivity and shape the information transmitted to the cortex.

HIGHLIGHTS

Chronic dual-color calcium imaging reveals diverse visual tuning of collicular axonal boutons.Nearby collicular and retinal boutons often share feature preferences at ∼10 µm scaleSilencing of collicular input suppresses visual responses in the majority of thalamic neurons.Silencing of collicular input reduces motion selectivity in thalamic neurons.

Slow off responses in the rat superior colliculus neurons may contribute to the predator detection

A slowly moving dark spot imitating the shadow of a hovering bird of prey has been shown to induce freezing in rodents. Such visually triggered behaviours are usually initiated in the superior colliculus (SC); therefore, it is likely that such slowly moving dark spots can produce responses in SC neurons. In SC, two types of visual responses are typically distinguished: ON responses are produced by an increase in image brightness, and OFF responses are produced by a decrease in image brightness. Typically, OFF responses are very brief, lasting only a few hundred milliseconds, and may be poorly suited for the detection of slowly moving dark spots. Here, we report that, in the majority of SC neurons of urethane-anaesthetized rats, in addition to these brief OFF responses, very slow OFF responses lasting over 5 s were present; thus, OFF responses that occurred > 1 s after the stimulus offset were termed 'slow OFF' response, while brief, less than 1 s long OFF responses were called 'fast OFF' response. Although the slow OFF responses were of similar amplitude as the fast OFF responses (∼5 Hz), the optimal size (producing the maximal response) was larger for the slow OFF responses (20° for the slow and 10° for the fast OFF responses). Correlation analysis revealed that both the fast and the slow components of the OFF response contribute to the response to a slowly moving spot. Elimination of visual cortex inputs increased the amplitude and duration of the slow OFF responses, indicating that they originate in the retina. It is concluded that in rodent SC, a new type of OFF response that is well suited for predator detection is present.

The superior colliculus: New insights into an evolutionarily ancient structure

The superior colliculus is a structure located in the dorsal midbrain with well conserved function and connectivity across species. Essential for survival, the superior colliculus has evolved to trigger rapid orientation and avoidance movements in response to external stimuli. The increasing recognition of the widespread connectivity of the superior colliculus, not only with brainstem and spinal cord, but also with virtually all brain structures, has rekindled the interest on this structure and revealed novel roles in the past few years. In this review, we focus on the most recent advancements in understanding its cellular composition, connectivity and function, with a particular focus on how the cellular diversity and connectivity arises during development, as well as on its recent role in the emergence of sensory circuits.

Post-Critical Period Transcriptional and Physiological Adaptations of Thalamocortical Connections after Sensory Loss

Unilateral whisker denervation activates plasticity mechanisms and circuit adaptations in adults. Single nucleus RNA sequencing and multiplex fluorescence in situ hybridization revealed differentially expressed genes related to altered glutamate receptor distributions and synaptogenesis in thalamocortical (TC) recipient layer 4 (L4) neurons of the sensory cortex, specifically those receiving input from the intact whiskers after whisker denervation. Electrophysiology detected increased spontaneous excitatory events at L4 neurons, confirming an increase in synaptic connections. Elevated expression levels of Gria2 mRNA and functional GluA2 subunit of AMPA receptors at the TC synapse indicate the presence of stabilized and potentiated TC synapses to L4 excitatory neurons along the intact pathway after unilateral whisker denervation. These adaptations likely underlie the increased cortical activity observed in rodents during intact whisker sensation after unilateral whisker denervation. Our findings provide new insights into the mechanisms by which the adult brain supports recovery after unilateral sensory loss.

Analysis methods for large-scale neuronal recordings

Simultaneous recordings from hundreds or thousands of neurons are becoming routine because of innovations in instrumentation, molecular tools, and data processing software. Such recordings can be analyzed with data science methods, but it is not immediately clear what methods to use or how to adapt them for neuroscience applications. We review, categorize, and illustrate diverse analysis methods for neural population recordings and describe how these methods have been used to make progress on longstanding questions in neuroscience. We review a variety of approaches, ranging from the mathematically simple to the complex, from exploratory to hypothesis-driven, and from recently developed to more established methods. We also illustrate some of the common statistical pitfalls in analyzing large-scale neural data.

Genetically defined neuron types underlying visuomotor transformation in the superior colliculus

The superior colliculus (SC) is a conserved midbrain structure that is important for transforming visual and other sensory information into motor actions. Decades of investigations in numerous species have made the SC and its nonmammalian homologue, the optic tectum, one of the best studied structures in the brain, with rich information now available regarding its anatomical organization, its extensive inputs and outputs and its important functions in many reflexive and cognitive behaviours. Excitingly, recent studies using modern genomic and physiological approaches have begun to reveal the diverse neuronal subtypes in the SC, as well as their unique functions in visuomotor transformation. Studies have also started to uncover how subtypes of SC neurons form intricate circuits to mediate visual processing and visually guided behaviours. Here, we review these recent discoveries on the cell types and neuronal circuits underlying visuomotor transformations mediated by the SC. We also highlight the important future directions made possible by these new developments.

Brainstem inhibitory neurons enhance behavioral feature selectivity by sharpening the tuning of excitatory neurons

The brainstem is a hub for sensorimotor integration, which mediates crucial innate behaviors. This brain region is characterized by a rich population of GABAergic inhibitory neurons, required for the proper expression of these innate behaviors. However, what roles these inhibitory neurons play in innate behaviors and how they function are still not fully understood. Here, we show that inhibitory neurons in the nucleus of the optic tract and dorsal-terminal nuclei (NOT-DTN) of the mouse can modulate the innate eye movement optokinetic reflex (OKR) by shaping the tuning properties of excitatory NOT-DTN neurons. Specifically, we demonstrate that although these inhibitory neurons do not directly induce OKR, they enhance the visual feature selectivity of OKR behavior, which is mediated by the activity of excitatory NOT-DTN neurons. Moreover, consistent with the sharpening role of inhibitory neurons in OKR behavior, they have broader tuning relative to excitatory neurons. Last, we demonstrate that inhibitory NOT-DTN neurons directly provide synaptic inhibition to nearby excitatory neurons and sharpen their tuning in a sustained manner, accounting for the enhanced feature selectivity of OKR behavior. In summary, our findings uncover a fundamental principle underlying the computational role of inhibitory neurons in brainstem sensorimotor circuits.

Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq

The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing. For complete details on the use and execution of this protocol, please refer to Cheung et al.1.

Molecular Organization of Autonomic, Respiratory, and Spinally-Projecting Neurons in the Mouse Ventrolateral Medulla

The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control, serving as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the molecular and cellular organization of the VLM has remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing in male and female mice. The dataset was enriched with targeted sequencing of spinally-projecting and adrenergic/noradrenergic VLM neurons. Based on differentially expressed genes, the resulting dataset of 114,805 VLM cells identifies 23 subtypes of neurons, excluding those in the inferior olive, and five subtypes of astrocytes. Spinally-projecting neurons were found to be abundant in seven subtypes of neurons, which were validated through in situ hybridization. These subtypes included adrenergic/noradrenergic neurons, serotonergic neurons, and neurons expressing gene markers associated with premotor neurons in the ventromedial medulla. Further analysis of adrenergic/noradrenergic neurons and serotonergic neurons identified nine and six subtypes, respectively, within each class of monoaminergic neurons. Marker genes that identify the neural network responsible for breathing were concentrated in two subtypes of neurons, delineated from each other by markers for excitatory and inhibitory neurons. These datasets are available for public download and for analysis with a user-friendly interface. Collectively, this study provides a fine-scale molecular identification of cells in the VLM, forming the foundation for a better understanding of the VLM's role in vital functions and motor control.

Excitatory Projections of Wide Field Collicular Neurons to the Nucleus of the Optic Tract in the Rat

The superficial layers of the mammalian superior colliculus (SC) contain neurons that are generally responsive to visual stimuli but can differ considerably in morphology and response properties. To elucidate the structure and function of these neurons, we combined extracellular recording and juxtacellular labeling, detailed anatomical reconstruction, and ultrastructural analysis of the synaptic contacts of labeled neurons, using transmission electron microscopy. Our labeled neurons project to different brainstem nuclei. Of particular importance are neurons that fit the morphological criteria of the wide field (WF) neurons and whose dendrites are horizontally oriented. They display a rather characteristic axonal projection pattern to the nucleus of optic tract (NOT); thus, we call them superior collicular WF projecting to the NOT (SCWFNOT) neurons. We corroborated the morphological characterization of this neuronal type as a distinct neuronal class with the help of unsupervised hierarchical cluster analysis. Our ultrastructural data demonstrate that SCWFNOT neurons establish excitatory connections with their targets in the NOT. Although, in rodents, the literature about the WF neurons has focused on their extensive projection to the lateral posterior nucleus of the thalamus, as a conduit for information to reach the visual association areas of the cortex, our data suggest that this subclass of WF neurons may participate in the optokinetic nystagmus.

Transformation of Motion Pattern Selectivity from Retina to Superior Colliculus

The superior colliculus (SC) is a prominent and conserved visual center in all vertebrates. In mice, the most superficial lamina of the SC is enriched with neurons that are selective for the moving direction of visual stimuli. Here, we study how these direction selective neurons respond to complex motion patterns known as plaids, using two-photon calcium imaging in awake male and female mice. The plaid pattern consists of two superimposed sinusoidal gratings moving in different directions, giving an apparent pattern direction that lies between the directions of the two component gratings. Most direction selective neurons in the mouse SC respond robustly to the plaids and show a high selectivity for the moving direction of the plaid pattern but not of its components. Pattern motion selectivity is seen in both excitatory and inhibitory SC neurons and is especially prevalent in response to plaids with large cross angles between the two component gratings. However, retinal inputs to the SC are ambiguous in their selectivity to pattern versus component motion. Modeling suggests that pattern motion selectivity in the SC can arise from a nonlinear transformation of converging retinal inputs. In contrast, the prevalence of pattern motion selective neurons is not seen in the primary visual cortex (V1). These results demonstrate an interesting difference between the SC and V1 in motion processing and reveal the SC as an important site for encoding pattern motion.

Differential Expression Analysis Identifies Candidate Synaptogenic Molecules for Wiring Direction-Selective Circuits in the Retina

An organizational feature of neural circuits is the specificity of synaptic connections. A striking example is the direction-selective (DS) circuit of the retina. There are multiple subtypes of DS retinal ganglion cells (DSGCs) that prefer motion along one of four preferred directions. This computation is mediated by selective wiring of a single inhibitory interneuron, the starburst amacrine cell (SAC), with each DSGC subtype preferentially receiving input from a subset of SAC processes. We hypothesize that the molecular basis of this wiring is mediated in part by unique expression profiles of DSGC subtypes. To test this, we first performed paired recordings from isolated mouse retinas of both sexes to determine that postnatal day 10 (P10) represents the age at which asymmetric synapses form. Second, we performed RNA sequencing and differential expression analysis on isolated P10 ON-OFF DSGCs tuned for either nasal or ventral motion and identified candidates which may promote direction-specific wiring. We then used a conditional knock-out strategy to test the role of one candidate, the secreted synaptic organizer cerebellin-4 (Cbln4), in the development of DS tuning. Using two-photon calcium imaging, we observed a small deficit in directional tuning among ventral-preferring DSGCs lacking Cbln4, though whole-cell voltage-clamp recordings did not identify a significant change in inhibitory inputs. This suggests that Cbln4 does not function primarily via a cell-autonomous mechanism to instruct wiring of DS circuits. Nevertheless, our transcriptomic analysis identified unique candidate factors for gaining insights into the molecular mechanisms that instruct wiring specificity in the DS circuit.

Predation without direction selectivity

Across the animal kingdom, visual predation relies on motion-sensing neurons in the superior colliculus (SC) and its orthologs. These neurons exhibit complex stimulus preferences, including direction selectivity, which is thought to be critical for tracking the unpredictable escape routes of prey. The source of direction selectivity in the SC is contested, and its contributions to predation have not been tested experimentally. Here, we use type-specific cell removal to show that narrow-field (NF) neurons in the mouse SC guide predation. In vivo recordings demonstrate that direction-selective responses of NF cells are independent of recently reported stimulus-edge effects. Monosynaptic retrograde tracing reveals that NF cells receive synaptic input from direction-selective ganglion cells. When we eliminate direction selectivity in the retina of adult mice, direction-selective responses in the SC, including in NF cells, are lost. However, eliminating retinal direction selectivity does not affect the hunting success or strategies of mice, even when direction selectivity is removed after mice have learned to hunt, and despite abolishing the gaze-stabilizing optokinetic reflex. Thus, our results identify the retinal source of direction selectivity in the SC. They show that NF cells in the SC guide predation, an essential spatial orienting task, independent of their direction selectivity, revealing behavioral multiplexing of complex neural feature preferences and highlighting the importance of feature-selective manipulations for neuroethology.

Mapping the Retina onto the Brain

Vision begins in the retina, which extracts salient features from the environment and encodes them in the spike trains of retinal ganglion cells (RGCs), the output neurons of the eye. RGC axons innervate diverse brain areas (>50 in mice) to support perception, guide behavior, and mediate influences of light on physiology and internal states. In recent years, complete lists of RGC types (∼45 in mice) have been compiled, detailed maps of their dendritic connections drawn, and their light responses surveyed at scale. We know less about the RGCs' axonal projection patterns, which map retinal information onto the brain. However, some organizing principles have emerged. Here, we review the strategies and mechanisms that govern developing RGC axons and organize their innervation of retinorecipient brain areas.

Multipotent progenitors instruct ontogeny of the superior colliculus

The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.

Enhancement and contextual modulation of visuospatial processing by thalamocollicular projections from ventral lateral geniculate nucleus

In the mammalian visual system, the ventral lateral geniculate nucleus (vLGN) of the thalamus receives salient visual input from the retina and sends prominent GABAergic axons to the superior colliculus (SC). However, whether and how vLGN contributes to fundamental visual information processing remains largely unclear. Here, we report in mice that vLGN facilitates visually-guided approaching behavior mediated by the lateral SC and enhances the sensitivity of visual object detection. This can be attributed to the extremely broad spatial integration of vLGN neurons, as reflected in their much lower preferred spatial frequencies and broader spatial receptive fields than SC neurons. Through GABAergic thalamocollicular projections, vLGN specifically exerts prominent surround suppression of visuospatial processing in SC, leading to a fine tuning of SC preferences to higher spatial frequencies and smaller objects in a context-dependent manner. Thus, as an essential component of the central visual processing pathway, vLGN serves to refine and contextually modulate visuospatial processing in SC-mediated visuomotor behaviors via visually-driven long-range feedforward inhibition.

Characterization of primary visual cortex input to specific cell types in the superior colliculus

The superior colliculus is a critical brain region involved in processing visual information. It receives visual input directly from the retina, as well as via a projection from primary visual cortex. Here we determine which cell types in the superficial superior colliculus receive visual input from primary visual cortex in mice. Neurons in the superficial layers of the superior colliculus were classified into four groups - Wide-field, narrow-field, horizontal and stellate - based on their morphological and electrophysiological properties. To determine functional connections between V1 and these four different cell types we expressed Channelrhodopsin2 in primary visual cortex and then optically stimulated these axons while recording from different neurons in the superficial superior colliculus using whole-cell patch-clamp recording in vitro. We found that all four cell types in the superficial layers of the superior colliculus received monosynaptic (direct) input from V1. Wide-field neurons were more likely than other cell types to receive primary visual cortex input. Our results provide information on the cell specificity of the primary visual cortex to superior colliculus projection, increasing our understanding of how visual information is processed in the superior colliculus at the single cell level.

Retinal input integration in excitatory and inhibitory neurons in the mouse superior colliculus in vivo

The superior colliculus (SC) is a midbrain structure that receives inputs from retinal ganglion cells (RGCs). The SC contains one of the highest densities of inhibitory neurons in the brain but whether excitatory and inhibitory SC neurons differentially integrate retinal activity in vivo is still largely unknown. We recently established a recording approach to measure the activity of RGCs simultaneously with their postsynaptic SC targets in vivo, to study how SC neurons integrate RGC activity. Here, we employ this method to investigate the functional properties that govern retinocollicular signaling in a cell type-specific manner by identifying GABAergic SC neurons using optotagging in VGAT-ChR2 mice. Our results demonstrate that both excitatory and inhibitory SC neurons receive comparably strong RGC inputs and similar wiring rules apply for RGCs innervation of both SC cell types, unlike the cell type-specific connectivity in the thalamocortical system. Moreover, retinal activity contributed more to the spiking activity of postsynaptic excitatory compared to inhibitory SC neurons. This study deepens our understanding of cell type-specific retinocollicular functional connectivity and emphasizes that the two major brain areas for visual processing, the visual cortex and the SC, differently integrate sensory afferent inputs.