Behavioral state coding by molecularly defined paraventricular hypothalamic cell type ensembles

Single-cell and spatial omics: exploring hypothalamic heterogeneity

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

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.

Single-cell genomics meets systems neuroscience: Insights from mapping the brain circuitry of stress

Responses to external and internal dangers is essential for survival and homeostatic regulation. Hypothalamic corticotropin-releasing hormone neurons (CRHNs) play a pivotal role in regulating neuroendocrine responses to fear and stress. In recent years, the application of neurogenetic tools, such as fiber photometry, chemogenetics and optogenetics, have provided new insights into the dynamic neuronal responses of CRHNs during stressful events, offering new perspectives into their functional significance in mediating neurobehavioural responses to stress. Transsynaptic viral tracers have facilitated the comprehensive mapping of neuronal inputs to CRHNs. Furthermore, the development and application of innovative single-cell genomic tools combined with viral tracing have begun to pave the way for a deeper understanding of the transcriptional profiles of neural circuit components, enabling molecular-anatomical circuit mapping. Here, I will discuss how these systems neuroscience approaches and novel single-cell genomic methods are advancing the molecular and functional mapping of stress neurocircuits, their associated challenges and future directions.

Lateral hypothalamus and eating: cell types, molecular identity, anatomy, temporal dynamics and functional roles

The lateral hypothalamus (LH) is a central hub orchestrating eating behavior through its complex cellular, anatomical and temporal organization. The LH is characterized by high heterogeneity and functional complexity, with many aspects still unexplored. Here we synthesize recent advances in understanding the role of the LH in eating regulation across multiple dimensions. At the cellular level, the LH contains diverse neuronal populations that contribute to distinct roles in behavior. Anatomically, we divided the LH into four regions-anteromedial, anterolateral, posteromedial and posterolateral-each with unique cellular compositions, circuit organizations and projection patterns. By integrating the temporal dynamics of each LH cell type during eating behavior, we identified how various LH cell types are involved in regulating the appetitive and consummatory phases of eating behavior. The LH also plays vital roles in associative learning and different types of eating behavior, including homeostatic, pleasure-induced and stress-induced eating. These insights into LH organization and function provide promising directions for therapeutic interventions in eating disorders and obesity, including drugs, deep brain stimulation and gene therapy.

Neural cell competition sculpting brain from cradle to grave

Darwinian selection, operating within the cellular ecosystem of multicellular organisms, drives a pervasive surveillance mechanism of cell-cell competition that shapes tissue architecture and function. While cell competition eliminates suboptimal cells to ensure tissue integrity across various tissues, neuronal competition specifically sculpts neural networks to establish precise circuits for sensory, motor and cognitive functions. However, our understanding of cell competition across diverse neural cell types in both developmental and pathological contexts remains limited. Here, we review recent advances on the phenomenon, and mechanisms and potential functions of neural cell competition (NCC), ranging from neural progenitors, neurons, astrocytes and oligodendrocytes to microglia. Physiological NCC governs cellular survival, proliferation, arborization, organization, function and territorial colonization, whereas dysregulated NCC may cause neurodevelopmental disorders, accelerate aging, exacerbate neurodegenerative diseases and drive brain tumor progression. Future work that leverages cell competition mechanisms may help to improve cognition and curb diseases.

Projectome-based characterization of hypothalamic peptidergic neurons in male mice

The hypothalamus coordinately regulates physiological homeostasis and innate behaviors, yet the detailed arrangement of hypothalamic axons remains unclear. Here we mapped the whole-brain projections of over 7,000 hypothalamic neurons expressing distinct neuropeptides in male mice, identifying 2 main classes and 31 types using single-neuron projectome analysis. These classes/types exhibited regionally biased soma distribution and specific neuropeptide enrichment. Notably, many projectome types extended long-range axon collaterals to distinct brain regions, allowing single axons to co-regulate multiple targets. We uncovered topographic organization of certain peptidergic axons at specific targets, along with diverse single-neuron projectome patterns in Orexin, Agrp and Pomc populations. Furthermore, hypothalamic peptidergic neurons showed correlated innervation of subdomains in the periaqueductal gray and organized into modular subnetworks within the hypothalamus, providing a structural basis for coordinated outputs. This dataset highlights the complexity of hypothalamic axonal projections and lays a foundation for future investigation of the circuit mechanisms underlying hypothalamic functions.

Pathogen infection induces sickness behaviors through neuromodulators linked to stress and satiety in C. elegans

When animals are infected by a pathogen, peripheral sensors of infection signal to the brain to induce adaptive behavioral changes known as sickness behaviors. While the pathways that signal from the periphery to the brain have been intensively studied, how central circuits are reconfigured to elicit these behavioral changes is not well understood. Here we find that neuromodulatory systems linked to stress and satiety are recruited during chronic pathogen infection to alter the behavior of Caenorhabditis elegans. Upon infection by the bacterium Pseudomonas aeruginosa PA14, C. elegans decrease feeding, then display reversible bouts of quiescence, and eventually die. The ALA neuron and its neuropeptides FLP-7, FLP-24, and NLP-8, which control stress-induced sleep in uninfected animals, promote the PA14-induced feeding reduction. However, the ALA neuropeptide FLP-13 instead delays quiescence and death in infected animals. Cell-specific genetic perturbations show that the neurons that release FLP-13 to delay quiescence in infected animals are distinct from ALA. A brain-wide imaging screen reveals that infection-induced quiescence involves ASI and DAF-7/TGF-beta, which control satiety-induced quiescence in uninfected animals. Our results suggest that a common set of neuromodulators are recruited across different physiological states, acting from distinct neural sources and in distinct combinations to drive state-dependent behaviors.

Dopaminergic neurons in the paraventricular hypothalamus extend the food consumption phase

Feeding behavior is controlled by various neural networks in the brain that are involved in different feeding phases: Food procurement, consumption, and termination. However, the specific neural circuits controlling the food consumption phase remain poorly understood. Here, we investigated the roles of dopaminergic neurons in the paraventricular nucleus of the hypothalamus (PVH) in the feeding behavior in mice. Our results indicated that the PVH dopaminergic neurons were critical for extending the food consumption phase and involved in the development of obesity through epigenetic mechanisms. These neurons synchronized with proopiomelanocortin neurons during consumption, were stimulated by proopiomelanocortin activation, and projected to the lateral habenula (LHb), where dopamine receptor D2 was involved in the increase in food consumption. In addition, upregulated tyrosine hydroxylase (TH) expression in PVH was associated with obesity and indispensable for obesity induction in mice lacking Dnmt3a. Taken together, our results highlight the roles of PVH dopaminergic neurons in promoting food consumption and obesity induction.

The paraventricular nucleus of the hypothalamus: a key node in the control of behavioural states

The paraventricular nucleus (PVN) of the hypothalamus contains diverse populations of neuropeptide-producing neurons. These include neurons that synthesise oxytocin, vasopressin, corticotropin-releasing hormone, thyrotropin-releasing hormone and somatostatin. While it is well established that these neurons control the secretion of neuroendocrine hormones, there is growing evidence that they also control the expression of important homeostatic behaviours. Here we review recent data showing a critical role of PVN neurons in controlling arousal, social behaviour, defensive behaviour and pain. Collectively, this suggests that the PVN is a key node in a wider neural network controlling behavioural states.

Advances in Spatial Omics Technologies

Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.

Spatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortex

How early sensory experience during "critical periods" of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent [S. Cheng et al., Cell 185, 311-327.e24 (2022)]. Here, we characterize the spatial organization of L2/3 cell types with and without visual experience. Spatial transcriptomic profiling based on 500 genes recapitulates the zonation of L2/3 cell types along the pial-ventricular axis in V1. By applying multitasking theory, we suggest that the spatial zonation of L2/3 cell types is linked to the continuous nature of their gene expression profiles, which can be represented as a 2D manifold bounded by three archetypal cell types. By comparing normally reared and dark reared L2/3 cells, we show that visual deprivation-induced transcriptomic changes comprise two independent gene programs. The first, induced specifically in the visual cortex, includes immediate-early genes and genes associated with metabolic processes. It manifests as a change in cell state that is orthogonal to cell-type-specific gene expression programs. By contrast, the second program impacts L2/3 cell-type identity, regulating a subset of cell-type-specific genes and shifting the distribution of cells within the L2/3 cell-type manifold. Through an integrated analysis of spatial transcriptomics with single-nucleus RNA-seq data, we describe how vision patterns cortical L2/3 cell types during the critical period.

GPCRs in hypothalamic neurons and their roles in controlling food intake and metabolism

G-protein coupled receptor (GPCR) subtypes within the hypothalamus play a pivotal role in maintaining body homeostasis, particularly in the regulation of food intake and energy metabolism. This review provides an overview of classical loss and gain-of-function studies on GPCRs related to feeding and metabolism, with a focus on emerging cell-type-specific investigations. These studies reveal that diverse GPCR-expressing neuronal populations are intricately linked to feeding and energy balance. We also discuss recent findings that highlight the interaction of distinct peptide-GPCR systems in modulating complex feeding behaviors.

The regulation of glutamatergic nervous system in sleep-wake states and general anesthesia

The sleep-wake states and general anesthesia share many neurophysiological similarities, as both involve reversible changes in consciousness and modulation of brain activity. This paper reviews the role of glutamatergic neurons, the brain's primary excitatory neurons, in regulating sleep-wake states and general anesthesia. We discuss the involvement of glutamatergic neurons across various brain regions, including the brainstem, basal forebrain, thalamus, hypothalamus, and cortex, highlighting their contributions to physiological sleep-wake and anesthesia modulation. Recent advancements in techniques such as optogenetics, chemogenetics, and neural tracing have enhanced our understanding of these neurons' functions. Understanding these mechanisms can lead to improved therapeutic strategies for sleep disorders and more precise anesthetic practices, providing new avenues for clinical intervention.

Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex

Task learning involves learning associations between stimuli and outcomes and storing these relationships in memory. While this information can be reliably decoded from population activity, individual neurons encoding this representation can drift over time. The circuit or molecular mechanisms underlying this drift and its role in learning are unclear. We performed two-photon calcium imaging in the perirhinal cortex during task training. Using post hoc spatial transcriptomics, we measured immediate-early gene (IEG) expression and assigned monitored neurons to excitatory or inhibitory subtypes. We discovered an IEG-defined network spanning multiple subtypes that form stimulus-outcome associations. Targeted deletion of brain-derived neurotrophic factor in the perirhinal cortex disrupted IEG expression and impaired task learning. Representational drift slowed with prolonged training. Pre-existing representations were strengthened while stimulus-reward associations failed to form. Our findings reveal the cell types and molecules regulating long-term network stability that is permissive for task learning and memory allocation.

VGluT3 BNST neurons transmit GABA and restrict feeding without affecting rewarding or aversive processing

The bed nucleus of the stria terminalis (BNST) is involved in feeding, reward, aversion, and anxiety-like behavior. We identify BNST neurons defined by the expression of vesicular glutamate transporter 3, VGluT3. VGluT3 neurons were localized to anteromedial BNST, were molecularly distinct from accumbal VGluT3 neurons, and co-express vesicular GABA transporter (VGaT). Cell-type specific presynaptic processes were identified in arcuate nucleus (ARC) and the paraventricular nucleus of the hypothalamus (PVN), regions critical for feeding and homeostatic regulation. Whole-cell patch-clamp electrophysiology revealed that, while these neurons co-express VGluT3 and VGaT, they functionally transmit GABA to both ARC and PVN, with rare glutamate co-transmission to ARC. Neuronal recordings of VGluT3 BNST neurons showed greater calcium-dependent signaling in response to sucrose consumption while sated compared with fasted. When fasted, optogenetic stimulation of BNST VGluT3 neurons decreased sucrose consumption using several stimulation conditions but not when stimulation occurred prior to sucrose access, suggesting that BNST VGluT3 activation concurrent with consumption in the fasted state reduces feeding. BNST VGluT3 activation during anxiety-like paradigms (novelty-suppressed feeding, open field, and elevated zero maze) and real-time place conditioning resulted in no changes in anxiety-like or reward/aversion behavior. We interpret these data such that VGluT3 BNST neurons represent a unique cellular population within the BNST that provides inhibitory input to hypothalamic regions to decrease feeding without affecting anxiety-like or reward/aversion behavior.

The neurobiology of parenting and infant-evoked aggression

Parenting behavior comprises a variety of adult-infant and adult-adult interactions across multiple timescales. The state transition from nonparent to parent requires an extensive reorganization of individual priorities and physiology and is facilitated by combinatorial hormone action on specific cell types that are integrated throughout interconnected and brainwide neuronal circuits. In this review, we take a comprehensive approach to integrate historical and current literature on each of these topics across multiple species, with a focus on rodents. New and emerging molecular, circuit-based, and computational technologies have recently been used to address outstanding gaps in our current framework of knowledge on infant-directed behavior. This work is raising fundamental questions about the interplay between instinctive and learned components of parenting and the mutual regulation of affiliative versus agonistic infant-directed behaviors in health and disease. Whenever possible, we point to how these technologies have helped gain novel insights and opened new avenues of research into the neurobiology of parenting. We hope this review will serve as an introduction for those new to the field, a comprehensive resource for those already studying parenting, and a guidepost for designing future studies.

Flexible adjustment of oxytocin neuron activity in mouse dams revealed by microendoscopy

Oxytocin (OT) neurons in the hypothalamic paraventricular nucleus (PVH) play an important role in various physiological and behavioral processes, including the initiation of milk ejection and the regulation of maternal behaviors. However, their activity patterns at the single-cell level remain poorly understood. Using microendoscopic Ca2+ imaging in freely moving mouse dams, we demonstrate highly correlated pulsatile activity among individual OT neurons during lactation. The number of OT neurons engaged in the pulsatile activity significantly increased, along with a broadening of individual waveforms in the mid-lactation stage. Notably, only ~10% of the imaged OT neurons exhibited a significantly elevated response during pup retrieval, a hallmark of maternal behaviors, with a magnitude smaller than that observed during lactation. Collectively, these findings demonstrate the utility of microendoscopic imaging for PVH OT neurons and highlight the flexible adjustments of their individual activity patterns in freely behaving mouse dams.

Implementation and validation of single-cell genomics experiments in neuroscience

Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.

Hypothalamic corticotropin-releasing hormone neurons modulate sevoflurane anesthesia and the post-anesthesia stress responses

General anesthesia (GA) is an indispensable procedure necessary for safely and compassionately administering a significant number of surgical procedures and invasive diagnostic tests. However, the undesired stress response associated with GA causes delayed recovery and even increased morbidity in the clinic. Here, a core hypothalamic ensemble, corticotropin-releasing hormone neurons in the paraventricular nucleus of the hypothalamus (PVHCRH neurons), is discovered to play a role in regulating sevoflurane GA. Chemogenetic activation of these neurons delay the induction of and accelerated emergence from sevoflurane GA, whereas chemogenetic inhibition of PVHCRH neurons accelerates induction and delays awakening. Moreover, optogenetic stimulation of PVHCRH neurons induce rapid cortical activation during both the steady and deep sevoflurane GA state with burst-suppression oscillations. Interestingly, chemogenetic inhibition of PVHCRH neurons relieve the sevoflurane GA-elicited stress response (e.g., excessive self-grooming and elevated corticosterone level). These findings identify PVHCRH neurons modulate states of anesthesia in sevoflurane GA, being a part of anesthesia regulatory network of sevoflurane.

Dysfunctional astrocyte glutamate uptake in the hypothalamic paraventricular nucleus contributes to visceral pain and anxiety-like behavior in mice with chronic pancreatitis

Abdominal visceral pain is a predominant symptom in patients with chronic pancreatitis (CP); however, the underlying mechanism of pain in CP remains elusive. We hypothesized that astrocytes in the hypothalamic paraventricular nucleus (PVH) contribute to CP pain pathogenesis. A mouse model of CP was established by repeated intraperitoneal administration of caerulein to induce abdominal visceral pain. Abdominal mechanical stimulation, open field and elevated plus maze tests were performed to assess visceral pain and anxiety-like behavior. Fiber photometry, brain slice Ca2+ imaging, electrophysiology, and immunohistochemistry were used to investigate the underlying mechanisms. Mice with CP displayed long-term abdominal mechanical allodynia and comorbid anxiety, which was accompanied by astrocyte glial fibrillary acidic protein reactivity, elevated Ca2+ signaling, and astroglial glutamate transporter-1 (GLT-1) deficits in the PVH. Specifically, reducing astrocyte Ca2+ signaling in the PVH via chemogenetics significantly rescued GLT-1 deficits and alleviated mechanical allodynia and anxiety in mice with CP. Furthermore, we found that GLT-1 deficits directly contributed to the hyperexcitability of VGLUT2PVH neurons in mice with CP, and that pharmacological activation of GLT-1 alleviated the hyperexcitability of VGLUT2PVH neurons, abdominal visceral pain, and anxiety in these mice. Taken together, our data suggest that dysfunctional astrocyte glutamate uptake in the PVH contributes to visceral pain and anxiety in mice with CP, highlighting GLT-1 as a potential therapeutic target for chronic pain in patients experiencing CP.

Link Brain-Wide Projectome to Neuronal Dynamics in the Mouse Brain

Knowledge about the neuronal dynamics and the projectome are both essential for understanding how the neuronal network functions in concert. However, it remains challenging to obtain the neural activity and the brain-wide projectome for the same neurons, especially for neurons in subcortical brain regions. Here, by combining in vivo microscopy and high-definition fluorescence micro-optical sectioning tomography, we have developed strategies for mapping the brain-wide projectome of functionally relevant neurons in the somatosensory cortex, the dorsal hippocampus, and the substantia nigra pars compacta. More importantly, we also developed a strategy to achieve acquiring the neural dynamic and brain-wide projectome of the molecularly defined neuronal subtype. The strategies developed in this study solved the essential problem of linking brain-wide projectome to neuronal dynamics for neurons in subcortical structures and provided valuable approaches for understanding how the brain is functionally organized via intricate connectivity patterns.

From Mammals to Insects: Exploring the Genetic and Neural Basis of Eating Behavior

Obesity and anorexia are life-threatening diseases that are still poorly understood at the genetic and neuronal levels. Patients suffering from these conditions experience disrupted regulation of food consumption, leading to extreme weight gain or loss and, in severe situations, death from metabolic dysfunction. Despite the development of various behavioral and pharmacological interventions, current treatments often yield limited and short-lived success. To address this, a deeper understanding of the genetic and neural mechanisms underlying food perception and appetite regulation is essential for identifying new drug targets and developing more effective treatment methods. This review summarizes the progress of past research in understanding the genetic and neural mechanisms controlling food consumption and appetite regulation, focusing on two key model organisms: the fruit fly Drosophila melanogaster and the mouse Mus musculus. These studies investigate how the brain senses energy and nutrient deficiency, how sensory signals trigger appetitive behaviors, and how food intake is regulated through interconnected neural circuits in the brain.

Early perturbations to fluid homeostasis alter development of hypothalamic feeding circuits with context-specific changes in ingestive behavior

Drinking and feeding are tightly coordinated homeostatic events and the paraventricular nucleus of the hypothalamus (PVH) represents a possible node of neural integration for signals related to energy and fluid homeostasis. We used TRAP2;Ai14 and Fos labeling to visualize neurons in the PVH and median preoptic nucleus (MEPO) responding to both water deprivation and hunger. Moreover, we determined that structural and functional development of dehydration-sensitive inputs to the PVH from the MEPO precedes those of agouti-related peptide (AgRP) neurons, which convey hunger signals and are known to be developmentally programmed by nutrition. We also determined that osmotic hyperstimulation of neonatal mice led to enhanced AgRP inputs to the PVH in adulthood, as well as disruptions to ingestive behaviors during high-fat diet feeding and dehydration-anorexia. Thus, development of feeding circuits is impacted not only by nutritional signals, but also by early perturbations to fluid homeostasis with context-specific consequences for coordination of ingestive behavior.

A line attractor encoding a persistent internal state requires neuropeptide signaling

Internal states drive survival behaviors, but their neural implementation is poorly understood. Recently, we identified a line attractor in the ventromedial hypothalamus (VMH) that represents a state of aggressiveness. Line attractors can be implemented by recurrent connectivity or neuromodulatory signaling, but evidence for the latter is scant. Here, we demonstrate that neuropeptidergic signaling is necessary for line attractor dynamics in this system by using cell-type-specific CRISPR-Cas9-based gene editing combined with single-cell calcium imaging. Co-disruption of receptors for oxytocin and vasopressin in adult VMH Esr1+ neurons that control aggression diminished attack, reduced persistent neural activity, and eliminated line attractor dynamics while only slightly reducing overall neural activity and sex- or behavior-specific tuning. These data identify a requisite role for neuropeptidergic signaling in implementing a behaviorally relevant line attractor in mammals. Our approach should facilitate mechanistic studies in neuroscience that bridge different levels of biological function and abstraction.

Dexmedetomidine Promotes NREM Sleep by Depressing Oxytocin Neurons in the Paraventricular Nucleus in Mice

Dexmedetomidine (DEX) is a highly selective α2-adrenoceptor agonist with sedative effects on sleep homeostasis. Oxytocin-expressing (OXT) neurons in the paraventricular nucleus (PVN) of the hypothalamus (PVNOXT) regulate sexual reproduction, drinking, sleep-wakefulness, and other instinctive behaviors. To investigate the effect of DEX on the activity and signal transmission of PVNOXT in regulating the sleep-wakefulness cycle. Here, we employed OXT-cre mice to selectively target and express the designer receptors exclusively activated by designer drugs (DREADD)-based chemogenetic tool hM3D(Gq) in PVNOXT neurons. Combining chemogenetic methods with electroencephalogram (EEG) /electromyogram (EMG) recordings, we found that cannula injection of DEX in PVN significantly increased the duration of non-rapid eye movement (NREM) sleep in mice. Furthermore, the chemogenetic activation of PVNOXT neurons using i.p. injection of clozapine N-oxide (CNO) after cannula injection of DEX to PVN led to a substantial increase in wakefulness. Electrophysiological results showed that DEX decreased the frequency of action potential (AP) and the spontaneous excitatory postsynaptic current (sEPSC) of PVNOXT neurons through α2-adrenoceptors. Therefore, these results identify that DEX promotes sleep and maintains sleep homeostasis by inhibiting PVNOXT neurons through the α2-adrenoceptor.

Control of sodium appetite by hindbrain aldosterone-sensitive neurons

Mineralocorticoids play a key role in hydromineral balance by regulating sodium retention and potassium wasting. Through favoring sodium, mineralocorticoids can cause hypertension from fluid overload under conditions of hyperaldosteronism, such as aldosterone-secreting tumors. An often-overlooked mechanism by which aldosterone functions to increase sodium is through stimulation of salt appetite. To drive sodium intake, aldosterone targets neurons in the hindbrain which uniquely express 11β-hydroxysteroid dehydrogenase type 2 (HSD2). This enzyme is a necessary precondition for aldosterone-sensing cells as it metabolizes glucocorticoids - preventing their activation of the mineralocorticoid receptor. In this review, we will consider the role of hindbrain HSD2 neurons in regulating sodium appetite by discussing HSD2 expression in the brain, regulation of hindbrain HSD2 neuron activity, and the circuitry mediating the effects of these aldosterone-sensitive neurons. Reducing the activity of hindbrain HSD2 neurons may be a viable strategy to reduce sodium intake and cardiovascular risk, particularly for conditions of hyperaldosteronism.

Neurobiological mechanisms underlying oxytocin-mediated parental behavior in rodents

Parental behavior is essential for mammalian offspring to survive. Because of this significance, elucidating the neurobiological mechanisms that facilitate parental behavior has received strong interest. Decades of studies utilizing pharmacology and molecular biology have revealed that in addition to its facilitatory effects on parturition and lactation, oxytocin (OT) promotes the expression of parental behavior in rodents. Recent studies have also described the modulation of sensory processing by OT and the interaction of the OT system with other brain regions associated with parental behavior. However, the precise neurobiological mechanisms underlying the facilitation of caregiving behaviors by OT remain unclear. In this Review, I summarize the findings from rats and mice with a view toward integrating past and recent progress. I then review recent advances in the understanding of the molecular, cellular, and circuit mechanisms of OT-mediated parental behavior. Based on these observations, I propose a hypothetical model that would explain the mechanisms underlying OT-mediated parental behavior. Finally, I conclude by discussing some major remaining questions and propose potential future research directions.

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.

Molecular underpinnings underlying behaviors changes in the brain of juvenile common carp (Cyrinus carpio) in response to warming

INTRODUCTION

Global warming is increasing interest in how aquatic animals can adjust their physiological performance and cope with temperature changes. Therefore, understanding the behavioral changes and molecular underpinnings in fish under warming is crucial for both the individual and groups survival. This could provide experimental evidence and resource for evaluating the impact of global warming.

OBJECTIVE

Three genetic families of common carp (Cyprinus carpio) were generated. These juveniles were constructed short-term (4 days) and long-term (30 days) warming groups to investigate the effects of warming on behavioral responses and to elucidate the potential underlying mechanisms of warming-driven behavior.

METHODS

Behavioral tests were used to explore the effects of short- and long-term exposure to warming on the swimming behavior of C. carpio. Brain transcriptome combined with measurement of nervous system activity was used to further investigated the comprehensive neuromolecular mechanisms under warming.

RESULTS

Long-term warming groups had a more significant impact on the decline of swimming behavior in juvenile C. carpio. Furthermore, brain comparative transcriptomic analysis combined with measurement of nervous system activity revealed that genes involved in cytoskeletal organization, mitochondrial regulation, and energy metabolism are major regulators of behavior in the juvenile under warming. Importantly, especially in the long-term warming groups, enrichment analysis of associated gene expression suggested functional alterations of synaptic transmission and signal transduction leading to swimming function impairment in the central nervous system, as revealed by behavioral tests.

CONCLUSIONS

Our study provides evidence of the neurogenomic mechanism underlying the decreased swimming activity in juvenile C. carpio under warming. These findings have important implications for understanding the impacts of climate change on aquatic ecosystems and the organisms that inhabit them.

Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks

Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 μm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D in situ quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 200-μm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring, and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.

Navigating Central Oxytocin Transport: Known Realms and Uncharted Territories

Complex mechanisms govern the transport and action of oxytocin (Oxt), a neuropeptide and hormone that mediates diverse physiologic processes. While Oxt exerts site-specific and rapid effects in the brain via axonal and somatodendritic release, volume transmission via CSF and the neurovascular interface can act as an additional mechanism to distribute Oxt signals across distant brain regions on a slower timescale. This review focuses on modes of Oxt transport and action in the CNS, with particular emphasis on the roles of perivascular spaces, the blood-brain barrier (BBB), and circumventricular organs in coordinating the triadic interaction among circulating blood, CSF, and parenchyma. Perivascular spaces, critical conduits for CSF flow, play a pivotal role in Oxt diffusion and distribution within the CNS and reciprocally undergo Oxt-mediated structural and functional reconstruction. While the BBB modulates the movement of Oxt between systemic and cerebral circulation in a majority of brain regions, circumventricular organs without a functional BBB can allow for diffusion, monitoring, and feedback regulation of bloodborne peripheral signals such as Oxt. Recognition of these additional transport mechanisms provides enhanced insight into the systemic propagation and regulation of Oxt activity.

Stress integration by an ascending adrenergic-melanocortin circuit

Stress is thought to be an important contributing factor for eating disorders; however, neural substrates underlying the complex relationship between stress and appetite are not fully understood. Using in vivo recordings from awake behaving mice, we show that various acute stressors activate catecholaminergic nucleus tractus solitarius (NTSTH) projections in the paraventricular hypothalamus (PVH). Remarkably, the resulting adrenergic tone inhibits MC4R-expressing neurons (PVHMC4R), which are known for their role in feeding suppression. We found that PVHMC4R silencing encodes negative valence in sated mice and is required for avoidance induced by visceral malaise. Collectively, these findings establish PVHMC4R neurons as an effector of stress-activated brainstem adrenergic input in addition to the well-established hypothalamic-pituitary-adrenal axis. Convergent modulation of stress and feeding by PVHMC4R neurons implicates NTSTH → PVHMC4R input in stress-associated appetite disorders.

Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.

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.

Space-feature measures on meshes for mapping spatial transcriptomics

Advances in the development of largely automated microscopy methods such as MERFISH for imaging cellular structures in mouse brains are providing spatial detection of micron resolution gene expression. While there has been tremendous progress made in the field of Computational Anatomy (CA) to perform diffeomorphic mapping technologies at the tissue scales for advanced neuroinformatic studies in common coordinates, integration of molecular- and cellular-scale populations through statistical averaging via common coordinates remains yet unattained. This paper describes the first set of algorithms for calculating geodesics in the space of diffeomorphisms, what we term space-feature-measure LDDMM, extending the family of large deformation diffeomorphic metric mapping (LDDMM) algorithms to accommodate a space-feature action on marked particles which extends consistently to the tissue scales. It leads to the derivation of a cross-modality alignment algorithm of transcriptomic data to common coordinate systems attached to standard atlases. We represent the brain data as geometric measures, termed as space-feature measures supported by a large number of unstructured points, each point representing a small volume in space and carrying a list of densities of features elements of a high-dimensional feature space. The shape of space-feature measure brain spaces is measured by transforming them by diffeomorphisms. The metric between these measures is obtained after embedding these objects in a linear space equipped with the norm, yielding a so-called "chordal metric".

Maternal dietary fat during lactation shapes single nucleus transcriptomic profile of postnatal offspring hypothalamus in a sexually dimorphic manner in mice

Maternal overnutrition during lactation predisposes offspring to develop metabolic diseases and exacerbates the relevant syndromes in males more than females in later life. The hypothalamus is a heterogenous brain region that regulates energy balance. Here we combined metabolic trait quantification of mother and offspring mice under low and high fat diet (HFD) feeding during lactation, with single nucleus transcriptomic profiling of their offspring hypothalamus at peak lacation to understand the cellular and molecular alterations in response to maternal dietary pertubation. We found significant expansion in neuronal subpopulations including histaminergic (Hdc), arginine vasopressin/retinoic acid receptor-related orphan receptor β (Avp/Rorb) and agouti-related peptide/neuropeptide Y (AgRP/Npy) in male offspring when their mothers were fed HFD, and increased Npy-astrocyte interactions in offspring responding to maternal overnutrition. Our study provides a comprehensive offspring hypothalamus map at the peak lactation and reveals how the cellular subpopulations respond to maternal dietary fat in a sex-specific manner during development.

Reciprocal activity of AgRP and POMC neurons governs coordinated control of feeding and metabolism

Agouti-related peptide (AgRP)-expressing and proopiomelanocortin (POMC)-expressing neurons reciprocally regulate food intake. Here, we combine non-interacting recombinases to simultaneously express functionally opposing chemogenetic receptors in AgRP and POMC neurons for comparing metabolic responses in male and female mice with simultaneous activation of AgRP and inhibition of POMC neurons with isolated activation of AgRP neurons or isolated inhibition of POMC neurons. We show that food intake is regulated by the additive effect of AgRP neuron activation and POMC neuron inhibition, while systemic insulin sensitivity and gluconeogenesis are differentially modulated by isolated-versus-simultaneous regulation of AgRP and POMC neurons. We identify a neurocircuit engaging Npy1R-expressing neurons in the paraventricular nucleus of the hypothalamus, where activated AgRP neurons and inhibited POMC neurons cooperate to promote food consumption and activate Th+ neurons in the nucleus tractus solitarii. Collectively, these results unveil how food intake is precisely regulated by the simultaneous bidirectional interplay between AgRP and POMC neurocircuits.

Neural control of fluid homeostasis is engaged below 10°C in hibernation

Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) hibernate for several months each winter without access to water,1 but the mechanisms that maintain fluid homeostasis during hibernation are poorly understood. In torpor, when body temperature (TB) reaches 4°C, squirrels decrease metabolism, slow heart rate, and reduce plasma levels of the antidiuretic hormones arginine vasopressin (AVP) and oxytocin (OXT).1 Squirrels spontaneously undergo interbout arousal (IBA) every 2 weeks, temporarily recovering an active-like metabolism and a TB of 37°C for up to 48 h.1,2 Despite the low levels of AVP and OXT during torpor, profound increases in blood pressure and heart rate during the torpor-IBA transition are not associated with massive fluid loss, suggesting the existence of a mechanism that protects against diuresis at a low TB. Here, we demonstrate that the antidiuretic hormone release pathway is activated by hypothalamic supraoptic nucleus (SON) neurons early in the torpor-arousal transition. SON neuron activity, dense-core vesicle release from the posterior pituitary, and plasma hormone levels all begin to increase before TB reaches 10°C. In vivo fiber photometry of SON neurons from hibernating squirrels, together with RNA sequencing and c-FOS immunohistochemistry, confirms that SON is electrically, transcriptionally, and translationally active to monitor blood osmolality throughout the dynamic torpor-arousal transition. Our work emphasizes the importance of the antidiuretic pathway during the torpor-arousal transition and reveals that the neurophysiological mechanism that coordinates the hormonal response to retain fluid is active at an extremely low TB, which is prohibitive for these processes in non-hibernators.

Geometric transformation adaptive optics (GTAO) for volumetric deep brain imaging through gradient-index lenses

The advance of genetic function indicators has enabled the observation of neuronal activities at single-cell resolutions. A major challenge for the applications on mammalian brains is the limited optical access depth. Currently, the method of choice to access deep brain structures is to insert miniature optical components. Among these validated miniature optics, the gradient-index (GRIN) lens has been widely employed for its compactness and simplicity. However, due to strong fourth-order astigmatism, GRIN lenses suffer from a small imaging field of view, which severely limits the measurement throughput and success rate. To overcome these challenges, we developed geometric transformation adaptive optics (GTAO), which enables adaptable achromatic large-volume correction through GRIN lenses. We demonstrate its major advances through in vivo structural and functional imaging of mouse brains. The results suggest that GTAO can serve as a versatile solution to enable large-volume recording of deep brain structures and activities through GRIN lenses.

An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types

The hypothalamic paraventricular nucleus (PVN) is a highly complex brain region that is crucial for homeostatic regulation through neuroendocrine signaling, outflow of the autonomic nervous system, and projections to other brain areas. In the past years, single-cell datasets of the hypothalamus have contributed immensely to the current understanding of the diverse hypothalamic cellular composition. While the PVN has been adequately classified functionally, its molecular classification is currently still insufficient. To address this, we created a detailed atlas of PVN transcriptomic cell types by integrating various PVN single-cell datasets into a recently published hypothalamus single-cell transcriptome atlas. Furthermore, we functionally profiled transcriptomic cell types, based on relevant literature, existing retrograde tracing data, and existing single-cell data of a PVN-projection target region. Finally, we validated our findings with immunofluorescent stainings. In our PVN atlas dataset, we identify the well-known different neuropeptide types, each composed of multiple novel subtypes. We identify Avp-Tac1, Avp-Th, Oxt-Foxp1, Crh-Nr3c1, and Trh-Nfib as the most important neuroendocrine subtypes based on markers described in literature. To characterize the preautonomic functional population, we integrated a single-cell retrograde tracing study of spinally projecting preautonomic neurons into our PVN atlas. We identify these (presympathetic) neurons to cocluster with the Adarb2+ clusters in our dataset. Further, we identify the expression of receptors for Crh, Oxt, Penk, Sst, and Trh in the dorsal motor nucleus of the vagus, a key region that the pre-parasympathetic PVN neurons project to. Finally, we identify Trh-Ucn3 and Brs3-Adarb2 as some centrally projecting populations. In conclusion, our study presents a detailed overview of the transcriptomic cell types of the murine PVN and provides a first attempt to resolve functionality for the identified populations.

Gene panel selection for targeted spatial transcriptomics

Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.

Molecular organization of neuronal cell types and neuromodulatory systems in the zebrafish telencephalon

The function of neuronal networks is determined not only by synaptic connectivity but also by neuromodulatory systems that broadcast information via distributed connections and volume transmission. To understand the molecular constraints that organize neuromodulatory signaling in the telencephalon of adult zebrafish, we used transcriptomics and additional approaches to delineate cell types, to determine their phylogenetic conservation, and to map the expression of marker genes at high granularity. The combinatorial expression of GPCRs and cell-type markers indicates that all neuronal cell types are subject to modulation by multiple monoaminergic systems and distinct combinations of neuropeptides. Individual cell types were associated with multiple (typically >30) neuromodulatory signaling networks but expressed only a few diagnostic GPCRs at high levels, suggesting that different neuromodulatory systems act in combination, albeit with unequal weights. These results provide a detailed map of cell types and brain areas in the zebrafish telencephalon, identify core components of neuromodulatory networks, highlight the cell-type specificity of neuropeptides and GPCRs, and begin to decipher the logic of combinatorial neuromodulation.

Neuroscience of reward: Paradoxical roles for corticotrophin-releasing factor

The brain has long been known to control stress and reward through complex and interconnected circuitry. A new study now reveals a group of hypothalamic neurons that paradoxically mediate both reward and aversion.

Designing a Hybrid Chain Reaction Probe for Multiplex Transcripts Assay with High-Level Imaging

The hybrid chain reaction (HCR), an isothermal and enzyme-free amplification strategy, has found extensive use in fluorescent in situ hybridization (FISH) assays. However, the existing HCRs are limited, being time-consuming processes and low-efficiency imaging due to weak signal, significantly restricting their application in transcriptomic assays. To address the limitations, we developed nine orthogonal HCR hairpin-pair (hp) probes in this study to enable efficient signal amplification for multiplex assays. To enhance the efficiency and imaging quality of multiplex assays using these HCR probes, we employed two strategies. First, we coupled fluorescent molecules to HCR hairpins via disulfide bonds, facilitating easy removal through chemical cleavage. As a result, the workflow was greatly simplified. Second, we combined HCR with in situ rolling circle amplification (ISRCA), creating ISRCA-HCR, which achieved a 17-fold signal amplification. ISRCA-HCR demonstrated a high-level imaging capability for spatial cell type assays. This study shows the application for cell typing based on the developed HCR probes, enabling accurate and high-level signal amplification for multiplex FISH imaging. This provides an effective research tool for transcriptome and spatial cell type analysis.

Hypothalamic CRH neurons represent physiological memory of positive and negative experience

Recalling a salient experience provokes specific behaviors and changes in the physiology or internal state. Relatively little is known about how physiological memories are encoded. We examined the neural substrates of physiological memory by probing CRHPVN neurons of mice, which control the endocrine response to stress. Here we show these cells exhibit contextual memory following exposure to a stimulus with negative or positive valence. Specifically, a negative stimulus invokes a two-factor learning rule that favors an increase in the activity of weak cells during recall. In contrast, the contextual memory of positive valence relies on a one-factor rule to decrease activity of CRHPVN neurons. Finally, the aversive memory in CRHPVN neurons outlasts the behavioral response. These observations provide information about how specific physiological memories of aversive and appetitive experience are represented and demonstrate that behavioral readouts may not accurately reflect physiological changes invoked by the memory of salient experiences.

Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

Head-mounted miniscopes have allowed for functional fluorescence imaging in freely moving animals. However, current capabilities of state-of-the-art technology can record only up to two, spectrally distinct fluorophores. This severely limits the number of cell types identifiable in a functional imaging experiment. Here we present a pipeline that enables the distinction of nine neuronal subtypes from regions defined by behaviorally relevant cells during in vivo GCaMP imaging. These subtypes are identified utilizing unique fluorophores that are co-expressed with GCaMP, unmixed by spectral imaging on a confocal microscope and co-registering these spectral fingerprints with functional data obtained on miniaturized microscopes. This method facilitates detailed analyses of circuit-level encoding of behavior.

Deep-brain optical recording of neural dynamics during behavior

In vivo fluorescence recording techniques have produced landmark discoveries in neuroscience, providing insight into how single cell and circuit-level computations mediate sensory processing and generate complex behaviors. While much attention has been given to recording from cortical brain regions, deep-brain fluorescence recording is more complex because it requires additional measures to gain optical access to harder to reach brain nuclei. Here we discuss detailed considerations and tradeoffs regarding deep-brain fluorescence recording techniques and provide a comprehensive guide for all major steps involved, from project planning to data analysis. The goal is to impart guidance for new and experienced investigators seeking to use in vivo deep fluorescence optical recordings in awake, behaving rodent models.

Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing

Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter release in individual synapses. Yet, the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths of more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300-400 µm of the neocortex. To obviate this limitation, we shape the focal volume, generated by the excitation beam, by modulating the incident wavefront via guidestar-assisted adaptive optics. Here, we describe the construction, calibration and operation of a two-photon microscope that incorporates adaptive optics to restore diffraction-limited resolution at depths close to 900 µm in the mouse cortex. Our setup detects a guidestar formed by the excitation of a red-shifted dye in blood serum, used to directly measure the wavefront. We incorporate predominantly commercially available optical, optomechanical, mechanical and electronic components, and supply computer-aided design models of other customized components. The resulting adaptive optics two-photon microscope is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in the mouse neocortex by imaging the morphology of somatostatin-expressing neurons that lie 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons and thalamocortical glutamate transmission to L4 neurons. The protocol requires ~30 d to complete and is suitable for users with graduate-level expertise in optics.

Cell type specificity for circuit output in the midbrain dopaminergic system

Midbrain dopaminergic neurons are a relatively small group of neurons in the mammalian brain controlling a wide range of behaviors. In recent years, increasingly sophisticated tracing, imaging, transcriptomic, and machine learning approaches have provided substantial insights into the anatomical, molecular, and functional heterogeneity of dopaminergic neurons. Despite this wealth of new knowledge, it remains unclear whether and how the diverse features defining dopaminergic subclasses converge to delineate functional ensembles within the dopaminergic system. Here, we review recent studies investigating various aspects of dopaminergic heterogeneity and discuss how development, behavior, and disease influence subtype characteristics. We then outline what further approaches could be pursued to gain a more inclusive picture of dopaminergic diversity, which could be crucial to understanding the functional architecture of this system.

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

In mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3, including several brain regions (for example, refs. 1-11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data. Using this approach, we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of this atlas to the mouse brain common coordinate framework allowed systematic quantifications of the cell-type composition and organization in individual brain regions. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes of cells. Finally, this high-resolution spatial map of cells, each with a transcriptome-wide expression profile, allowed us to infer cell-type-specific interactions between hundreds of cell-type pairs and predict molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a foundation for functional investigations of neural circuits and their dysfunction in health and disease.