Development of the mammalian main olfactory bulb

Comprehensive analysis of immunoglobulin expression in the mouse brain from embryonic to adult stages

Immunoglobulin (Ig) is a critical molecule in the body's defense against foreign substances such as bacteria and viruses. While traditionally considered B cell specific, studies have reported that Ig is also expressed by non-B cells. However, it is not known to what extent Ig is expressed in the brain and which type of variable regions are expressed. In this study, we elucidated the expression profile of Igs from embryonic to adult stages using single-cell RNA sequencing data and Ig repertoire analysis. Our results revealed that microglia express Ighm transcripts from embryonic to adult stages. These transcripts contain the upstream region of the Ighj region. In addition, Ighm is expressed in the layer 6 corticothalamic neurons, some of which co-express Ighg2c in the adult brain. In particular, we were able to generate a comprehensive profile of Ig variable region expression from embryonic to adult stages. Furthermore, the response of Ighm expression in microglia to lipopolysaccharide is markedly different from that in B cells, suggesting a novel, brain-specific role for the Ig gene, distinct from its classical function in the immune system.

Olfactory bulb interneurons - The developmental timeline and targeting defined by embryonic neurogenesis

The generation of mouse olfactory bulb (OB) interneurons (INs) is initiated in the embryo but continues throughout life. It is generally agreed that OB INs generated postnatally affect the connectivity of the OB, depending on the timeline of neurogenesis. Here, we focused on OB INs generated embryonically, which have generally received less attention than those generated in the adult. Birthdates of embryonic INs were differentiated by maternal injections of thymidine analogs and their final destinations and phenotypes in the OB analyzed by immunohistochemistry. We found that the first embryonic INs were generated at embryonic day 10 (E10) and continued through the entire embryonic development. Analysis in adult tissues showed that embryonic INs were retained and were distributed across all layers of the OB. Interestingly, an initial lateral preference in cell density was seen in INs generated during E11-E13. Although INs are broadly distributed in the OB, we found that within the granule cell layer (GCL), OB INs distributed mostly in the superficial GCL. Immunostaining for calbindin, parvalbumin, tyrosine hydroxylase, 5T4 and calretinin were lacking co-expression with thymidine analogs labeled cells, suggesting that maturation of embryonic INs occurred slowly following birth. We studied the embryonic neuroblasts migration and differentiation by labeling IN progenitor cells in the lateral ganglionic eminence using in utero electroporation. We found that IN neuroblasts reached the primordial OB as early as E13 and began to differentiate apical dendrites by E15, which extended into the developing external plexiform layer. We established E16 as the embryonic stage at which the prototypical chain of migrating neuroblasts denoting the embryonic rostral migratory stream (RMS) was visible. Collectively, our data highlight the importance of studying OB INs in isolated time windows to better understand the formation of circuits that define the olfactory system function.

Neurogenesis dynamics in the olfactory bulb: deciphering circuitry organization, function, and adaptive plasticity

Adult neurogenesis persists after birth in the subventricular zone, with new neurons migrating to the granule cell layer and glomerular layers of the olfactory bulb, where they integrate into existing circuitry as inhibitory interneurons. The generation of these new neurons in the olfactory bulb supports both structural and functional plasticity, aiding in circuit remodeling triggered by memory and learning processes. However, the presence of these neurons, coupled with the cellular diversity within the olfactory bulb, presents an ongoing challenge in understanding its network organization and function. Moreover, the continuous integration of new neurons in the olfactory bulb plays a pivotal role in regulating olfactory information processing. This adaptive process responds to changes in epithelial composition and contributes to the formation of olfactory memories by modulating cellular connectivity within the olfactory bulb and interacting intricately with higher-order brain regions. The role of adult neurogenesis in olfactory bulb functions remains a topic of debate. Nevertheless, the functionality of the olfactory bulb is intricately linked to the organization of granule cells around mitral and tufted cells. This organizational pattern significantly impacts output, network behavior, and synaptic plasticity, which are crucial for olfactory perception and memory. Additionally, this organization is further shaped by axon terminals originating from cortical and subcortical regions. Despite the crucial role of olfactory bulb in brain functions and behaviors related to olfaction, these complex and highly interconnected processes have not been comprehensively studied as a whole. Therefore, this manuscript aims to discuss our current understanding and explore how neural plasticity and olfactory neurogenesis contribute to enhancing the adaptability of the olfactory system. These mechanisms are thought to support olfactory learning and memory, potentially through increased complexity and restructuring of neural network structures, as well as the addition of new granule granule cells that aid in olfactory adaptation. Additionally, the manuscript underscores the importance of employing precise methodologies to elucidate the specific roles of adult neurogenesis amidst conflicting data and varying experimental paradigms. Understanding these processes is essential for gaining insights into the complexities of olfactory function and behavior.

Timing Matters: Lessons From Perinatal Neurogenesis in the Olfactory Bulb

In the olfactory bulb (OB), odorant receptor-specific input converges into glomeruli. Subsequently, the coding of odor information is fine-tuned by local synaptic circuits within the glomeruli and the deeper external plexiform layer (EPL) in the OB. Deciphering the organization of inhibitory granule cells (GCs) in the EPL relative to the secondary dendrites of projection neurons is pivotal for understanding odor processing. We conducted a detailed investigation of GCs, focusing on the timing of neurogenesis, laminar distribution, and synaptogenesis between GCs and projection neurons. In summary, GCs develop following a developmental continuum with an outside-in maturation pattern from embryogenesis to adulthood. GCs born 1 week after birth display a unique sublayer-specific distribution pattern, marking a transition between embryonic or neonatal and adult stages. Integration into reciprocal synaptic circuits occurred 10 days post-neurogenesis. We conclude that the timing of neurogenesis dictates the anatomical configuration of GCs within the OB, which, in turn, regulates preferential synaptic integration with either mitral cell or tufted cell secondary dendrites.

Olfactory Development and Dysfunction: Involvement of Microglia

Olfactory deficits are increasingly recognized in a variety of neurological, neurodevelopmental, psychiatric, and viral diseases. While the pathology underlying olfactory loss is likely to differ across diseases, one shared feature may be an immune response mediated by microglia. Microglia orchestrate the brain's response to environmental insults and maintain neurodevelopmental homeostasis. Here, we explore the potential involvement of microglia in olfactory development and loss in disease. The effects of microglia-mediated immune response during development may be of special relevance to the olfactory system, which is unique in both its vulnerability to environmental insults as well as its extended period of neurogenesis and neuronal migration.

Ex Vivo Functional Characterization of Mouse Olfactory Bulb Projection Neurons Reveals a Heterogeneous Continuum

Mitral cells (MCs) and tufted cells (TCs) in the olfactory bulb (OB) act as an input convergence hub and transmit information to higher olfactory areas. Since first characterized, they have been classed as distinct projection neurons based on size and location: laminarly arranged MCs with a diameter larger than 20 µm in the mitral layer (ML) and smaller TCs spread across both the ML and external plexiform layers (EPL). Recent in vivo work has shown that these neurons encode complementary olfactory information, akin to parallel channels in other sensory systems. Yet, many ex vivo studies still collapse them into a single class, mitral/tufted, when describing their physiological properties and impact on circuit function. Using immunohistochemistry and whole-cell patch-clamp electrophysiology in fixed or acute slices from adult mice, we attempted to align in vivo and ex vivo data and test a soma size-based classifier of bulbar projection neurons using passive and intrinsic firing properties. We found that there is no clear separation between cell types based on passive or active properties. Rather, there is a heterogeneous continuum with three loosely clustered subgroups: TCs in the EPL, and putative tufted or putative MCs in the ML. These findings illustrate the large functional heterogeneity present within the OB projection neurons and complement existing literature highlighting how heterogeneity in sensory systems is preponderant and possibly used in the OB to decode complex olfactory information.

On the Fila Olfactoria and the Cribriform Region of the Crocodylia

In mammals the fila olfactoria, fascicles of axons coursing from sensory neurons in the olfactory epithelium to the glomeruli of the olfactory bulb, not only have a topographic projection pattern but also serve as routes for cerebrospinal fluid (CSF) drainage from around the brain. Les is known about the fila olfactoria in nonmammalian taxa. This work explores the fila olfactoria of the American alligator (Alligator mississippiensis) using a combination of gross dissection, histology, Diffusible Iodine-based contrast-enhanced computed tomography, latex corrosion casting, and India ink tracers. In Crocodylians, as in other nonmammalian vertebrates, the fila olfactoria courses through a foramen in the nasal capsule rather than an ethmoidal cribriform plate. In Alligator this foramen is filled by dense connective tissue; prominent perineural spaces extend through the connective tissue, effectively making it perforate like the cribriform plate. Latex or India ink introduced into the cranial CSF pass through the dense connective to reach the submucosa of the olfactory epithelium, suggesting that Crocodylians have the same cranial CSF drainage pattern as mammals. In Alligator, the fila olfactoria is asymmetric, with more fascicles entering the ventral and lateral surfaces of the olfactory bulb than the dorsal or medial surfaces. If individual fascicles of the fila olfactoria are traced in Alligator, a clear topographic projection emerges; with medial and lateral polarity maintained between olfactory epithelium and olfactory bulb, and a rostral-caudal polarity projecting as dorsal-ventral on the olfactory bulb.

Olfactory testing in infants with perinatal asphyxia: Enhancing encephalopathy risk stratification for future health outcomes

Perinatal asphyxia (PA) is a leading cause of neonatal morbidity and mortality, often resulting in long-term neurodevelopmental challenges. Despite advancements in perinatal care, predicting long-term outcomes remains difficult. Early diagnosis is essential for timely interventions to reduce brain injury, with tools such as Magnetic Resonance Imaging, brain ultrasound, and emerging biomarkers playing a possible key role. Olfaction, one of the earliest senses to develop, may provide valuable insights into long-term neurodevelopmental outcomes following PA due to its intricate neural connections with regions responsible for memory, emotion, and homeostasis. Newborns demonstrate early olfactory abilities, such as recognizing maternal odors, which are vital for bonding, feeding, and emotional regulation. These responses are processed by a network of brain regions, including the olfactory bulb (OB), piriform cortex, amygdala, and orbitofrontal cortex. Hypoxic injury to these regions, particularly the OB, may disrupt olfactory processing in infants with PA, potentially affecting their cognitive and social development. Investigating the relationship between olfactory system development and perinatal brain injury could lead to innovative diagnostic and therapeutic approaches. Further research, including clinical and animal studies, is necessary to fully explore the potential of olfactory assessments in predicting outcomes after PA. This educational review explores and discusses the potential of olfaction as a predictor of long-term outcomes and a tool for risk stratification following PA, opening new pathways for interventions and improved care.

An overview on olfaction in the biological, analytical, computational, and machine learning fields

Recently, the comprehension of odor perception has advanced, unveiling the mysteries of the molecular receptors within the nasal passages and the intricate mechanisms governing signal transmission between these receptors, the olfactory bulb, and the brain. This review provides a comprehensive panorama of odors, encompassing various topics ranging from the structural and molecular underpinnings of odorous substances to the physiological intricacies of olfactory perception. It extends to elucidate the analytical methods used for their identification and explores the frontiers of computational methodologies.

Ion Channels in Odor Information Processing of Neural Circuits of the Vertebrate Olfactory Bulb

Olfactory disorders and their associated complications present a considerable challenge to an individual's quality of life and emotional wellbeing. The current range of treatments, including surgical procedures, pharmacological interventions, and behavioral training, frequently proves ineffective in restoring olfactory function. The olfactory bulb (OB) is essential for odor processing and plays a pivotal role in the development of these disorders. Despite the acknowledged significance of ion channels in sensory functions and related pathologies, their specific involvement in OB remains unexplored. This review presents an overview of the functions of various ion channel families in regulating neuronal excitability, synaptic transmission, and the complex processes of olfactory perception. The objective of this review was to elucidate the role of ion channels in olfactory function, providing new insights into the diagnosis and treatment of olfactory dysfunction.

Differential functional change in olfactory bulb and olfactory eloquent areas in Parkinson's disease

Olfactory dysfunction, or hyposmia, frequently occurs as a prodromal symptom and ongoing sign of Parkinson's disease. Functional MRI is a powerful tool for studying functional changes in the olfactory brain regions in patients with Parkinson's disease. However, existing studies show inconsistent results and no study has measured olfactory functional MRI abnormalities in the human olfactory bulb directly. This is mainly due to the well-known susceptibility artefacts in conventional functional MRI images that affect several key olfactory-eloquent brain regions, and especially the olfactory bulb. In this study, olfactory functional MRI was performed using a recently developed functional MRI approach that can minimize susceptibility artefacts and measure robust functional MRI signals in the human olfactory bulb during olfactory stimulation. Experiments were performed on high magnetic field (7 T) in 24 early (<5 years of parkinsonian symptoms) Parkinson's disease patients and 31 matched healthy controls. Our data showed increased functional MRI signal changes (ΔS/S) in the olfactory bulb in patients with early Parkinson's disease, which correlated with behavioural olfactory measures. Temporally, functional MRI signals in the olfactory bulb returned to the pre-stimulus state earlier after reaching peak amplitude in patients with early Parkinson's disease, implicating a faster olfactory habituation effect. The piriform cortex showed reduced numbers of activated voxels in patients with early Parkinson's disease, which correlated with behavioural olfactory assessment. Several secondary olfactory regions including the orbitofrontal cortex, temporal pole and amygdala exhibited reduced numbers of activated voxels and increased functional MRI signal changes in patients with early Parkinson's disease. Our data also showed that functional MRI results are highly dependent on voxel selection in the functional analysis. In summary, we demonstrate differential spatial and temporal characteristics of olfactory functional MRI signals between the primary and secondary olfactory regions in patients with early Parkinson's disease. These results may assist the development of novel quantitative biomarkers (especially in the early stages of Parkinson's disease) to track and predict disease progression, as well as potential treatment targets for early intervention.

The Organism as the Niche: Physiological States Crack the Code of Adult Neural Stem Cell Heterogeneity

Neural stem cells (NSCs) persist in the adult mammalian brain and are able to give rise to new neurons and glia throughout life. The largest stem cell niche in the adult mouse brain is the ventricular-subventricular zone (V-SVZ) lining the lateral ventricles. Adult NSCs in the V-SVZ coexist in quiescent and actively proliferating states, and they exhibit a regionalized molecular identity. The importance of such spatial diversity is just emerging, as depending on their position within the niche, adult NSCs give rise to distinct subtypes of olfactory bulb interneurons and different types of glia. However, the functional relevance of stem cell heterogeneity in the V-SVZ is still poorly understood. Here, we put into perspective findings highlighting the importance of adult NSC diversity for brain plasticity, and how the body signals to brain stem cells in different physiological states to regulate their behavior.

Olfactory neurogenesis plays different parts at successive stages of life, implications for mental health

The olfactory bulb is a unique site of continuous neurogenesis, primarily generating inhibitory interneurons, a process that begins at birth and extends through infancy and adulthood. This review examines the characteristics of olfactory bulb neurogenesis, focusing on granule cells, the most numerous interneurons, and how their age and maturation affect their function. Adult-born granule cells, while immature, contribute to the experience-dependent plasticity of the olfactory circuit by enabling structural and functional synaptic changes. In contrast, granule cells born early in life form the foundational elements of the olfactory bulb circuit, potentially facilitating innate olfactory information processing. The implications of these neonatal cells on early life olfactory memory and their impact on adult perception, particularly in response to aversive events and susceptibility to emotional disorders, warrant further investigation.

The olfactory network of larval Xenopus laevis regenerates accurately after olfactory nerve transection

Across vertebrate species, the olfactory epithelium (OE) exhibits the uncommon feature of lifelong neuronal turnover. Epithelial stem cells give rise to new neurons that can adequately replace dying olfactory receptor neurons (ORNs) during developmental and adult phases and after lesions. To relay olfactory information from the environment to the brain, the axons of the renewed ORNs must reconnect with the olfactory bulb (OB). In Xenopus laevis larvae, we have previously shown that this process occurs between 3 and 7 weeks after olfactory nerve (ON) transection. In the present study, we show that after 7 weeks of recovery from ON transection, two functionally and spatially distinct glomerular clusters are reformed in the OB, akin to those found in non-transected larvae. We also show that the same odourant response tuning profiles observed in the OB of non-transected larvae are again present after 7 weeks of recovery. Next, we show that characteristic odour-guided behaviour disappears after ON transection but recovers after 7-9 weeks of recovery. Together, our findings demonstrate that the olfactory system of larval X. laevis regenerates with high accuracy after ON transection, leading to the recovery of odour-guided behaviour.

The transcriptomic and spatial organization of telencephalic GABAergic neuronal types

The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.

Sensory Stimulation-dependent Npas4 Expression in the Olfactory Bulb during Early Postnatal Development

The development of the olfactory system is influenced by sensory inputs, and it maintains neuronal generation and plasticity throughout the lifespan. The olfactory bulb contains a higher proportion of interneurons than other brain regions, particularly during the early postnatal period of neurogenesis. Although the relationship between sensory stimulation and olfactory bulb development during the postnatal period has been well studied, the molecular mechanisms have yet to be identified. In this study, we used western blotting and immunohistochemistry to analyze the expression of the transcription factor Npas4, a neuron-specific immediate-early gene that acts as a developmental regulator in many brain regions. We found that Npas4 is highly expressed in olfactory bulb interneurons during the early postnatal stages and gradually decreases toward the late postnatal stages. Npas4 expression was observed in all olfactory bulb layers, including the rostral migratory stream, where newborn neurons are generated and migrate to the olfactory bulb. Under sensory deprivation, the olfactory bulb size and the number of olfactory bulb interneurons were reduced. Furthermore, Npas4 expression and the expression of putative Npas4 downstream molecules were decreased. Collectively, these findings indicate that Npas4 expression induced by sensory input plays a role in the formation of neural circuits with excitatory mitral/tufted cells by regulating the survival of olfactory bulb interneurons during the early stages of postnatal development.

Olfactory bulb anomalies in KBG syndrome mouse model and patients

ANKRD11 (ankyrin repeat domain 11) is a chromatin regulator and the only gene associated with KBG syndrome, a rare neurodevelopmental disorder. We have previously shown that Ankrd11 regulates murine embryonic cortical neurogenesis. Here, we show a novel olfactory bulb phenotype in a KBG syndrome mouse model and two diagnosed patients. Conditional knockout of Ankrd11 in murine embryonic neural stem cells leads to aberrant postnatal olfactory bulb development and reduced size due to reduction of the olfactory bulb granule cell layer. We further show that the rostral migratory stream has incomplete migration of neuroblasts, reduced cell proliferation as well as aberrant differentiation of neurons. This leads to reduced neuroblasts and neurons in the olfactory bulb granule cell layer. In vitro, Ankrd11-deficient neural stem cells from the postnatal subventricular zone display reduced migration, proliferation, and neurogenesis. Finally, we describe two clinically and molecularly confirmed KBG syndrome patients with anosmia and olfactory bulb and groove hypo-dysgenesis/agenesis. Our report provides evidence that Ankrd11 is a novel regulator of olfactory bulb development and neuroblast migration. Moreover, our study highlights a novel clinical sign of KBG syndrome linked to ANKRD11 perturbations in mice and humans.

Deficits in olfactory system neurogenesis in neurodevelopmental disorders

The role of neurogenesis in neurodevelopmental disorders (NDDs) merits much attention. The complex process by which stem cells produce daughter cells that in turn differentiate into neurons, migrate various distances, and form synaptic connections that are then refined by neuronal activity or experience is integral to the development of the nervous system. Given the continued postnatal neurogenesis that occurs in the mammalian olfactory system, it provides an ideal model for understanding how disruptions in distinct stages of neurogenesis contribute to the pathophysiology of various NDDs. This review summarizes and discusses what is currently known about the disruption of neurogenesis within the olfactory system as it pertains to attention-deficit/hyperactivity disorder, autism spectrum disorder, Down syndrome, Fragile X syndrome, and Rett syndrome. Studies included in this review used either human subjects, mouse models, or Drosophila models, and lay a compelling foundation for continued investigation of NDDs by utilizing the olfactory system.

The neurobiological effects of senescence on dopaminergic system: A comprehensive review

Over time, the body undergoes a natural, multifactorial, and ongoing process named senescence, which induces changes at the molecular, cellular, and micro-anatomical levels in many body systems. The brain, being a highly complex organ, is particularly affected by this process, potentially impairing its numerous functions. The brain relies on chemical messengers known as neurotransmitters to function properly, with dopamine being one of the most crucial. This catecholamine is responsible for a broad range of critical roles in the central nervous system, including movement, learning, cognition, motivation, emotion, reward, hormonal release, memory consolidation, visual performance, sexual drive, modulation of circadian rhythms, and brain development. In the present review, we thoroughly examine the impact of senescence on the dopaminergic system, with a primary focus on the classic delimitations of the dopaminergic nuclei from A8 to A17. We provide in-depth information about their anatomy and function, particularly addressing how senescence affects each of these nuclei.

Different electrophysiological profiles of genetically labelled dopaminergic neurons in the mouse midbrain and olfactory bulb

Dopaminergic (DA) neurons play pivotal roles in diverse brain functions, spanning movement, reward processing and sensory perception. DA neurons are most abundant in the midbrain (Substantia Nigra pars compacta [SNC] and Ventral Tegmental Area [VTA]) and the olfactory bulb (OB) in the forebrain. Interestingly, a subtype of OB DA neurons is capable of regenerating throughout life, while a second class is exclusively born during embryonic development. Compelling evidence in SNC and VTA also indicates substantial heterogeneity in terms of morphology, connectivity and function. To further investigate this heterogeneity and directly compare form and function of midbrain and forebrain bulbar DA neurons, we performed immunohistochemistry and whole-cell patch-clamp recordings in ex vivo brain slices from juvenile DAT-tdTomato mice. After confirming the penetrance and specificity of the dopamine transporter (DAT) Cre line, we compared soma shape, passive membrane properties, voltage sags and action potential (AP) firing across midbrain and forebrain bulbar DA subtypes. We found that each DA subgroup within midbrain and OB was highly heterogeneous, and that DA neurons across the two brain areas are also substantially different. These findings complement previous work in rats as well as gene expression and in vivo datasets, further questioning the existence of a single "dopaminergic" neuronal phenotype.

Illuminating the terminal nerve: Uncovering the link between GnRH-1 neuron and olfactory development

During embryonic development, the olfactory placode (OP) generates migratory neurons, including olfactory pioneer neurons, cells of the terminal nerve (TN), gonadotropin-releasing hormone-1 (GnRH-1) neurons, and other uncharacterized neurons. Pioneer neurons from the OP induce olfactory bulb (OB) morphogenesis. In mice, GnRH-1 neurons appear in the olfactory system around mid-gestation and migrate via the TN axons to different brain regions. The GnRH-1 neurons are crucial in controlling the hypothalamic-pituitary-gonadal axis. Kallmann syndrome is characterized by impaired olfactory system development, defective OBs, secretion of GnRH-1, and infertility. The precise mechanistic link between the olfactory system and GnRH-1 development remains unclear. Studies in humans and mice highlight the importance of the prokineticin-2/prokineticin-receptor-2 (Prokr2) signaling pathway in OB morphogenesis and GnRH-1 neuronal migration. Prokr2 loss-of-function mutations can cause Kallmann syndrome (KS), and hence the Prokr2 signaling pathway represents a unique model to decipher the olfactory/GnRH-1 connection. We discovered that Prokr2 is expressed in the TN neurons during the critical period of GnRH-1 neuron formation, migration, and induction of OB morphogenesis. Single-cell RNA sequencing identified that the TN is formed by neurons distinct from the olfactory neurons. The TN neurons express multiple genes associated with KS. Our study suggests that the aberrant development of pioneer/TN neurons might cause the KS spectrum.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.

A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains

Conventional methods fall short in unraveling the dynamics of rare cell types related to aging and diseases. Here we introduce EasySci, an advanced single-cell combinatorial indexing strategy for exploring age-dependent cellular dynamics in the mammalian brain. Profiling approximately 1.5 million single-cell transcriptomes and 400,000 chromatin accessibility profiles across diverse mouse brains, we identified over 300 cell subtypes, uncovering their molecular characteristics and spatial locations. This comprehensive view elucidates rare cell types expanded or depleted upon aging. We also investigated cell-type-specific responses to genetic alterations linked to Alzheimer's disease, identifying associated rare cell types. Additionally, by profiling 118,240 human brain single-cell transcriptomes, we discerned cell- and region-specific transcriptomic changes tied to Alzheimer's pathogenesis. In conclusion, this research offers a valuable resource for probing cell-type-specific dynamics in both normal and pathological aging.

epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains

During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical and pathological brain development. Here, we create high-resolution 3D atlases of the early postnatal mouse brain, using Allen CCFv3 anatomical labels, at postnatal days (P) 4, 6, 8, 10, 12, and 14, and determine the volumetric growth of different brain regions. We utilize 11 different cell type-specific transgenic animals to validate and refine anatomical labels. Moreover, we reveal region-specific density changes in γ-aminobutyric acid-producing (GABAergic), cortical layer-specific cell types, and microglia as key players in shaping early postnatal brain development. We find contrasting changes in GABAergic neuronal densities between cortical and striatal areas, stabilizing at P12. Moreover, somatostatin-expressing cortical interneurons undergo regionally distinct density reductions, while vasoactive intestinal peptide-expressing interneurons show no significant changes. Remarkably, microglia transition from high density in white matter tracks to gray matter at P10, and show selective density increases in sensory processing areas that correlate with the emergence of individual sensory modalities. Lastly, we create an open-access web-visualization (https://kimlab.io/brain-map/epDevAtlas) for cell-type growth charts and developmental atlases for all postnatal time points.

Pregnancy-responsive pools of adult neural stem cells for transient neurogenesis in mothers

Adult neural stem cells (NSCs) contribute to lifelong brain plasticity. In the adult mouse ventricular-subventricular zone, NSCs are heterogeneous and, depending on their location in the niche, give rise to different subtypes of olfactory bulb (OB) interneurons. Here, we show that multiple regionally distinct NSCs, including domains that are usually quiescent, are recruited on different gestation days during pregnancy. Synchronized activation of these adult NSC pools generates transient waves of short-lived OB interneurons, especially in layers with less neurogenesis under homeostasis. Using spatial transcriptomics, we identified molecular markers of pregnancy-associated interneurons and showed that some subsets are temporarily needed for own pup recognition. Thus, pregnancy triggers transient yet behaviorally relevant neurogenesis, highlighting the physiological relevance of adult stem cell heterogeneity.

Perceptual learning deficits mediated by somatostatin releasing inhibitory interneurons of olfactory bulb in an early life stress mouse model

Early life adversity (ELA) causes aberrant functioning of neural circuits affecting the health of an individual. While ELA-induced behavioural disorders resulting from sensory and cognitive disabilities can be assessed clinically, the neural mechanisms need to be probed using animal models by employing multi-pronged experimental approaches. As ELA can alter sensory perception, we investigated the effect of early weaning on murine olfaction. By implementing go/no-go odour discrimination paradigm, we observed olfactory learning and memory impairments in early life stressed (ELS) male mice. As olfactory bulb (OB) circuitry plays a critical role in odour learning, we studied the plausible changes in the OB of ELS mice. Lowered c-Fos activity in the external plexiform layer and a reduction in the number of dendritic processes of somatostatin-releasing, GABAergic interneurons (SOM-INs) in the ELS mice led us to hypothesise the underlying circuit. We recorded reduced synaptic inhibitory feedback on mitral/tufted (M/T) cells, in the OB slices from ELS mice, explaining the learning deficiency caused by compromised refinement of OB output. The reduction in synaptic inhibition was nullified by the photo-activation of ChR2-expressing SOM-INs in ELS mice. The role of SOM-INs was revealed by learning-dependent refinement of Ca2+dynamics quantified by GCaMP6f signals, which was absent in ELS mice. Further, the causal role of SOM-INs involving circuitry was investigated by optogenetic modulation during the odour discrimination learning. Photo-activating these neurons rescued the ELA-induced learning deficits. Conversely, photo-inhibition caused learning deficiency in control animals, while it completely abolished the learning in ELS mice, confirming the adverse effects mediated by SOM-INs. Our results thus establish the role of specific inhibitory circuit in pre-cortical sensory area in orchestrating ELA-dependent changes.

Illuminating the Terminal Nerve: Uncovering the Link between GnRH-1 and Olfactory Development

During embryonic development, the olfactory placode (OP) generates migratory neurons, including olfactory pioneer neurons, cells of the terminal nerve (TN), Gonadotropin-releasing hormone-1 (GnRH-1) neurons, and other uncharacterized neurons. Pioneer neurons from the olfactory placode induce olfactory bulb morphogenesis. In mice, GnRH-1 neurons appear in the olfactory system around mid-gestation and migrate via the terminal nerve axons to different brain regions. The GnRH-1 neurons are crucial in controlling the hypothalamic-pituitary-gonadal (HPG) axis. Kallmann syndrome is characterized by impaired olfactory system development, defective olfactory bulbs, defective secretion of GnRH-1, and infertility. The precise mechanistic link between the olfactory system and GnRH-1 development remains unclear. Studies in humans and mice highlight the importance of the Prokineticin-2/Prokineticin-Receptor-2 (Prokr2) signaling pathway in olfactory bulb morphogenesis and GnRH-1 neuronal migration. Prokr2 loss-of-function mutations can cause Kallmann syndrome, and hence the Prokr2 signaling pathway represents a unique model to decipher the olfactory/GnRH-1 connection. We discovered that Prokr2 is expressed in the TN neurons during the critical period of GnRH-1 neuron formation, migration, and induction of olfactory bulb morphogenesis. Single-cell RNA sequencing identified that the TN is formed by neurons that are distinct from the olfactory neurons. The TN neurons express multiple genes associated with KS. Our study suggests that the aberrant development of pioneer/TN neurons might cause the KS spectrum.

Key Points

1) Pioneer or terminal nerve neurons play a crucial role in initiating the development of the olfactory bulbs. We found that the Prokineticin Receptor-2 gene, associated with Kallmann syndrome, is expressed by the olfactory pioneer/terminal nerve neurons.2) We genetically traced, isolated, and conducted Single-cell RNA sequencing on terminal nerve neurons of rodents. This analysis revealed a significant enrichment of gene expression related to Kallmann syndrome.3) Our study indicates that the investigation of Pioneer/terminal nerve neurons should be a pivotal focal point for comprehending developmental defects affecting olfactory and GnRH-1 systems.

The tumor suppressor CREBBP and the oncogene MYCN cooperate to induce malignant brain tumors in mice

The tumor suppressor and chromatin modifier cAMP response element-binding protein binding protein (CREBBP) and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN), a member of the MYC oncogene family, are critically involved in brain development. Both genes are frequently mutated in the same tumor entities, including high-grade glioma and medulloblastoma. Therefore, we hypothesized that alterations in both genes cooperate to induce brain tumor formation. For further investigation, hGFAP-cre::Crebbp^Fl/Fl::lsl-MYCN mice were generated, which combine Crebbp deletion with overexpression of MYCN in neural stem cells (NSCs). Within eight months, these animals developed aggressive forebrain tumors. The first tumors were detectable in the olfactory bulbs of seven-day-old mice. This location raises the possibility that presumptive founder cells are derived from the ventricular-subventricular zone (V-SVZ). To examine the cellular biology of these tumors, single-cell RNA sequencing was performed, which revealed high intratumoral heterogeneity. Data comparison with reference CNS cell types indicated the highest similarity of tumor cells with transit-amplifying NSCs or activated NSCs of the V-SVZ. Consequently, we analyzed V-SVZ NSCs of our mouse model aiming to confirm that the tumors originate from this stem cell niche. Mutant V-SVZ NSCs showed significantly increased cell viability and proliferation as well as reduced glial and neural differentiation in vitro compared to control cells. In summary, we demonstrate the oncogenic potential of a combined loss of function of CREBBP and overexpression of MYCN in this cell population. hGFAP-cre::Crebbp^Fl/Fl::lsl-MYCN mice thus provide a valuable tool to study tumor-driving mechanisms in a key neural stem/ progenitor cell niche.

The Olfactory Bulb in Companion Animals-Anatomy, Physiology, and Clinical Importance

The Olfactory Bulb is a component of the Olfactory System, in which it plays an essential role as an interface between the peripheral components and the cerebral cortex responsible for olfactory interpretation and discrimination. It is in this element that the first selective integration of olfactory stimuli occurs through a complex cell interaction that forwards the received olfactory information to higher cortical centers. Considering its position in the organizational hierarchy of the olfactory system, it is now known that changes in the Olfactory Bulb can lead to olfactory abnormalities. Through imaging techniques, it was possible to establish relationships between the occurrence of changes secondary to brain aging and senility, neurodegenerative diseases, head trauma, and infectious diseases with a decrease in the size of the Olfactory Bulb and in olfactory acuity. In companion animals, this relationship has also been identified, with observations of relations between the cranial conformation, the disposition, size, and shape of the Olfactory Bulb, and the occurrence of structural alterations associated with diseases with different etiologies. However, greater difficulty in quantitatively assessing olfactory acuity in animals and a manifestly smaller number of studies dedicated to this topic maintain a lack of concrete and unequivocal results in this field of veterinary sciences. The aim of this work is to revisit the Olfactory Bulb in companion animals in all its dimensions, review its anatomy and histological characteristics, physiological integration in the olfactory system, importance as a potential early indicator of the establishment of specific pathologies, as well as techniques of imaging evaluation for its in vivo clinical exploration.

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.

Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST

Spatially resolved transcriptomics involves a set of emerging technologies that enable the transcriptomic profiling of tissues with the physical location of expressions. Although a variety of methods have been developed for data integration, most of them are for single-cell RNA-seq datasets without consideration of spatial information. Thus, methods that can integrate spatial transcriptomics data from multiple tissue slides, possibly from multiple individuals, are needed. Here, we present PRECAST, a data integration method for multiple spatial transcriptomics datasets with complex batch effects and/or biological effects between slides. PRECAST unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, while requiring only partially shared cell/domain clusters across datasets. Using both simulated and four real datasets, we show improved cell/domain detection with outstanding visualization, and the estimated aligned embeddings and cell/domain labels facilitate many downstream analyses. We demonstrate that PRECAST is computationally scalable and applicable to spatial transcriptomics datasets from different platforms.

Spatiotemporal dynamics of the development of mouse olfactory system from prenatal to postnatal period

Introduction

The olfactory epithelium (OE) and olfactory bulb (OB) are the major components of the olfactory system and play critical roles in olfactory perception. However, the embryonic development of OE and OB by using the olfactory specific genes has not been comprehensively investigated yet. Most previous studies were limited to a specific embryonic stage, and very little is known, till date, about the development of OE.

Methods

The current study aimed to explore the development of mouse olfactory system by spatiotemporal analysis of the histological features by using the olfactory specific genes of olfactory system from the prenatal to postnatal period.

Results

We found that OE is divided into endo-turbinate, ecto-turbinate, and vomeronasal organs, and that putative OB with putative main and accessory OB is formed in the early developmental stage. The OE and OB became multilayered in the later developmental stages, accompanied by the differentiation of olfactory neurons. Remarkably, we found the development of layers of olfactory cilia and differentiation of OE to progress dramatically after birth, suggesting that the exposure to air may facilitate the final development of OE.

Discussion

Overall, the present study laid the groundwork for a better understanding of the spatial and temporal developmental events of the olfactory system.

Rapid presynaptic maturation in naturally regenerating axons of the adult mouse olfactory nerve

Successful neuronal regeneration requires the reestablishment of synaptic connectivity. This process requires the reconstitution of presynaptic neurotransmitter release, which we investigate here in a model of entirely natural regeneration. After toxin-induced injury, olfactory sensory neurons in the adult mouse olfactory epithelium can regenerate fully, sending axons via the olfactory nerve to reestablish synaptic contact with postsynaptic partners in the olfactory bulb. Using electrophysiological recordings in acute slices, we find that, after initial recontact, functional connectivity in this system is rapidly established. Reconnecting presynaptic terminals have almost mature functional properties, including high release probability and strong capacity for presynaptic inhibition. Release probability then matures quickly, rendering reestablished terminals functionally indistinguishable from controls just 1 week after initial contact. These data show that successful synaptic regeneration in the adult mammalian brain is almost a "plug-and-play" process, with presynaptic terminals undergoing a rapid phase of functional maturation as they reintegrate into target networks.

Anatomical and Functional Connectivity at the Dendrodendritic Reciprocal Mitral Cell-Granule Cell Synapse: Impact on Recurrent and Lateral Inhibition

In the vertebrate olfactory bulb, reciprocal dendrodendritic interactions between its principal neurons, the mitral and tufted cells, and inhibitory interneurons in the external plexiform layer mediate both recurrent and lateral inhibition, with the most numerous of these interneurons being granule cells. Here, we used recently established anatomical parameters and functional data on unitary synaptic transmission to simulate the strength of recurrent inhibition of mitral cells specifically from the reciprocal spines of rat olfactory bulb granule cells in a quantitative manner. Our functional data allowed us to derive a unitary synaptic conductance on the order of 0.2 nS. The simulations predicted that somatic voltage deflections by even proximal individual granule cell inputs are below the detection threshold and that attenuation with distance is roughly linear, with a passive length constant of 650 μm. However, since recurrent inhibition in the wake of a mitral cell action potential will originate from hundreds of reciprocal spines, the summated recurrent IPSP will be much larger, even though there will be substantial mutual shunting across the many inputs. Next, we updated and refined a preexisting model of connectivity within the entire rat olfactory bulb, first between pairs of mitral and granule cells, to estimate the likelihood and impact of recurrent inhibition depending on the distance between cells. Moreover, to characterize the substrate of lateral inhibition, we estimated the connectivity via granule cells between any two mitral cells or all the mitral cells that belong to a functional glomerular ensemble (i.e., which receive their input from the same glomerulus), again as a function of the distance between mitral cells and/or entire glomerular mitral cell ensembles. Our results predict the extent of the three regimes of anatomical connectivity between glomerular ensembles: high connectivity within a glomerular ensemble and across the first four rings of adjacent glomeruli, substantial connectivity to up to eleven glomeruli away, and negligible connectivity beyond. Finally, in a first attempt to estimate the functional strength of granule-cell mediated lateral inhibition, we combined this anatomical estimate with our above simulation results on attenuation with distance, resulting in slightly narrowed regimes of a functional impact compared to the anatomical connectivity.

Developing and maintaining a nose-to-brain map of odorant identity

Olfactory sensory neurons (OSNs) in the olfactory epithelium of the nose transduce chemical odorant stimuli into electrical signals. These signals are then sent to the OSNs' target structure in the brain, the main olfactory bulb (OB), which performs the initial stages of sensory processing in olfaction. The projection of OSNs to the OB is highly organized in a chemospatial map, whereby axon terminals from OSNs expressing the same odorant receptor (OR) coalesce into individual spherical structures known as glomeruli. This nose-to-brain map of odorant identity is built from late embryonic development to early postnatal life, through a complex combination of genetically encoded, OR-dependent and activity-dependent mechanisms. It must then be actively maintained throughout adulthood as OSNs experience turnover due to external insult and ongoing neurogenesis. Our review describes and discusses these two distinct and crucial processes in olfaction, focusing on the known mechanisms that first establish and then maintain chemospatial order in the mammalian OSN-to-OB projection.

Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes

Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.