Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input–output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.

An essential step toward understanding brain function is to establish a cellular-resolution structural framework upon which multi-scale and multi-modal information spanning molecules, cells, circuits and systems can be integrated and interpreted. Here, through a collaborative effort from the Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based description of one brain structure - the primary motor cortex upper limb area (MOp-ul) of the mouse. Applying state-of-the-art labeling, imaging, computational, and neuroinformatics tools, we delineated the MOp-ul within the Mouse Brain 3D Common Coordinate Framework (CCF). We defined over two dozen MOp-ul projection neuron (PN) types by their anterograde targets; the spatial distribution of their somata defines 11 cortical sublayers, a significant refinement of the classic notion of cortical laminar organization. We further combine multiple complementary tracing methods (classic tract tracing, cell type-based anterograde, retrograde, and transsynaptic viral tracing, high-throughput BARseq, and complete single cell reconstruction) to systematically chart cell type-based MOp input-output streams. As PNs link distant brain regions at synapses as well as host cellular gene expression, our construction of a PN type resolution MOp-ul wiring diagram will facilitate an integrated analysis of motor control circuitry across the molecular, cellular, and systems levels. This work further provides a roadmap towards a cellular resolution description of mammalian brain architecture.

The cerebellum plays a key role in motor tasks, but its involvement in cognition is still being considered. Although there is an association of different psychiatric and cognitive disorders with cerebellar impairments, the lack of time-course studies has hindered the understanding of the involvement of cerebellum in cognitive and non-motor functions. Such association was here studied using the Purkinje Cell Degeneration mutant mouse, a model of selective and progressive cerebellar degeneration that lacks the cytosolic carboxypeptidase 1 (CCP1). The effects of the absence of this enzyme on the cerebellum of mutant mice were analyzed both in vitro and in vivo. These analyses were carried out longitudinally (throughout both the pre-neurodegenerative and neurodegenerative stages) and different motor and non-motor tests were performed. We demonstrate that the lack of CCP1 affects microtubule dynamics and flexibility, defects that contribute to the morphological alterations of the Purkinje cells (PCs), and to progressive cerebellar breakdown. Moreover, this degeneration led not only to motor defects but also to gradual cognitive impairments, directly related to the progression of cellular damage. Our findings confirm the cerebellar implication in non-motor tasks, where the formation of the healthy, typical PCs structure is necessary for normal cognitive and affective behavior.

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The cerebrovascular network and its mural cells must meet the dynamic energy demands of different neuronal cell types across the brain, but their spatial relationship among these cells is largely unknown. Here, we apply brain-wide mapping methods to create a comprehensive cellular-resolution resource comprising the distribution of and quantitative relationship between microvessels, pericytes, and glutamatergic and GABAergic neurons including neuronal nitric oxide synthase-positive (nNOS+) neurons and their subtypes in mice. Leveraging these data, we discovered region-specific signatures of vasculature and cell type compositions across cortical and subcortical areas, including strikingly contrasting correlations between the density of vasculature, pericytes, glutamatergic neurons and parvalbumin-positive interneurons versus nNOS+ neurons in the isocortex. We also found surprisingly low vasculature and pericyte density in the hippocampus, and distinctly high pericyte to vasculature ratio in the hypothalamus. These findings suggest that vascular density and mural cell composition is finely tuned to maintain regional energy homeostasis.

The mammalian olfactory bulb (OB) has all the features of a whole mammalian brain but in a more reduced space: neuronal lamination, sensory inputs, afferences, or efferences to other centers of the central nervous system, or a contribution of new neural elements. Therefore, it is widely considered as "a brain inside the brain." Although this rostral region has the same origin and general layering as the other cerebral cortices, some distinctive features make it very profitable in experimentation in neurobiology: the sensory inputs are driven directly on its surface, the main output can be accessed anatomically, and new elements appear in it throughout adult life. These three morphological characteristics have been manipulated to analyze further the response of the whole OB. The present review offers a general outlook into the consequences of such experimentation in the anatomy, connectivity and neurochemistry of the OB after (a) sensory deprivation, mainly by naris occlusion; (b) olfactory deinnervation by means of olfactory epithelium damage, olfactory nerve interruption, or even olfactory tract disruption; (c) the removal of the principal neurons of the OB; and (d) management of the arrival of newborn interneurons from the rostral migratory stream. These experiments were performed using surgical or chemical methods, but also by means of the analysis of genetic models, some of whose olfactory components are missing, colorless or mismatching within the wild-type scenario of odor processing. Anat Rec, 296:1383-1400, 2013. V C 2013 Wiley Periodicals, Inc.Key words: olfaction; olfactory bulb; neuronal lamination; nervous systemAbbreviations used: AON 5 accessory olfactory nucleus; BDNF 5 brain-derived neurotrophic factor; EGF 5 epidermal growth factor; FGF 5 fibroblast growth factor; LOT 5 lateral olfactory tract; MC 5 mitral cells; NCAM 5 neural cell adhesion molecule; OB 5 olfactory bulb; OMP 5 olfactory marker protein; ORN 5 olfactory receptor neuron; PCD 5 Purkinje cell degeneration; PSA-NCAM 5 polysialylated form of NCAM; RMS 5 rostral migratory stream; SVZ 5 subventricular zone; TGF 5 transforming growth factor.

Bone marrow stem cells are the best known stem cell type and have been employed for more than 50 years, especially in pathologies of the hematopoietic and immune systems. However, their therapeutic potential is much broader, and they can also be employed to palliate neural diseases. Apart from their plastic properties, these cells lack the legal or ethical constraints of other stem cell populations, that is, embryonic stem cells. Current research addressing the integration of bone marrow-derived cells into the neural circuits of the central nervous system, their features, and applications is a hotspot in neurobiology. Nevertheless, as in other leading research lines the efficacy and possibilities of their application depend on technical procedures, which are still far from being standardized. Accordingly, for efficient research this large range of variants should be taken into account as they could lead to unexpected results. Rather than focusing on clinical aspects, this review offers a compendium of the methodologies aimed at providing a guide for researchers who are working in the field of bone marrow transplantation in the central nervous system. It seeks to be useful for both introductory and trouble-shooting purposes, and in particular for dealing with the large array of bone marrow transplantation protocols available.