Whole-animal connectome and cell-type complement of the three-segmented Platynereis dumerilii larva

AbstractNervous systems coordinate effectors across the body during movements. We know little about the cellular-level structure of synaptic circuits for such body-wide control. Here we describe the whole-body synaptic connectome and cell-type complement of a three-segmented larva of the marine annelid Platynereis dumerilii. We reconstructed and annotated over 1,500 neurons and 6,500 non-neuronal cells in a whole-body serial electron microscopy dataset. The differentiated cells fall into 180 neuronal and 90 non-neuronal cell types. We analyse the modular network architecture of the entire nervous system and describe polysynaptic pathways from 428 sensory neurons to four effector systems – ciliated cells, glands, pigment cells and muscles. The complete somatic musculature and its innervation will be described in a companion paper. We also investigated intersegmental differences in cell-type complement, descending and ascending pathways, and mechanosensory and peptidergic circuits. Our work provides the basis for understanding whole-body coordination in annelids.

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Th2 Cytokine Modulates Herpesvirus Reactivation in a Cell Type Specific Manner

Journal of Virology ◽

10.1128/jvi.01946-20 ◽

2021 ◽

Author(s):

Guoxun Wang ◽

Christina Zarek ◽

Tyron Chang ◽

Lili Tao ◽

Alexandria Lowe ◽

...

Keyword(s):

B Cells ◽

Cell Types ◽

The Body ◽

Receptor Expression ◽

Conditional Knockout ◽

Interleukin 4 ◽

Virus Reactivation ◽

Cell Type ◽

Murine Gammaherpesvirus ◽

Cell Type Specific

Gammaherpesviruses, such as Epstein-Barr virus (EBV), Kaposi’s sarcoma associated virus (KSHV), and murine γ-herpesvirus 68 (MHV68), establish latent infection in B cells, macrophages, and non-lymphoid cells, and can induce both lymphoid and non-lymphoid cancers. Research on these viruses has relied heavily on immortalized B cell and endothelial cell lines. Therefore, we know very little about the cell type specific regulation of virus infection. We have previously shown that treatment of MHV68-infected macrophages with the cytokine interleukin-4 (IL-4) or challenge of MHV68-infected mice with an IL-4-inducing parasite leads to virus reactivation. However, we do not know if all latent reservoirs of the virus, including B cells, reactivate the virus in response to IL-4. Here we used an in vivo approach to address the question of whether all latently infected cell types reactivate MHV68 in response to a particular stimulus. We found that IL-4 receptor expression on macrophages was required for IL-4 to induce virus reactivation, but that it was dispensable on B cells. We further demonstrated that the transcription factor, STAT6, which is downstream of the IL-4 receptor and binds virus gene 50 N4/N5 promoter in macrophages, did not bind to the virus gene 50 N4/N5 promoter in B cells. These data suggest that stimuli that promote herpesvirus reactivation may only affect latent virus in particular cell types, but not in others. Importance Herpesviruses establish life-long quiescent infections in specific cells in the body, and only reactivate to produce infectious virus when precise signals induce them to do so. The signals that induce herpesvirus reactivation are often studied only in one particular cell type infected with the virus. However, herpesviruses establish latency in multiple cell types in their hosts. Using murine gammaherpesvirus-68 (MHV68) and conditional knockout mice, we examined the cell type specificity of a particular reactivation signal, interleukin-4 (IL-4). We found that IL-4 only induced herpesvirus reactivation from macrophages, but not from B cells. This work indicates that regulation of virus latency and reactivation is cell type specific. This has important implications for therapies aimed at either promoting or inhibiting reactivation for the control or elimination of chronic viral infections.

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Renal cell markers: lighthouses for managing renal diseases

AJP Renal Physiology ◽

10.1152/ajprenal.00182.2021 ◽

2021 ◽

Author(s):

Shivangi Agarwal ◽

Yashwanth R Sudhini ◽

Onur K Polat ◽

Jochen Reiser ◽

Mehmet Mete Altintas

Keyword(s):

High Efficiency ◽

Imaging Techniques ◽

Unmet Need ◽

Cell Types ◽

Whole Body ◽

Renal Diseases ◽

Cell Type ◽

Cell Markers ◽

Urine Production

Kidneys, one of the vital organs in our body, are responsible for maintaining whole-body homeostasis. The complexity of renal function (e.g., filtration, reabsorption, fluid and electrolyte regulation, urine production) demands diversity not only at the level of cell types but also in their overall distribution and structural framework within the kidney. To gain an in-depth molecular-level understanding of the renal system, it is imperative to discern the components of kidney and the types of cells residing in each of the sub-regions. Recent developments in labeling, tracing, and imaging techniques enabled us to mark, monitor and identify these cells in vivo with high efficiency in a minimally invasive manner. In this review, we have summarized different cell types, specific markers that are uniquely associated with those cell types, and their distribution in kidney, which altogether make kidneys so special and different. Cellular sorting based on the presence of certain proteins on the cell surface allowed for assignment of multiple markers for each cell type. However, different studies using different techniques have found contradictions in the cell-type specific markers. Thus, the term "cell marker" might be imprecise and sub-optimal, leading to uncertainty when interpreting the data. Therefore, we strongly believe that there is an unmet need to define the best cell markers for a cell type. Although, the compendium of renal-selective marker proteins presented in this review is a resource that may be useful to the researchers, we acknowledge that the list may not be necessarily exhaustive.

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Nature ◽

10.1038/s41586-021-03465-8 ◽

2021 ◽

Vol 598 (7879) ◽

pp. 111-119 ◽

Cited By ~ 1

Author(s):

Trygve E. Bakken ◽

Nikolas L. Jorstad ◽

Qiwen Hu ◽

Blue B. Lake ◽

Wei Tian ◽

...

Keyword(s):

Motor Cortex ◽

Primary Motor Cortex ◽

Neuronal Cell ◽

Cell Types ◽

Morphological Characterization ◽

Fine Motor ◽

Marker Genes ◽

Cell Type ◽

Regulatory Pathways ◽

Cellular Analysis

AbstractThe primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

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Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

Frontiers in Neuroanatomy ◽

10.3389/fnana.2021.787601 ◽

2022 ◽

Vol 15 ◽

Author(s):

Kyra T. Newmaster ◽

Fae A. Kronman ◽

Yuan-ting Wu ◽

Yongsoo Kim

Keyword(s):

Data Analysis ◽

Mouse Brain ◽

Neuronal Cell ◽

Cell Types ◽

Developmental Time ◽

Cell Type ◽

Level Data ◽

Primary Model ◽

Resolution Mapping ◽

High Level

The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.

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A community-based transcriptomics classification and nomenclature of neocortical cell types

Nature Neuroscience ◽

10.1038/s41593-020-0685-8 ◽

2020 ◽

Vol 23 (12) ◽

pp. 1456-1468 ◽

Cited By ~ 8

Author(s):

Rafael Yuste ◽

Michael Hawrylycz ◽

Nadia Aalling ◽

Argel Aguilar-Valles ◽

Detlev Arendt ◽

...

Keyword(s):

Data Aggregation ◽

Developmental Stages ◽

Cell Types ◽

The Body ◽

Cortical Circuits ◽

Cell Type ◽

Community Based ◽

Cortical Cells ◽

Molecular Features ◽

Definition Of

AbstractTo understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.

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Light microscopical and cytochemical study on the adhesive and epidermal gland cell secretions of the branchiobdellid Cambarincola fallax (Annelida: Clitellata)

Canadian Journal of Zoology ◽

10.1139/z88-303 ◽

1988 ◽

Vol 66 (9) ◽

pp. 2057-2064 ◽

Cited By ~ 14

Author(s):

S. R. Gelder ◽

J. P. Rowe

Keyword(s):

Basic Protein ◽

Gland Cell ◽

Attachment Site ◽

Cell Types ◽

The Body ◽

Protein Component ◽

Cell Type ◽

Gland Cells ◽

Adhesive Organs ◽

Epidermal Gland

Eight types of gland cells are present in six different epidermal glands in the branchiobdellid Cambarincola fallax. The anterior and posterior adhesive organs are both composed of viscid and releaser adhesive gland cell types, and their secretions open onto the anterior attachment site on the ventral surface of the ventral peristomial lip and onto the posterior attachment disc, respectively. The secretion granules of the viscid gland cell type are composed of neutral mucosubstances with basic proteins containing arginine and (or) lysine; the releaser gland cell type contains basic proteinaceous granules with a tryptophan component. These adhesive glands are very similar to duo-gland adhesive organs described elsewhere. Use of the term "sucker" should be discontinued as there is no suctorial mechanism at the anterior attachment site and only circumstantial evidence of such action at the posterior disc. Two epidermal gland cell types occur together in groups of two to four cells at sites scattered over the body surface except in trunk segments 6 and 7. One of these epidermal gland cell types produces granular secretions formed of neutral mucosubstances with a basic protein component, and the other produces globular secretions composed of a carboxylated acid mucosubstance. Secretions from the peristomial gland cells open onto the dorsal and ventral lips. The posterolateral gland cells form three pairs: two pairs in segment 8 and one pair in segment 9. Both peristomial and posterolateral gland cells have granular secretions composed of neutral mucosubstances with a basic protein component. The two types of clitellar gland cells are arranged in groups of 7 to 13 cells with a granular secretion type predominating over one with globular secretions. The granular type consists of neutral mucosubstances with amyloid-like and strong basic protein components, and the globular type consists of a carboxylated acid mucosubstance with a nonbasic protein component.

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A harmonized atlas of mouse spinal cord cell types and their spatial organization

Nature Communications ◽

10.1038/s41467-021-25125-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Daniel E. Russ ◽

Ryan B. Patterson Cross ◽

Li Li ◽

Stephanie C. Koch ◽

Kaya J. E. Matson ◽

...

Keyword(s):

Spinal Cord ◽

Single Cell ◽

Spatial Organization ◽

Neuronal Cell ◽

Cell Types ◽

Molecular Organization ◽

Cell Type ◽

Sequencing Data ◽

Mouse Spinal Cord ◽

Common Reference

AbstractSingle-cell RNA sequencing data can unveil the molecular diversity of cell types. Cell type atlases of the mouse spinal cord have been published in recent years but have not been integrated together. Here, we generate an atlas of spinal cell types based on single-cell transcriptomic data, unifying the available datasets into a common reference framework. We report a hierarchical structure of postnatal cell type relationships, with location providing the highest level of organization, then neurotransmitter status, family, and finally, dozens of refined populations. We validate a combinatorial marker code for each neuronal cell type and map their spatial distributions in the adult spinal cord. We also show complex lineage relationships among postnatal cell types. Additionally, we develop an open-source cell type classifier, SeqSeek, to facilitate the standardization of cell type identification. This work provides an integrated view of spinal cell types, their gene expression signatures, and their molecular organization.

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Complexity and graded regulation of neuronal cell-type–specific alternative splicing revealed by single-cell RNA sequencing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2013056118 ◽

2021 ◽

Vol 118 (10) ◽

pp. e2013056118

Author(s):

Huijuan Feng ◽

Daniel F. Moakley ◽

Shuonan Chen ◽

Melissa G. McKenzie ◽

Vilas Menon ◽

...

Keyword(s):

Alternative Splicing ◽

Single Cell ◽

Neuronal Cell ◽

Cell Types ◽

Gabaergic Neurons ◽

Cell Type ◽

Differential Splicing ◽

Single Cell Rna Sequencing ◽

Hierarchical Levels ◽

Cell Type Specific

The enormous cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell-type–specific gene-regulatory programs at the molecular level. Although prevalent in the brain, the contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge. Here, we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single-cell RNA-sequencing data. We found distinct splicing programs between glutamatergic and GABAergic neurons and between subclasses within each neuronal class. These programs consist of overlapping sets of alternative exons showing differential splicing at multiple hierarchical levels. Using an integrative approach, our analysis suggests that RNA-binding proteins (RBPs) Celf1/2, Mbnl2, and Khdrbs3 are preferentially expressed and more active in glutamatergic neurons, while Elavl2 and Qk are preferentially expressed and more active in GABAergic neurons. Importantly, these and additional RBPs also contribute to differential splicing between neuronal subclasses at multiple hierarchical levels, and some RBPs contribute to splicing dynamics that do not conform to the hierarchical structure defined by the transcriptional profiles. Thus, our results suggest graded regulation of AS across neuronal cell types, which may provide a molecular mechanism to specify neuronal identity and function that are orthogonal to established classifications based on transcriptional regulation.

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Cell type-specific biotin labeling in vivo resolves regional neuronal proteomic differences in mouse brain

10.1101/2021.08.03.454921 ◽

2021 ◽

Author(s):

Sruti Rayaprolu ◽

Sara Bitarafan ◽

Ranjita Betarbet ◽

Sydney N Sunna ◽

Lihong Cheng ◽

...

Keyword(s):

Mouse Brain ◽

Neurological Diseases ◽

Neuronal Cell ◽

Cell Types ◽

Proteomic Profiling ◽

Cell Type ◽

Specific Expression ◽

Cell Type Specific ◽

The Brain

Isolation and proteomic profiling of brain cell types, particularly neurons, pose several technical challenges which limit our ability to resolve distinct cellular phenotypes in neurological diseases. Therefore, we generated a novel mouse line that enables cell type-specific expression of a biotin ligase, TurboID, via Cre-lox strategy for in vivo proximity-dependent biotinylation of proteins. Using adenoviral-based and transgenic approaches, we show striking protein biotinylation in neuronal cell bodies and axons throughout the mouse brain. We quantified more than 2,000 neuron-derived proteins following enrichment that mapped to numerous subcellular compartments. Synaptic, transmembrane transporters, ion channel subunits, and disease-relevant druggable targets were among the most significantly enriched proteins. Remarkably, we resolved brain region-specific proteomic profiles of Camk2a neurons with distinct functional molecular signatures and disease associations that may underlie regional neuronal vulnerability. Leveraging the neuronal specificity of this in vivo biotinylation strategy, we used an antibody-based approach to uncover regionally unique patterns of neuron-derived signaling phospho-proteins and cytokines, particularly in the cortex and cerebellum. Our work provides a proteomic framework to investigate cell type-specific mechanisms driving physiological and pathological states of the brain as well as complex tissues beyond the brain.

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Single nucleus analysis of the chromatin landscape in mouse forebrain development

10.1101/159137 ◽

2017 ◽

Cited By ~ 2

Author(s):

Sebastian Preissl ◽

Rongxin Fang ◽

Yuan Zhao ◽

Ramya Raviram ◽

Yanxiao Zhang ◽

...

Keyword(s):

Neuronal Cell ◽

Cell Types ◽

Cellular Heterogeneity ◽

Regulatory Sequences ◽

Specific Cell ◽

Cell Type ◽

Tissue Samples ◽

Forebrain Development ◽

Cell Type Specific ◽

Accessible Chromatin

ABSTRACTGenome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes1–4. However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin5 and is optimized for nuclei from flash-frozen primary tissue samples (snATAC-seq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specific cis regulatory sequences and infer potential master transcriptional regulators of each cell population. Our results demonstrate the feasibility of a general approach for identifying cell-type-specific cis regulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals.

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