scholarly journals A multimodal cell census and atlas of the mammalian primary motor cortex

2020 ◽  
Author(s):  
◽  
Ricky S. Adkins ◽  
Andrew I. Aldridge ◽  
Shona Allen ◽  
Seth A. Ament ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Spatial Information ◽  
Molecular Genetic ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Open Chromatin ◽  
Cell Type ◽  
Spatially Resolved

ABSTRACTWe report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) 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. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

scholarly journals A multimodal cell census and atlas of the mammalian primary motor cortex

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 86-102 ◽  
Author(s):  
◽  
Edward M. Callaway ◽  
Hong-Wei Dong ◽  
Joseph R. Ecker ◽  
Michael J. Hawrylycz ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Spatial Information ◽  
Molecular Genetic ◽  
Cortical Cell ◽  
Neuronal Cell ◽  
Open Chromatin ◽  
Cell Type ◽  
Spatially Resolved

AbstractHere 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.

scholarly journals Multiscale Co-Expression in the Brain

2020 ◽  
Author(s):  
Benjamin D. Harris ◽  
Megan Crow ◽  
Stephan Fischer ◽  
Jesse Gillis
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Rna Sequencing ◽  
Primary Motor Cortex ◽  
Cell Types ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
The Brain ◽  
Regulatory Landscape

ABSTRACTSingle-cell RNA-sequencing (scRNAseq) data can reveal co-regulatory relationships between genes that may be hidden in bulk RNAseq due to cell type confounding. Using the primary motor cortex data from the Brain Initiative Cell Census Network (BICCN), we study cell type specific co-expression across 500,000 cells. Surprisingly, we find that the same gene-gene relationships that differentiate cell types are evident at finer and broader scales, suggesting a consistent multiscale regulatory landscape.

scholarly journals Spatially mapped single-cell chromatin accessibility

2019 ◽  
Author(s):  
Casey A. Thornton ◽  
Ryan M. Mulqueen ◽  
Andrew Nishida ◽  
Kristof A. Torkenczy ◽  
Eve G. Lowenstein ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Information ◽  
Three Dimensional ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Artery Occlusion ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Spatially Resolved ◽  
Typical Experiment

AbstractHigh-throughput single-cell epigenomic assays can resolve the heterogeneity of cell types and states in complex tissues, however, spatial orientation within the network of interconnected cells is lost. Here, we present a novel method for highly scalable, spatially resolved, single-cell profiling of chromatin states. We use high-density multiregional sampling to perform single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin (sciMAP-ATAC) to produce single-cell data of an equivalent quality to non-spatially resolved single-cell ATAC-seq, where each cell is localized to a three-dimensional position within the tissue. A typical experiment comprises between 96 and 384 spatially mapped tissue positions, each producing 10s to over 100 individual single-cell ATAC-seq profiles, and a typical resolution of 214 cubic microns; with the ability to tune the resolution and cell throughput to suit each target application. We apply sciMAP-ATAC to the adult mouse primary somatosensory cortex, where we profile cortical lamination and demonstrate the ability to analyze data from a single tissue position or compare a single cell type in adjacent positions. We also profile the human primary visual cortex, where we produce spatial trajectories through the cortex. Finally, we characterize the spatially progressive nature of cerebral ischemic infarct in the mouse brain using a model of transient middle cerebral artery occlusion. We leverage the spatial information to identify novel and known transcription factor activities that vary by proximity to the ischemic infarction core with cell type specificity.

scholarly journals Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex

2021 ◽  
Author(s):  
Shawn Zheng Kai Tan ◽  
Huseyin Kir ◽  
Brian Aevermann ◽  
Tom Gillespie ◽  
Michael Hawrylycz ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Cell Types ◽  
Use Cases ◽  
Data Driven ◽  
Cell Type ◽  
Data Standards ◽  
Brain Data ◽  
The Brain

Large scale single cell omics profiling is revolutionising our understanding of cell types, especially in complex organs like the brain. This presents both an opportunity and a challenge for cell ontologies. Annotation of cell types in single cell 'omics data typically uses unstructured free text, making comparison and mapping of annotation between datasets challenging. Annotation with cell ontologies is key to overcoming this challenge, but this will require meeting the challenge of extending cell ontologies representing classically defined cell types by defining and classifying cell types directly from data. Here we present the Brain Data Standards Ontology (BDSO), a data driven ontology that is built as an extension to the Cell Ontology (CL). It supports two major use cases: cell type annotation, and navigation, search, and organisation of a web application integrating single cell omics datasets for the mammalian primary motor cortex. The ontology is built using a semi-automated pipeline that interlinks cell type taxonomies and necessary and sufficient marker genes, and imports relevant ontology modules derived from external ontologies. Overall, the BDS ontology provides an underlying structure that supports these use cases, while remaining sustainable and extensible through automation as our knowledge of brain cell type expands.

scholarly journals Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 137-143 ◽  
Author(s):  
Meng Zhang ◽  
Stephen W. Eichhorn ◽  
Brian Zingg ◽  
Zizhen Yao ◽  
Kaelan Cotter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Cell Types ◽  
Mammalian Brain ◽  
Imaging Method ◽  
Retrograde Labelling ◽  
Spatially Resolved ◽  
Different Cell Types

AbstractA mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing allows systematic identification of cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1,2. Single-cell epigenomic profiling3,4 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation. Here we used a single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)5, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex. We profiled approximately 300,000 cells in the mouse primary motor cortex and its adjacent areas, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory but also most inhibitory neuronal clusters adopted laminar organizations. Intratelencephalic neurons formed a largely continuous gradient along the cortical depth axis, in which the gene expression of individual cells correlated with their cortical depths. Furthermore, we integrated MERFISH with retrograde labelling to probe projection targets of neurons of the mouse primary motor cortex and found that their cortical projections formed a complex network in which individual neuronal clusters project to multiple target regions and individual target regions receive inputs from multiple neuronal clusters.

scholarly journals Isoform cell-type specificity in the mouse primary motor cortex

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 195-199
Author(s):  
A. Sina Booeshaghi ◽  
Zizhen Yao ◽  
Cindy van Velthoven ◽  
Kimberly Smith ◽  
Bosiljka Tasic ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Cell Types ◽  
Cell Type Specificity ◽  
Spatially Resolved ◽  
Gene Level ◽  
Multiple Measurements ◽  
Isoform Specificity ◽  
Different Cell Types

AbstractFull-length SMART-seq1 single-cell RNA sequencing can be used to measure gene expression at isoform resolution, making possible the identification of specific isoform markers for different cell types. Used in conjunction with spatial RNA capture and gene-tagging methods, this enables the inference of spatially resolved isoform expression for different cell types. Here, in a comprehensive analysis of 6,160 mouse primary motor cortex cells assayed with SMART-seq, 280,327 cells assayed with MERFISH2 and 94,162 cells assayed with 10x Genomics sequencing3, we find examples of isoform specificity in cell types—including isoform shifts between cell types that are masked in gene-level analysis—as well as examples of transcriptional regulation. Additionally, we show that isoform specificity helps to refine cell types, and that a multi-platform analysis of single-cell transcriptomic data leveraging multiple measurements provides a comprehensive atlas of transcription in the mouse primary motor cortex that improves on the possibilities offered by any single technology.

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

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 111-119 ◽  
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.

scholarly journals Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets

2020 ◽  
Author(s):  
Zhen Miao ◽  
Michael S. Balzer ◽  
Ziyuan Ma ◽  
Hongbo Liu ◽  
Junnan Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Kidney Development ◽  
Developmental Stages ◽  
Major Gene ◽  
Cell Types ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Cell Type ◽  
Single Nucleotide Variants

AbstractDetermining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response.Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms.We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via interactive public websites.

scholarly journals A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anoushka Joglekar ◽  
Andrey Prjibelski ◽  
Ahmed Mahfouz ◽  
Paul Collier ◽  
Susan Lin ◽  
...  
Keyword(s):  
Single Cell ◽  
Brain Region ◽  
Cell Types ◽  
Brain Regions ◽  
Protein Isoforms ◽  
Cell Type ◽  
Anatomic Structure ◽  
Spatially Resolved ◽  
Long Read ◽  
Isoform Expression

AbstractSplicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 (www.isoformAtlas.com). Isoform tests for DIE show better performance than exon tests. We detect hundreds of DIE events traceable to cell types, often corresponding to functionally distinct protein isoforms. Mostly, one cell type is responsible for brain-region specific DIE. However, for fewer genes, multiple cell types influence DIE. Thus, regional identity can, although rarely, override cell-type specificity. Cell types indigenous to one anatomic structure display distinctive DIE, e.g. the choroid plexus epithelium manifests distinct transcription-start-site usage. Spatial transcriptomics and long-read sequencing yield a spatially resolved splicing map. Our methods quantify isoform expression with cell-type and spatial resolution and it contributes to further our understanding of how the brain integrates molecular and cellular complexity.

scholarly journals Single-cell regulatory landscape and disease vulnerability map of adult Macaque cortex

2020 ◽  
Author(s):  
Ying Lei ◽  
Mengnan Cheng ◽  
Zihao Li ◽  
Zhenkun Zhuang ◽  
Liang Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Neurological Diseases ◽  
Single Cells ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Nucleotide Polymorphisms ◽  
Cell Type

Non-human primates (NHP) provide a unique opportunity to study human neurological diseases, yet detailed characterization of the cell types and transcriptional regulatory features in the NHP brain is lacking. We applied a combinatorial indexing assay, sci-ATAC-seq, as well as single-nuclei RNA-seq, to profile chromatin accessibility in 43,793 single cells and transcriptomics in 11,477 cells, respectively, from prefrontal cortex, primary motor cortex and the primary visual cortex of adult cynomolgus monkey Macaca fascularis. Integrative analysis of these two datasets, resolved regulatory elements and transcription factors that specify cell type distinctions, and discovered area-specific diversity in chromatin accessibility and gene expression within excitatory neurons. We also constructed the dynamic landscape of chromatin accessibility and gene expression of oligodendrocyte maturation to characterize adult remyelination. Furthermore, we identified cell type-specific enrichment of differentially spliced gene isoforms and disease-associated single nucleotide polymorphisms. Our datasets permit integrative exploration of complex regulatory dynamics in macaque brain tissue at single-cell resolution.

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