scholarly journals Phenotypic variation within and across transcriptomic cell types in mouse motor cortex

2020 ◽  
Author(s):  
Federico Scala ◽  
Dmitry Kobak ◽  
Matteo Bernabucci ◽  
Yves Bernaerts ◽  
Cathryn René Cadwell ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Cortical Neurons ◽  
Adult Mouse ◽  
Cell Types ◽  
Neuronal Diversity ◽  
Patch Clamp Recording ◽  
Electrophysiological Properties ◽  
Single Cell Rna Sequencing ◽  
Electric Space ◽  
Almost All

Cortical neurons exhibit astounding diversity in gene expression as well as in morphological and electrophysiological properties. Most existing neural taxonomies are based on either transcriptomic or morpho-electric criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells. Here we used Patch-seq to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of over 1300 neurons in adult mouse motor cortex, providing a comprehensive morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (Vip, Pvalb, Sst, etc.) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well-separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neural types in the neocortex do not always form discrete entities. Instead, neurons follow a hierarchy consisting of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.

scholarly journals Phenotypic variation of transcriptomic cell types in mouse motor cortex

Nature ◽  
2020 ◽  
Author(s):  
Federico Scala ◽  
Dmitry Kobak ◽  
Matteo Bernabucci ◽  
Yves Bernaerts ◽  
Cathryn René Cadwell ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Cortical Neurons ◽  
Primary Motor Cortex ◽  
Cell Types ◽  
Neuronal Diversity ◽  
Patch Clamp Recording ◽  
Electrophysiological Properties ◽  
Neuronal Types ◽  
Electric Space ◽  
Almost All

AbstractCortical neurons exhibit extreme diversity in gene expression as well as in morphological and electrophysiological properties1,2. Most existing neural taxonomies are based on either transcriptomic3,4 or morpho-electric5,6 criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells7. Here we used Patch-seq8 to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of more than 1,300 neurons in adult mouse primary motor cortex, providing a morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (those expressing Vip, Pvalb, Sst and so on) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neuronal types in the neocortex do not always form discrete entities. Instead, neurons form a hierarchy that consists of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.

scholarly journals Q&A: using Patch-seq to profile single cells

BMC Biology ◽  
2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Cathryn R. Cadwell ◽  
Rickard Sandberg ◽  
Xiaolong Jiang ◽  
Andreas S. Tolias
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Patch Clamp ◽  
Single Cell ◽  
Single Cells ◽  
Cell Types ◽  
Patch Clamp Recording ◽  
Electrophysiological Properties ◽  
Whole Cell Patch Clamp ◽  
Single Cell Rna Sequencing

Abstract Individual neurons vary widely in terms of their gene expression, morphology, and electrophysiological properties. While many techniques exist to study single-cell variability along one or two of these dimensions, very few techniques can assess all three features for a single cell. We recently developed Patch-seq, which combines whole-cell patch clamp recording with single-cell RNA-sequencing and immunohistochemistry to comprehensively profile the transcriptomic, morphologic, and physiologic features of individual neurons. Patch-seq can be broadly applied to characterize cell types in complex tissues such as the nervous system, and to study the transcriptional signatures underlying the multidimensional phenotypes of single cells.

scholarly journals Single-Cell RNA Sequencing of the Adult Mouse Kidney: From Molecular Cataloging of Cell Types to Disease-Associated Predictions

2019 ◽  
Vol 73 (1) ◽  
pp. 140-142 ◽  
Author(s):  
Nils O. Lindström ◽  
Guilherme De Sena Brandine ◽  
Andrew Ransick ◽  
Andrew P. McMahon
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Adult Mouse ◽  
Cell Types ◽  
Mouse Kidney ◽  
Single Cell Rna Sequencing

scholarly journals Inhibition of Lithium Sensitive Orai1/ STIM1 Expression and Store Operated Ca2+ Entry in Chorea-Acanthocytosis Neurons by NF-κB Inhibitor Wogonin

2018 ◽  
Vol 51 (1) ◽  
pp. 278-289 ◽  
Author(s):  
Basma Sukkar ◽  
Stefan Hauser ◽  
Lisann Pelzl ◽  
Zohreh Hosseinzadeh ◽  
Itishri Sahu ◽  
...  
Keyword(s):  
Cell Death ◽  
Cortical Neurons ◽  
Lithium Treatment ◽  
Cell Types ◽  
Protein Abundance ◽  
Loss Of Function ◽  
Atpase Inhibitor ◽  
Patch Clamp Recording ◽  
Transcript Levels ◽  
Induced Pluripotent

Background/Aims: The neurodegenerative disease Chorea-Acanthocytosis (ChAc) is caused by loss-of-function-mutations of the chorein-encoding gene VPS13A. In ChAc neurons transcript levels and protein abundance of Ca2+ release activated channel moiety (CRAC) Orai1 as well as its regulator STIM1/2 are decreased, resulting in blunted store operated Ca2+-entry (SOCE) and enhanced suicidal cell death. SOCE is up-regulated and cell death decreased by lithium. The effects of lithium are paralleled by upregulation of serum & glucocorticoid inducible kinase SGK1 and abrogated by pharmacological SGK1 inhibition. In other cell types SGK1 has been shown to be partially effective by upregulation of NFκB, a transcription factor stimulating the expression of Orai1 and STIM. The present study explored whether pharmacological inhibition of NFκB interferes with Orai1/STIM1/2 expression and SOCE and their upregulation by lithium in ChAc neurons. Methods: Cortical neurons were differentiated from induced pluripotent stem cells generated from fibroblasts of ChAc patients and healthy volunteers. Orai1 and STIM1 transcript levels and protein abundance were estimated from qRT-PCR and Western blotting, respectively, cytosolic Ca2+-activity ([Ca2+]i) from Fura-2-fluorescence, SOCE from increase of [Ca2+]i following Ca2+ re-addition after Ca2+-store depletion with sarco-endoplasmatic Ca2+-ATPase inhibitor thapsigargin (1µM), as well as CRAC current utilizing whole cell patch clamp recording. Results: Orai1 and STIM1 transcript levels and protein abundance as well as SOCE and CRAC current were significantly enhanced by lithium treatment (2 mM, 24 hours). These effects were reversed by NFκB inhibitor wogonin (50 µM). Conclusion: The stimulation of expression and function of Orai1/STIM1/2 by lithium in ChAc neurons are disrupted by pharmacological NFκB inhibition.

scholarly journals A survey of human brain transcriptome diversity at the single cell level

2015 ◽  
Vol 112 (23) ◽  
pp. 7285-7290 ◽  
Author(s):  
Spyros Darmanis ◽  
Steven A. Sloan ◽  
Ye Zhang ◽  
Martin Enge ◽  
Christine Caneda ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cortical Neurons ◽  
Cell Types ◽  
Type I ◽  
Neuronal Populations ◽  
Brain Transcriptome ◽  
Single Cell Rna Sequencing ◽  
Whole Transcriptome

The human brain is a tissue of vast complexity in terms of the cell types it comprises. Conventional approaches to classifying cell types in the human brain at single cell resolution have been limited to exploring relatively few markers and therefore have provided a limited molecular characterization of any given cell type. We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained during surgical procedures where otherwise normal tissue was removed to gain access to deeper hippocampal pathology in patients with medical refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. We were able to divide neurons into individual communities and show that these communities preserve the categorization of interneuron subtypes that is typically observed with the use of classic interneuron markers. We then used single cell RNA sequencing on fetal human cortical neurons to identify genes that are differentially expressed between fetal and adult neurons and those genes that display an expression gradient that reflects the transition between replicating and quiescent fetal neuronal populations. Finally, we observed the expression of major histocompatibility complex type I genes in a subset of adult neurons, but not fetal neurons. The work presented here demonstrates the applicability of single cell RNA sequencing on the study of the adult human brain and constitutes a first step toward a comprehensive cellular atlas of the human brain.

scholarly journals Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Lucas T Gray ◽  
Zizhen Yao ◽  
Thuc Nghi Nguyen ◽  
Tae Kyung Kim ◽  
Hongkui Zeng ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Adult Mouse ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Binding Motifs ◽  
Mouse Cortex ◽  
Mouse Visual Cortex

Mammalian cortex is a laminar structure, with each layer composed of a characteristic set of cell types with different morphological, electrophysiological, and connectional properties. Here, we define chromatin accessibility landscapes of major, layer-specific excitatory classes of neurons, and compare them to each other and to inhibitory cortical neurons using the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We identify a large number of layer-specific accessible sites, and significant association with genes that are expressed in specific cortical layers. Integration of these data with layer-specific transcriptomic profiles and transcription factor binding motifs enabled us to construct a regulatory network revealing potential key layer-specific regulators, including Cux1/2, Foxp2, Nfia, Pou3f2, and Rorb. This dataset is a valuable resource for identifying candidate layer-specific cis-regulatory elements in adult mouse cortex.

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 Intrinsic electrophysiological properties predict variability in morphology and connectivity among striatal Parvalbumin-expressing Pthlh-cells

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Carolina Bengtsson Gonzales ◽  
Steven Hunt ◽  
Ana B. Munoz-Manchado ◽  
Chris J. McBain ◽  
Jens Hjerling-Leffler
Keyword(s):  
Cell Types ◽  
Inhibitory Interneuron ◽  
Classification Schemes ◽  
Electrophysiological Properties ◽  
Neuronal Populations ◽  
Neuronal Classification ◽  
Single Cell Rna Sequencing ◽  
Different Types ◽  
Types Of Information ◽  
Activity Dependent

Abstract Determining the cellular content of the nervous system in terms of cell types and the rules of their connectivity represents a fundamental challenge to the neurosciences. The recent advent of high-throughput techniques, such as single-cell RNA-sequencing has allowed for greater resolution in the identification of cell types and/or states. Although most of the current neuronal classification schemes comprise discrete clusters, several recent studies have suggested that, perhaps especially, within the striatum, neuronal populations exist in continua, with regards to both their molecular and electrophysiological properties. Whether these continua are stable properties, established during development, or if they reflect acute differences in activity-dependent regulation of critical genes is currently unknown. We set out to determine whether gradient-like molecular differences in the recently described Pthlh-expressing inhibitory interneuron population, which contains the Pvalb-expressing cells, correlate with differences in morphological and connectivity properties. We show that morphology and long-range inputs correlate with a spatially organized molecular and electrophysiological gradient of Pthlh-interneurons, suggesting that the processing of different types of information (by distinct anatomical striatal regions) has different computational requirements.

scholarly journals Parvalbumin-Positive Basket Interneurons in Monkey and Rat Prefrontal Cortex

2008 ◽  
Vol 100 (4) ◽  
pp. 2348-2360 ◽  
Author(s):  
N. V. Povysheva ◽  
A. V. Zaitsev ◽  
D. C. Rotaru ◽  
G. Gonzalez-Burgos ◽  
D. A. Lewis ◽  
...  
Keyword(s):  
Prefrontal Cortex ◽  
Cortical Neurons ◽  
Input Resistance ◽  
Cell Types ◽  
Threshold Current ◽  
Electrophysiological Properties ◽  
Basket Cells ◽  
Physiological Properties ◽  
Axonal Arbor ◽  
Fast Spiking

Differences in the developmental origin and relative proportions of biochemically distinct classes of cortical neurons have been found between rodents and primates. In addition, species differences in the properties of certain cell types, such as neurogliaform cells, have also been reported. Consequently, in this study we compared the anatomical and physiological properties of parvalbumin (PV)-positive basket interneurons in the prefrontal cortex of macaque monkeys and rats. The somal size, total dendritic length, and horizontal and vertical spans of the axonal arbor were similar in monkeys and rats. Physiologically, PV basket cells could be identified as fast-spiking interneurons in both species, based on their short spike and high-frequency firing without adaptation. However, important interspecies differences in the intrinsic physiological properties were found. In monkeys, basket cells had a higher input resistance and a lower firing threshold, and they generated more spikes at near-threshold current intensities than those in rats. Thus monkey basket cells appeared to be more excitable. In addition, rat basket cells consistently fired the first spike with a substantial delay and generated spike trains interrupted by quiescent periods more often than monkey basket cells. The frequency of miniature excitatory postsynaptic potentials in basket cells was considerably higher in rats than that in monkeys. These differences between rats and monkeys in the electrophysiological properties of PV-positive basket cells may contribute to the differential patterns of neuronal activation observed in rats and monkeys performing working-memory tasks.

scholarly journals Activity of motor cortex neurons during backward locomotion

2011 ◽  
Vol 105 (6) ◽  
pp. 2698-2714 ◽  
Author(s):  
P. V. Zelenin ◽  
T. G. Deliagina ◽  
G. N. Orlovsky ◽  
A. Karayannidou ◽  
E. E. Stout ◽  
...  
Keyword(s):  
Motor Cortex ◽  
Cortical Neurons ◽  
Cortical Activity ◽  
The Other ◽  
Bipedal Locomotion ◽  
Related Activity ◽  
Quadrupedal Locomotion ◽  
Functional Roles ◽  
Recorded Activity ◽  
Almost All

Forward walking (FW) and backward walking (BW) are two important forms of locomotion in quadrupeds. Participation of the motor cortex in the control of FW has been intensively studied, whereas cortical activity during BW has never been investigated. The aim of this study was to analyze locomotion-related activity of the motor cortex during BW and compare it with that during FW. For this purpose, we recorded activity of individual neurons in the cat during BW and FW. We found that the discharge frequency in almost all neurons was modulated in the rhythm of stepping during both FW and BW. However, the modulation patterns during BW and FW were different in 80% of neurons. To determine the source of modulating influences (forelimb controllers vs. hindlimb controllers), the neurons were recorded not only during quadrupedal locomotion but also during bipedal locomotion (with either forelimbs or hindlimbs walking), and their modulation patterns were compared. We found that during BW (like during FW), modulation in some neurons was determined by inputs from limb controllers of only one girdle, whereas the other neurons received inputs from both girdles. The combinations of inputs could depend on the direction of locomotion. Most often (in 51% of forelimb-related neurons and in 34% of the hindlimb-related neurons), the neurons received inputs only from their own girdle when this girdle was leading and from both girdles when this girdle was trailing. This reconfiguration of inputs suggests flexibility of the functional roles of individual cortical neurons during different forms of locomotion.

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