scholarly journals Identification of a regeneration-organizing cell in the Xenopus tail

Science ◽  
2019 ◽  
Vol 364 (6441) ◽  
pp. 653-658 ◽  
Author(s):  
C. Aztekin ◽  
T. W. Hiscock ◽  
J. C. Marioni ◽  
J. B. Gurdon ◽  
B. D. Simons ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Transcriptional Profiling ◽  
Cellular Mechanism ◽  
Cell Type ◽  
Genetic Ablation ◽  
Tail Development ◽  
Naturally Occurring ◽  
Early Embryos ◽  
Single Cell Rna Sequencing ◽  
Wound Epidermis

Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.

The development of the tectum in Xenopus laevis: an autoradiographic study

Development ◽  
1972 ◽  
Vol 28 (1) ◽  
pp. 87-115
Author(s):  
K. Straznicky ◽  
R. M. Gaze
Keyword(s):  
Xenopus Laevis ◽  
Dna Synthesis ◽  
Optic Tectum ◽  
Tritiated Thymidine ◽  
Dorsal Surface ◽  
Autoradiographic Study ◽  
Cell Type ◽  
Pole Cells ◽  
Serial Addition ◽  
The Times

The development of the optic tectum in Xenopus laevis has been studied by the use of autoradiography with tritiated thymidine. The first part of the adult tectum to form is the rostroventral pole; cells in this position undergo their final DNA synthesis between stages 35 and 45 or shortly thereafter. Next, the cells comprising the ventrolateral border of the tectum form. These cells undergo their final DNA synthesis at or shortly after stage 45. Finally the cells comprising the dorsal surface of the adult tectum form, mainly between stages 50–55. This part of the tectum originates from the serial addition of strips of cells medially, which displace the pre-existing tissue laterally and rostrally. The formation of the tectum is virtually complete by stage 58. The tectum in Xenopus thus forms in topographical order from rostroventral to caudo-medial. The distribution of labelled cells, several stages after the time of injection of isotope, indicates that, at any one time, a segment of tectum is forming which runs normal to the tectal surface and includes all layers from the ventricular layer out to the surface. In Xenopus, therefore, the times of origin of tectal cells appear to be related not to cell type or tectal layer but to the topographical position of the cells across the surface of the tectum.

Critical downstream analysis steps for single-cell RNA sequencing data

2021 ◽  
Author(s):  
Zilong Zhang ◽  
Feifei Cui ◽  
Chen Lin ◽  
Lingling Zhao ◽  
Chunyu Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Noisy Data ◽  
Single Cell Level ◽  
Cell Type ◽  
Sequencing Data ◽  
Cell Level ◽  
Bioinformatics Tool ◽  
Single Cell Rna Sequencing ◽  
Downstream Analysis

Abstract Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at the single-cell level. Currently, many analysis tools are available to better utilize these relatively noisy data. In this review, we summarize the most widely used methods for critical downstream analysis steps (i.e. clustering, trajectory inference, cell-type annotation and integrating datasets). The advantages and limitations are comprehensively discussed, and we provide suggestions for choosing proper methods in different situations. We hope this paper will be useful for scRNA-seq data analysts and bioinformatics tool developers.

scholarly journals Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205883 ◽  
Author(s):  
Joseph C. Mays ◽  
Michael C. Kelly ◽  
Steven L. Coon ◽  
Lynne Holtzclaw ◽  
Martin F. Rath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pineal Gland ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
Mammalian Pineal Gland ◽  
Daily Patterns

scholarly journals Super-cells untangle large and complex single-cell transcriptome networks

2021 ◽  
Author(s):  
Mariia Bilous ◽  
Loc Tran ◽  
Chiara Cianciaruso ◽  
Santiago J Carmona ◽  
Mikael J Pittet ◽  
...  
Keyword(s):  
Single Cell ◽  
Coarse Graining ◽  
Cell Populations ◽  
Cell Type ◽  
Large Numbers ◽  
Single Cell Rna Sequencing ◽  
Gene Correlation ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Single-cell RNA sequencing (scRNA-seq) technologies offer unique opportunities for exploring heterogeneous cell populations. However, in-depth single-cell transcriptomic characterization of complex tissues often requires profiling tens to hundreds of thousands of cells. Such large numbers of cells represent an important hurdle for downstream analyses, interpretation and visualization. Here we develop a network-based coarse-graining framework where highly similar cells are merged into super-cells. We demonstrate that super-cells not only preserve but often improve the results of downstream analyses including visualization, clustering, differential expression, cell type annotation, gene correlation, imputation, RNA velocity and data integration. By capitalizing on the redundancy inherent to scRNA-seq data, super-cells significantly facilitate and accelerate the construction and interpretation of single-cell atlases, as demonstrated by the integration of 1.46 million cells from COVID-19 patients in less than two hours on a standard desktop.

scholarly journals Identifying common and novel cell types in single-cell RNA-sequencing data using FR-Match

2021 ◽  
Author(s):  
Yun Zhang ◽  
Brian Aevermann ◽  
Rohan Gala ◽  
Richard H. Scheuermann
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Sample Type ◽  
Cell Type ◽  
Sequencing Data ◽  
Excellent Performance ◽  
Single Cell Rna Sequencing ◽  
Accurate Performance ◽  
Cross Platform ◽  
Tissue Region

Reference cell type atlases powered by single cell transcriptomic profiling technologies have become available to study cellular diversity at a granular level. We present FR-Match for matching query datasets to reference atlases with robust and accurate performance for identifying novel cell types and non-optimally clustered cell types in the query data. This approach shows excellent performance for cross-platform, cross-sample type, cross-tissue region, and cross-data modality cell type matching.

scholarly journals Single-Cell RNA-Sequencing Identifies Infrapatellar Fat Pad Macrophage Polarization in Acute Synovitis/Fat Pad Fibrosis and Cell Therapy

2021 ◽  
Vol 8 (11) ◽  
pp. 166
Author(s):  
Dimitrios Kouroupis ◽  
Thomas M. Best ◽  
Lee D. Kaplan ◽  
Diego Correa ◽  
Anthony J. Griswold
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Transcriptional Profiling ◽  
Macrophage Polarization ◽  
Myeloid Cells ◽  
Cellular Heterogeneity ◽  
Joint Disease ◽  
Infrapatellar Fat Pad ◽  
Fat Pad ◽  
Single Cell Rna Sequencing

The pathogenesis and progression of knee inflammatory pathologies is modulated partly by residing macrophages in the infrapatellar fat pad (IFP), thus, macrophage polarization towards pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes is important in joint disease pathologies. Alteration of M1/M2 balance contributes to the initiation and progression of joint inflammation and can be potentially altered with mesenchymal stem cell (MSC) therapy. In an acute synovial/IFP inflammation rat model a single intra-articular injection of IFP-MSC was performed, having as controls (1) diseased rats not receiving IFP-MSC and (2) non-diseased rats. After 4 days, cell specific transcriptional profiling via single-cell RNA-sequencing was performed on isolated IFP tissue from each group. Eight transcriptomically distinct cell populations were identified within the IFP across all three treatment groups with a noted difference in the proportion of myeloid cells across the groups. Largely myeloid cells consisted of macrophages (>90%); one M1 sub-cluster highly expressing pro-inflammatory markers and two M2 sub-clusters with one of them expressing higher levels of canonical M2 markers. Notably, the diseased samples (11.9%) had the lowest proportion of cells expressing M2 markers relative to healthy (14.8%) and MSC treated (19.4%) samples. These results suggest a phenotypic polarization of IFP macrophages towards the pro-inflammatory M1 phenotype in an acute model of inflammation, which are alleviated by IFP-MSC therapy inducing a switch towards an alternate M2 status. Understanding the IFP cellular heterogeneity and associated transcriptional programs may offer insights into novel therapeutic strategies for disabling joint disease pathologies.

scholarly journals Fibroblastic reticular cells provide a supportive niche for lymph node-resident macrophages

2021 ◽  
Author(s):  
Joshua D'Rozario ◽  
Konstantin Knoblich ◽  
Mechthild Luetge ◽  
Christian Perez Shibayama ◽  
Hung-Wei Cheng ◽  
...  
Keyword(s):  
Lymph Node ◽  
Key Factors ◽  
Rapid Loss ◽  
Major Site ◽  
Genetic Ablation ◽  
Functional Assays ◽  
Single Cell Rna Sequencing ◽  
Reticular Cells ◽  
Macrophage Populations ◽  
Fibroblastic Reticular Cells

The lymph node (LN) is home to resident macrophage populations that are essential for immune function and homeostasis. The T cell paracortical zone is a major site of macrophage efferocytosis of apoptotic cells, but key factors controlling this niche are undefined. Here we show that fibroblastic reticular cells (FRCs) are an essential component of the LN macrophage niche. Macrophages co-localised with FRCs in human LNs, and murine single-cell RNA-sequencing revealed that most reticular cells expressed master macrophage regulator CSF1. Functional assays showed that CSF1R signalling was sufficient to support macrophage development. In the presence of LPS, FRCs underwent a mechanistic switch and maintained support through CSF1R-independent mechanisms. These effects were conserved between mouse and human systems. Rapid loss of macrophages and monocytes from LNs was observed upon genetic ablation of FRCs. These data reveal a critically important role for FRCs in the creation of the parenchymal macrophage niche within LNs.

Localization of migraine susceptibility genes in human brain by single-cell RNA sequencing

Cephalalgia ◽  
2018 ◽  
Vol 38 (13) ◽  
pp. 1976-1983 ◽  
Author(s):  
William Renthal
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Cell Types ◽  
Susceptibility Genes ◽  
Brain Cell ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Brain Cell Types

Background Migraine is a debilitating disorder characterized by severe headaches and associated neurological symptoms. A key challenge to understanding migraine has been the cellular complexity of the human brain and the multiple cell types implicated in its pathophysiology. The present study leverages recent advances in single-cell transcriptomics to localize the specific human brain cell types in which putative migraine susceptibility genes are expressed. Methods The cell-type specific expression of both familial and common migraine-associated genes was determined bioinformatically using data from 2,039 individual human brain cells across two published single-cell RNA sequencing datasets. Enrichment of migraine-associated genes was determined for each brain cell type. Results Analysis of single-brain cell RNA sequencing data from five major subtypes of cells in the human cortex (neurons, oligodendrocytes, astrocytes, microglia, and endothelial cells) indicates that over 40% of known migraine-associated genes are enriched in the expression profiles of a specific brain cell type. Further analysis of neuronal migraine-associated genes demonstrated that approximately 70% were significantly enriched in inhibitory neurons and 30% in excitatory neurons. Conclusions This study takes the next step in understanding the human brain cell types in which putative migraine susceptibility genes are expressed. Both familial and common migraine may arise from dysfunction of discrete cell types within the neurovascular unit, and localization of the affected cell type(s) in an individual patient may provide insight into to their susceptibility to migraine.

Regional specification within the mesoderm of early embryos of Xenopus laevis

Development ◽  
1987 ◽  
Vol 100 (2) ◽  
pp. 279-295 ◽  
Author(s):  
L. Dale ◽  
J.M. Slack
Keyword(s):  
Xenopus Laevis ◽  
Marginal Zone ◽  
Mesoderm Induction ◽  
Intermediate Type ◽  
Cell Stage ◽  
Early Embryos ◽  
Significant Difference ◽  
Cell Embryo ◽  
Single Blastomeres

We have further analysed the roles of mesoderm induction and dorsalization in the formation of a regionally specified mesoderm in early embryos of Xenopus laevis. First, we have examined the regional specificity of mesoderm induction by isolating single blastomeres from the vegetalmost tier of the 32-cell embryo and combining each with a lineage-labelled (FDA) animal blastomere tier. Whereas dorsovegetal (D1) blastomeres induce ‘dorsal-type’ mesoderm (notochord and muscle), laterovegetal and ventrovegetal blastomeres (D2–4) induce either ‘intermediate-type’ (muscle, mesothelium, mesenchyme and blood) or ‘ventral-type’ (mesothelium, mesenchyme and blood) mesoderm. No significant difference in inductive specificity between blastomeres D2, 3 and 4 could be detected. We also show that laterovegetal and ventrovegetal blastomeres from early cleavage stages can have a dorsal inductive potency partially activated by operative procedures, resulting in the induction of intermediate-type mesoderm. Second, we have determined the state of specification of ventral blastomeres by isolating and culturing them in vitro between the 4-cell stage and the early gastrula stage. The majority of isolates from the ventral half of the embryo gave extreme ventral types of differentiation at all stages tested. Although a minority of cases formed intermediate-type and dorsal-type mesoderms we believe these to result from either errors in our assessment of the prospective DV axis or from an enhancement, provoked by microsurgery, of some dorsal inductive specificity. The results of induction and isolation experiments suggest that only two states of specification exist in the mesoderm of the pregastrula embryo, a dorsal type and a ventral type. Finally we have made a comprehensive series of combinations between different regions of the marginal zone using FDA to distinguish the components. We show that, in combination with dorsal-type mesoderm, ventral-type mesoderm becomes dorsalized to the level of intermediate-type mesoderm. Dorsal-type mesoderm is not ventralized in these combinations. Dorsalizing activity is confined to a restricted sector of the dorsal marginal zone, it is wider than the prospective notochord and seems to be graded from a high point at the dorsal midline. The results of these experiments strengthen the case for the three-signal model proposed previously, i.e. dorsal and ventral mesoderm inductions followed by dorsalization, as the simplest explanation capable of accounting for regional specification within the mesoderm of early Xenopus embryos.

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