scholarly journals Single Cell Transcriptome-Based Dissection of Lineage Fate Decisions in Myelopoiesis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1395-1395
Author(s):  
Andre Olsson ◽  
H. Leighton Grimes ◽  
Virendra K Chaudhri ◽  
Philip Dexheimer ◽  
Bruce J Aronow ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Molecular Mechanisms ◽  
Conflicts Of Interest ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Cell Data ◽  
Insight Into

Abstract In spite of tremendous advances in the analysis of hematopoietic progenitors and transcription factors that give rise to different lineages, molecular insight into the mechanisms that underlie cell fate choice at the level of individual cells is lacking. We utilized single-cell RNA sequencing of murine granulocyte-monocyte progenitors (GMPs) to analyze the molecular basis of cell fate choice. Over 200 libraries were generated with average read depths of 4 million per library and an expressed gene call of over 3,800 genes with FPKM >3. Our data reveal a varied but coherent spectrum of gene expression patterns in individual murine GMPs. The majority of cells could be clustered into ones expressing either granulocytic or monocytic genes, suggesting that they were primed for lineage determination. A minority of GMPs expressed a mixed-lineage pattern of genes. The single-cell data suggested an antagonistic transcription factor circuit involving Gfi1 and IRF8 that was validated with both loss- and gain-of-function experiments in GMPs. Our data highlight the utility of single cell RNA-Seq analysis to reveal molecular mechanisms controlling lineage fate decisions in hematopoiesis. Disclosures No relevant conflicts of interest to declare.

scholarly journals The Drosophila Embryo at Single Cell Transcriptome Resolution

2017 ◽  
Author(s):  
Nikos Karaiskos ◽  
Philipp Wahle ◽  
Jonathan Alles ◽  
Anastasiya Boltengagen ◽  
Salah Ayoub ◽  
...  
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Drosophila Embryo ◽  
Evolutionary Changes ◽  
Cell Transcriptome ◽  
Mechanisms Of Development ◽  
In Situ Hybridizations ◽  
Single Cell Transcriptome

ABSTRACTDrosophila is a premier model system for understanding the molecular mechanisms of development. By the onset of morphogenesis, ~6000 cells express distinct gene combinations according to embryonic position. Despite extensive mRNA in situ screens, combinatorial gene expression within individual cells is largely unknown. Therefore, it is difficult to comprehensively identify the coding and non-coding transcripts that drive patterning and to decipher the molecular basis of cellular identity. Here, we single-cell sequence precisely staged embryos, measuring >3100 genes per cell. We produce a ‘transcriptomic blueprint’ of development – a virtual embryo where 3D locations of sequenced cells are confidently identified. Our “Drosophila-Virtual-Expression-eXplorer” performs virtual in situ hybridizations and computes expression gradients. Using DVEX, we predict spatial expression and discover patterned lncRNAs. DEVX is sensitive enough to detect subtle evolutionary changes in expression patterns between Drosophila species. We believe DVEX is a prototype for powerful single cell studies in complex tissues.

scholarly journals Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

2021 ◽  
Author(s):  
Davide Simone ◽  
Frank Penkava ◽  
Anna Ridley ◽  
Stephen Nicholas Sansom ◽  
Hussein Mohamed Al-Mossawi ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Treg Subset ◽  
Inflammatory Site ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Regulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

scholarly journals Single-cell transcriptome analysis of the zebrafish embryonic trunk

2021 ◽  
Author(s):  
Sanjeeva S Metikala ◽  
Satish Casie Chetty ◽  
Saulius Sumanas
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Cell Lineage ◽  
Cell Types ◽  
Rna Seq ◽  
Cell Lineages ◽  
Distinct Cell ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Different Cell Types

During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.

scholarly journals Single-cell transcriptome analysis of the zebrafish embryonic trunk

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254024
Author(s):  
Sanjeeva Metikala ◽  
Satish Casie Chetty ◽  
Saulius Sumanas
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Cell Lineage ◽  
Cell Types ◽  
Rna Seq ◽  
Cell Lineages ◽  
Distinct Cell ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Different Cell Types

During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.

scholarly journals Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Davide Simone ◽  
Frank Penkava ◽  
Anna Ridley ◽  
Stephen Sansom ◽  
M. Hussein Al-Mossawi ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Treg Subset ◽  
Inflammatory Site ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractRegulatory T cells (Tregs) play an important role in controlling inflammation and limiting autoimmunity, but their phenotypes at inflammatory sites in human disease are poorly understood. We here analyze the single-cell transcriptome of >16,000 Tregs obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis and three patients with psoriatic arthritis, closely related forms of inflammatory spondyloarthritis. We identify multiple Treg clusters with distinct transcriptomic profiles, including, among others, a regulatory CD8+ subset expressing cytotoxic markers/genes, and a Th17-like RORC+ Treg subset characterized by IL-10 and LAG-3 expression. Synovial Tregs show upregulation of interferon signature and TNF receptor superfamily genes, and marked clonal expansion, consistent with tissue adaptation and antigen contact respectively. Individual synovial Treg clones map to different clusters indicating cell fate divergence. Finally, we demonstrate that LAG-3 directly inhibits IL-12/23 and TNF secretion by patient-derived monocytes, a mechanism with translational potential in SpA. Our detailed characterization of Tregs at an important inflammatory site illustrates the marked specialization of Treg subpopulations.

Single Cell RNA seq for Analysis of Cell Fate Decisions

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. SCI-20-SCI-20
Author(s):  
H. Leighton Grimes ◽  
Singh Harinder ◽  
Andre Olsson ◽  
Nathan Salomonis ◽  
Bruce J. Aronow ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Clustering Analysis ◽  
Conflicts Of Interest ◽  
Regulatory Gene ◽  
Rna Seq ◽  
Regulatory State ◽  
Cell Fate Decisions ◽  
General Utility ◽  
Developmental Hierarchy

Abstract Single-cell RNA-Seq has the potential to become a dominant approach in probing diverse and complex developmental compartments. Its unbiased and comprehensive nature could enable developmental ordering of cellular and regulatory gene hierarchies without prior knowledge. To test general utility we performed single-cell RNA-seq of murine hematopoietic progenitors focusing on the myeloid developmental hierarchy. Using novel unsupervised clustering analysis, ICDS, we correctly ordered known hierarchical states as well as revealed rare intermediates. Regulatory state analysis suggested that the transcription factors Gfi1 and Irf8 function antagonistically to control homeostatic neutrophil and macrophage production, respectively. This prediction was validated by complementary genetic and genomic experiments in granulocyte-macrophage progenitors. Using knock-in reporters for Gfi1 and Irf8 and clonogenic analyses coupled with single-cell RNA-seq we distinguished regulatory states of bi-potential progenitors from their lineage specifying or committed progeny. Thus single-cell RNA-Seq is a powerful developmental tool to characterize hierarchical and rare cellular states along with the regulators that control their dynamics. Disclosures No relevant conflicts of interest to declare.

scholarly journals A single cell transcriptome atlas of the developing zebrafish hindbrain

2019 ◽  
Author(s):  
Monica Tambalo ◽  
Richard Mitter ◽  
David G. Wilkinson
Keyword(s):  
Single Cell ◽  
Neuronal Differentiation ◽  
Cell Types ◽  
Spatial Patterning ◽  
Rna Seq ◽  
Valuable Resource ◽  
Dorsoventral Axis ◽  
Single Cell Rna Sequencing ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractSegmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at bounderies and segment centres, in part mediated by Fgf20 signaling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

scholarly journals Lifelong single-cell profiling of cranial neural crest diversification

2021 ◽  
Author(s):  
Peter Fabian ◽  
Kuo-Chang Tseng ◽  
Mathi Thiruppathy ◽  
Claire Arata ◽  
Hung-Jhen Chen ◽  
...  
Keyword(s):  
Neural Crest ◽  
Single Cell ◽  
Cell Fate ◽  
Intrinsic Property ◽  
Chromatin Accessibility ◽  
Specific Cell ◽  
List Type ◽  
Cranial Neural Crest ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractThe cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being an intrinsic property of cranial neural crest, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse neural crest lineage potential.HighlightsSingle-cell transcriptome and chromatin atlas of cranial neural crestProgressive emergence of region-specific cell fate competencyChromatin accessibility mapping identifies candidate lineage regulatorsGata3 function linked to gill-specific respiratory programGraphical Abstract

scholarly journals Single-Cell Transcriptome Analysis of Human Adipose-Derived Stromal Cells Identifies a Contractile Cell Subpopulation

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Elize Wolmarans ◽  
Juanita Mellet ◽  
Chrisna Durandt ◽  
Fourie Joubert ◽  
Michael S. Pepper
Keyword(s):  
Single Cell ◽  
Transcriptome Analysis ◽  
Stromal Cells ◽  
Exploratory Study ◽  
Expression Patterns ◽  
Cell Subpopulation ◽  
Adipose Derived Stromal Cells ◽  
Cell Transcriptome ◽  
Population Doublings ◽  
Single Cell Transcriptome

The potential for human adipose-derived stromal cells (hASCs) to be used as a therapeutic product is being assessed in multiple clinical trials. However, much is still to be learned about these cells before they can be used with confidence in the clinical setting. An inherent characteristic of hASCs that is not well understood is their heterogeneity. The aim of this exploratory study was to characterize the heterogeneity of freshly isolated hASCs after two population doublings (P2) using single-cell transcriptome analysis. A minimum of two subpopulations were identified at P2. A major subpopulation was identified as contractile cells which, based on gene expression patterns, are likely to be pericytes and/or vascular smooth muscle cells (vSMCs).

scholarly journals Single-Cell Transcriptomics-Based Study of Transcriptional Regulatory Features in the Mouse Brain Vasculature

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Wei-Wei Lin ◽  
Lin-Tao Xu ◽  
Yi-Sheng Chen ◽  
Ken Go ◽  
Chenyu Sun ◽  
...  
Keyword(s):  
Single Cell ◽  
Mouse Brain ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Rna Seq ◽  
Brain Vasculature ◽  
Transcriptional Regulatory ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Background. The critical role of vascular health on brain function has received much attention in recent years. At the single-cell level, studies on the developmental processes of cerebral vascular growth are still relatively few. Techniques for constructing gene regulatory networks (GRNs) based on single-cell transcriptome expression data have made significant progress in recent years. Herein, we constructed a single-cell transcriptional regulatory network of mouse cerebrovascular cells. Methods. The single-cell RNA-seq dataset of mouse brain vessels was downloaded from GEO (GSE98816). This cell clustering was annotated separately using singleR and CellMarker. We then used a modified version of the SCENIC method to construct GRNs. Next, we used a mouse version of SEEK to assess whether genes in the regulon were coexpressed. Finally, regulatory module analysis was performed to complete the cell type relationship quantification. Results. Single-cell RNA-seq data were used to analyze the heterogeneity of mouse cerebrovascular cells, whereby four cell types including endothelial cells, fibroblasts, microglia, and oligodendrocytes were defined. These subpopulations of cells and marker genes together characterize the molecular profile of mouse cerebrovascular cells. Through these signatures, key transcriptional regulators that maintain cell identity were identified. Our findings identified genes like Lmo2, which play an important role in endothelial cells. The same cell type, for instance, fibroblasts, was found to have different regulatory networks, which may influence the functional characteristics of local tissues. Conclusions. In this study, a transcriptional regulatory network based on single-cell analysis was constructed. Additionally, the study identified and profiled mouse cerebrovascular cells using single-cell transcriptome data as well as defined TFs that affect the regulatory network of the mouse brain vasculature.

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