scholarly journals A single cell transcriptional atlas of early synovial joint development

2019 ◽  
Author(s):  
Qin Bian ◽  
Yu-Hao Cheng ◽  
Jordan P Wilson ◽  
Dong Won Kim ◽  
Hong Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Knee Joint ◽  
Single Cell ◽  
Lineage Tracing ◽  
Transcriptional Networks ◽  
Rna Seq ◽  
Synovial Joint ◽  
Isolated Populations ◽  
Joint Development

SUMMARYSynovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 6,202 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and functional analysis of prospectively isolated populations, we have inferred the underlying transcriptional networks of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.

scholarly journals A single cell transcriptional atlas of early synovial joint development

Development ◽  
2020 ◽  
Vol 147 (14) ◽  
pp. dev185777 ◽  
Author(s):  
Qin Bian ◽  
Yu-Hao Cheng ◽  
Jordan P. Wilson ◽  
Emily Y. Su ◽  
Dong Won Kim ◽  
...  
Keyword(s):  
Knee Joint ◽  
Single Cell ◽  
Lineage Tracing ◽  
Rna Seq ◽  
Synovial Joint ◽  
Isolated Populations ◽  
Joint Development

ABSTRACTSynovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage-tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 7329 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization and in vitro characterization of prospectively isolated populations, we have identified the transcriptional profiles of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.

scholarly journals Signaling and transcriptional networks governing late synovial joint development

2021 ◽  
Author(s):  
Qin Bian ◽  
Yu-Hao Cheng ◽  
Emily Y. Su ◽  
Yuqi Tan ◽  
Dong Won Kim ◽  
...  
Keyword(s):  
Articular Cartilage ◽  
Single Cell ◽  
Articular Chondrocytes ◽  
Cruciate Ligament ◽  
Fibrous Tissue ◽  
Cell Types ◽  
Transcriptional Networks ◽  
Synovial Joint ◽  
Joint Development ◽  
Cell Type Specific

Background: During synovial joint development, cavitation marks the end of the emergence of new cell types and the onset of the consolidation of cell type specific programs. However, the transcriptional programs that regulate this crucial stage prior to joint maturation are incompletely characterized. Gdf5-lineage cells give rise to the majority of joint constituents such as articular cartilage, meniscus, ligament, and tendon. Therefore, to explore pre-maturation of the synovial joint, we performed single cell RNA-Seq analysis of 1,306 Gdf5-lineage cells from the murine knee joint at E17.5. Results: Using computational analytics and in situ hybridization, we identified nine sub-states contributing to articular cartilage, meniscus, cruciate ligament, synovium, lining, and surrounding fibrous tissue. We identified a common progenitor population that is predicted to give rise to ligamentaocytes, articular chondrocytes, and lining cells. We further found that while a large number of signaling pathways orchestrate the differentiation of this progenitor to either ligamentocytes or to lining cells, only continued FGF signaling guides these cells to a default chondrocyte fate. Conclusions: Our single cell transcriptional atlas is a resource that can be used to better understand and further study synovial joint development and the reactivation of embryonic programs in diseases such as osteoarthritis.

scholarly journals Single-cell RNA-seq reveals spatially restricted multicellular fibrotic niches during lung fibrosis

2019 ◽  
Author(s):  
Nikita Joshi ◽  
Satoshi Watanabe ◽  
Rohan Verma ◽  
Renea P. Jablonski ◽  
Ching-I Chen ◽  
...  
Keyword(s):  
Single Cell ◽  
Alveolar Macrophages ◽  
Lineage Tracing ◽  
Fibroblast Proliferation ◽  
Rna Seq ◽  
Autocrine Signaling ◽  
Spatial Methods ◽  
Pharmacological Blockade ◽  
Established Population ◽  
Organ Fibrosis

AbstractOntologically distinct populations of macrophages differentially contribute to organ fibrosis through unknown mechanisms. We applied lineage tracing, spatial methods and single-cell RNA-seq to a spatially-restricted model of asbestos-induced pulmonary fibrosis. We demonstrate that while tissue-resident interstitial macrophages, tissue-resident alveolar macrophages, and monocyte-derived alveolar macrophages are present in the fibrotic niche, only monocyte-derived alveolar macrophages are causally related to fibrosis. Monocyte-derived alveolar macrophages were specifically localized to fibrotic regions in the proximity of fibroblasts where they expressed molecules known to drive fibroblast proliferation, including PDGFA. Moreover, we identified autocrine M-CSF/M-CSFR signaling in monocyte-derived alveolar macrophages as a novel mechanism promoting their self-maintenance and persistence in the fibrotic niche. Pharmacological blockade of M-CSF signaling led to disappearance of the established population of monocyte-derived alveolar macrophages. Thus, our data indicate that monocyte-derived alveolar macrophages are specifically recruited to the fibrotic niche where they are maintained by autocrine signaling and drive fibrosis by stimulating fibroblast proliferation.

scholarly journals Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted heart

2021 ◽  
Author(s):  
Julia Hesse ◽  
Christoph Owenier ◽  
Tobias Lautwein ◽  
Ria Zalfen ◽  
Jonas F. Weber ◽  
...  
Keyword(s):  
Single Cell ◽  
Stromal Cells ◽  
Lineage Tracing ◽  
Sarcomeric Proteins ◽  
Proliferating Cells ◽  
Paracrine Factors ◽  
Epicardial Cells ◽  
Cardiac Specification ◽  
Rna In Situ Hybridization

AbstractIn the adult heart, the epicardium becomes activated after injury, contributing to cardiac healing by secretion of paracrine factors. Here we analyzed by single-cell RNA sequencing combined with RNA in situ hybridization and lineage tracing of WT1+ cells the cellular composition, location, and hierarchy of epicardial stromal cells (EpiSC) in comparison to activated myocardial fibroblasts/stromal cells in infarcted mouse hearts. We identified 11 transcriptionally distinct EpiSC populations, that can be classified in three groups each containing a cluster of proliferating cells. Two groups expressed cardiac specification makers and sarcomeric proteins suggestive of cardiomyogenic potential. Transcripts of HIF-1α and HIF-responsive genes were enriched in EpiSC consistent with an epicardial hypoxic niche. Expression of paracrine factors was not limited to WT1+ cells but was a general feature of activated cardiac stromal cells. Our findings provide the cellular framework by which myocardial ischemia may trigger in EpiSC the formation of cardioprotective/regenerative responses.

scholarly journals Early lineage specification defines alveolar epithelial ontogeny in the murine lung

2019 ◽  
Vol 116 (10) ◽  
pp. 4362-4371 ◽  
Author(s):  
David B. Frank ◽  
Ian J. Penkala ◽  
Jarod A. Zepp ◽  
Aravind Sivakumar ◽  
Ricardo Linares-Saldana ◽  
...  
Keyword(s):  
Epithelial Cell ◽  
Single Cell ◽  
Branching Morphogenesis ◽  
Lineage Tracing ◽  
Transcriptional Networks ◽  
Alveolar Type ◽  
Sequencing Analysis ◽  
Alveolar Cells ◽  
Lineage Specification ◽  
Alveolar Epithelial

During the stepwise specification and differentiation of tissue-specific multipotent progenitors, lineage-specific transcriptional networks are activated or repressed to orchestrate cell specification. The gas-exchange niche in the lung contains two major epithelial cell types, alveolar type 1 (AT1) and AT2 cells, and the timing of lineage specification of these cells is critical for the correct formation of this niche and postnatal survival. Integrating cell-specific lineage tracing studies, spatially specific mRNA transcript and protein expression, and single-cell RNA-sequencing analysis, we demonstrate that specification of alveolar epithelial cell fate begins concomitantly with the proximal–distal specification of epithelial progenitors and branching morphogenesis earlier than previously appreciated. By using a newly developed dual-lineage tracing system, we show that bipotent alveolar cells that give rise to AT1 and AT2 cells are a minor contributor to the alveolar epithelial population. Furthermore, single-cell assessment of the transcriptome identifies specified AT1 and AT2 progenitors rather than bipotent cells during sacculation. These data reveal a paradigm of organ formation whereby lineage specification occurs during the nascent stages of development coincident with broad tissue-patterning processes, including axial patterning of the endoderm and branching morphogenesis.

scholarly journals Developmental landscape of  human forebrain at a single-cell level unveils early waves of oligodendrogenesis

2021 ◽  
Author(s):  
David van Bruggen ◽  
Fabio Baldivia Pohl ◽  
Christoffer Mattsson Langseth ◽  
Petra Kukanja ◽  
Hower Lee ◽  
...  
Keyword(s):  
Single Cell ◽  
Network Inference ◽  
Regulatory Mechanisms ◽  
Oligodendrocyte Precursor Cells ◽  
Second Trimester ◽  
Rna Seq ◽  
Cell Level ◽  
Human Central Nervous System ◽  
Oligodendrocyte Precursor

Oligodendrogenesis in the human central nervous system has been mainly observed at the second trimester of gestation, a much later developmental stage compared to mouse. Here we characterize the transcriptomic neural diversity in the human forebrain at post conceptual weeks (PCW) 8 to 10, using single-cell RNA-Seq. We find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level with single-cell ATAC-Seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of fifty key genes using In Situ Sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mouse and human and describe regulatory mechanisms required for human OPC specification.

scholarly journals Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq

2017 ◽  
Author(s):  
Garth R. Ilsley ◽  
Ritsuko Suyama ◽  
Takeshi Noda ◽  
Nori Satoh ◽  
Nicholas M. Luscombe
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Expression Patterns ◽  
Cell Types ◽  
Specific Gene ◽  
Rna Seq ◽  
Cell Stage ◽  
Specific Expression ◽  
Temporal Gene Expression

AbstractSingle-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. Recently, single-cell RNA-seq has been applied to developing embryos, which offers great potential for finding and characterising genes controlling the course of development along with their expression patterns. In this study, we applied single-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computational search for cell-specific gene expression patterns. We recovered many known expression patterns from our single-cell RNA-seq data and despite extensive previous screens, we succeeded in finding new cell-specific patterns, which we validated by in situ and single-cell qPCR.

scholarly journals Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution

2021 ◽  
Vol 9 ◽  
Author(s):  
Ernesto Marín-Sedeño ◽  
Xabier Martínez de Morentin ◽  
Jose M. Pérez-Pomares ◽  
David Gómez-Cabrero ◽  
Adrián Ruiz-Villalba
Keyword(s):  
Single Cell ◽  
Single Gene ◽  
Cell Lineage ◽  
Cell Types ◽  
Lineage Tracing ◽  
Cardiac Cell ◽  
Rna Seq ◽  
Cardiovascular Research ◽  
Cell Diversity ◽  
Unbiased Manner

During the last decade, extensive efforts have been made to comprehend cardiac cell genetic and functional diversity. Such knowledge allows for the definition of the cardiac cellular interactome as a reasonable strategy to increase our understanding of the normal and pathologic heart. Previous experimental approaches including cell lineage tracing, flow cytometry, and bulk RNA-Seq have often tackled the analysis of cardiac cell diversity as based on the assumption that cell types can be identified by the expression of a single gene. More recently, however, the emergence of single-cell RNA-Seq technology has led us to explore the diversity of individual cells, enabling the cardiovascular research community to redefine cardiac cell subpopulations and identify relevant ones, and even novel cell types, through their cell-specific transcriptomic signatures in an unbiased manner. These findings are changing our understanding of cell composition and in consequence the identification of potential therapeutic targets for different cardiac diseases. In this review, we provide an overview of the continuously changing cardiac cellular landscape, traveling from the pre-single-cell RNA-Seq times to the single cell-RNA-Seq revolution, and discuss the utilities and limitations of this technology.

scholarly journals Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

2020 ◽  
Author(s):  
Jeffrey J. Quinn ◽  
Matthew G. Jones ◽  
Ross A. Okimoto ◽  
Shigeki Nanjo ◽  
Michelle M. Chan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Single Cell ◽  
Cancer Progression ◽  
Cell Lineage ◽  
Lineage Tracing ◽  
Rna Seq ◽  
Disease Etiology ◽  
Cell Lineages ◽  
Transient Events

AbstractCancer progression is characterized by rare, transient events which are nonetheless highly consequential to disease etiology and mortality. Detailed cell phylogenies can recount the history and chronology of these critical events – including metastatic seeding. Here, we applied our Cas9-based lineage tracer to study the subclonal dynamics of metastasis in a lung cancer xenograft mouse model, revealing the underlying rates, routes, and drivers of metastasis. We report deeply resolved phylogenies for tens of thousands of metastatically disseminated cancer cells. We observe surprisingly diverse metastatic phenotypes, ranging from metastasis-incompetent to aggressive populations. These phenotypic distinctions result from pre-existing, heritable, and characteristic differences in gene expression, and we demonstrate that these differentially expressed genes can drive invasiveness. Furthermore, metastases transit via diverse, multidirectional tissue routes and seeding topologies. Our work demonstrates the power of tracing cancer progression at unprecedented resolution and scale.One Sentence SummarySingle-cell lineage tracing and RNA-seq capture diverse metastatic behaviors and drivers in lung cancer xenografts in mice.

scholarly journals Agonist-induced Functional Analysis and Cell Sorting, a novel tool to select and analyze neurons: Fragile X as a proof of concept

2020 ◽  
Author(s):  
Sara Castagnola ◽  
Julie Cazareth ◽  
Kevin Lebrigand ◽  
Marielle Jarjat ◽  
Virginie Magnone ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Single Cell ◽  
Cell Sorting ◽  
Fragile X ◽  
Developmental Time ◽  
Simultaneous Recording ◽  
Individual Response ◽  
Proof Of Concept ◽  
Rna Seq ◽  
Selection Parameters

ABSTRACTTo get a better insight into the dynamic interaction between cells and their environment, we developed the agonist-induced Functional Analysis and Cell Sorting (aiFACS) technique, which allows the simultaneous recording and sorting of cells in real-time according to their immediate and individual response to a stimulus. By modulating the aiFACS selection parameters, testing different developmental times, using various stimuli and multiplying the analysis of readouts, it is possible to analyze cell populations of any tissue, including tumors. The association of aiFACS to single-cell transcriptomic allows to build a tissue cartography based on specific functional response/s of cells.As proof of concept, we used aiFACS on the dissociated mouse brain, a highly heterogenous tissue, enriching it in interneurons upon stimulation with an agonist of the glutamate receptors and upon sorting based on calcium levels. Further single-cell RNA-seq of these aiFACS-selected interneurons resulted in a nine-cluster classification. Furthermore, we used aiFACS on interneurons derived from the brain of the Fmr1-KO mouse, a rodent model of Fragile X syndrome. We show here that these interneurons manifest a generalized defective pharmacological response compared to wild type, affecting all the analyzed cell clusters at one specific post-natal developmental time.

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