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 A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages

2019 ◽  
Vol 55 (1) ◽  
pp. 1900646 ◽  
Author(s):  
Nikita Joshi ◽  
Satoshi Watanabe ◽  
Rohan Verma ◽  
Renea P. Jablonski ◽  
Ching-I Chen ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Alveolar Macrophages ◽  
Lineage Tracing ◽  
Single Cell Rna Sequencing ◽  
Pharmacological Blockade ◽  
Macrophage Colony ◽  
Druggable Targets

Ontologically distinct populations of macrophages differentially contribute to organ fibrosis through unknown mechanisms.We applied lineage tracing, single-cell RNA sequencing and single-molecule fluorescence in situ hybridisation to a spatially restricted model of asbestos-induced pulmonary fibrosis.We demonstrate that tissue-resident alveolar macrophages, tissue-resident peribronchial and perivascular interstitial macrophages, and monocyte-derived alveolar macrophages are present in the fibrotic niche. Deletion of monocyte-derived alveolar macrophages but not tissue-resident alveolar macrophages ameliorated asbestos-induced lung fibrosis. Monocyte-derived alveolar macrophages were specifically localised to fibrotic regions in the proximity of fibroblasts where they expressed molecules known to drive fibroblast proliferation, including platelet-derived growth factor subunit A. Using single-cell RNA sequencing and spatial transcriptomics in both humans and mice, we identified macrophage colony-stimulating factor receptor (M-CSFR) signalling as one of the novel druggable targets controlling self-maintenance and persistence of these pathogenic monocyte-derived alveolar macrophages. Pharmacological blockade of M-CSFR signalling led to the disappearance of monocyte-derived alveolar macrophages and ameliorated fibrosis.Our findings suggest that inhibition of M-CSFR signalling during fibrosis disrupts an essential fibrotic niche that includes monocyte-derived alveolar macrophages and fibroblasts during asbestos-induced fibrosis.

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 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 Single cell profiling of Hofbauer cells and fetal brain microglia reveals shared programs and functions

2021 ◽  
Author(s):  
Alexis M Ceasrine ◽  
Rebecca Batorsky ◽  
Lydia L. Shook ◽  
Sezen Kislal ◽  
Evan A. Bordt ◽  
...  
Keyword(s):  
Single Cell ◽  
Fetal Brain ◽  
Lineage Tracing ◽  
Rna Seq ◽  
Neurodevelopmental Outcomes ◽  
Female Fetus ◽  
Hofbauer Cells ◽  
Single Cell Profiling ◽  
Placental Macrophages ◽  
Noninvasive Biomarkers

SummaryMaternal immune activation is associated with adverse offspring neurodevelopmental outcomes, many of which are mediated by in utero microglial programming. Microglia remain inaccessible at birth and throughout development, thus identification of noninvasive biomarkers that can reflect fetal brain microglial programming may permit screening and intervention during critical developmental windows. Here we used lineage tracing to demonstrate the shared ontogeny between fetal brain macrophages (microglia) and fetal placental macrophages (Hofbauer cells). Single-cell RNA sequencing of murine fetal brain and placental macrophages demonstrated shared transcriptional programs. Comparison with human datasets demonstrated that placental resident macrophage signatures are highly conserved between mice and humans. Single-cell RNA-seq identified sex differences in fetal microglial and Hofbauer cell programs, and robust differences between placenta-associated maternal macrophage/monocyte (PAMM) populations in the context of a male versus a female fetus. We propose that Hofbauer cells, which are easily accessible at birth, provide novel insights into fetal brain microglial programs, potentially facilitating the early identification of offspring most vulnerable to neurodevelopmental disorders.

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 Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos

2018 ◽  
Author(s):  
Fernando Biase ◽  
Qiuyang Wu ◽  
Riccardo Calandrelli ◽  
Marcelo Rivas-Astroza ◽  
Shuigeng Zhou ◽  
...  
Keyword(s):  
Cell Division ◽  
Single Cell ◽  
Cell Fate ◽  
Fluorescent Protein ◽  
Lineage Tracing ◽  
Preimplantation Embryos ◽  
Marker Genes ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Cell Stage

SUMMARYSingle-cell RNA-seq experiments cannot record cell division history and therefore cannot directly connect intercellular differences at a later developmental stage to their progenitor cells. We developed Rainbow-seq to combine cell division lineage tracing with single-cell RNA-seq. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA-seq experiment to simultaneously read single-cell transcriptomes and decode the lineage marker genes. We traced the lineages deriving from each blastomere in two-cell mouse embryos and observed inequivalent contributions to the embryonic and abembryonic poles in 72% of the blastocysts evaluated. Rainbow-seq on four- and eight-cell embryos with lineage tracing triggered at two-cell stage exhibited remarkable transcriptome-wide differences between the two cell lineages at both stages, including genes involved in negative regulation of transcription and signaling. These data provide critical insights on cell fate choices in cleavage embryos. Rainbow-seq bridged a critical gap between cellular division history and single-cell RNA-seq assays.

scholarly journals Single-Cell and Bulk Transcriptome Data Integration Reveals Dysfunctional Cell Types and Aberrantly Expressed Genes in Hypertrophic Scar

2022 ◽  
Vol 12 ◽  
Author(s):  
Shunuo Zhang ◽  
Yixin Zhang ◽  
Peiru Min
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Regulatory Network ◽  
Hypertrophic Scar ◽  
Cell Types ◽  
Integrative Analysis ◽  
Rna Seq ◽  
Autocrine Signaling ◽  
Communication Analysis ◽  
Cell Cell

Hypertrophic scar (HS) is a common skin disorder characterized by excessive extracellular matrix (ECM) deposition. However, it is still unclear how the cellular composition, cell-cell communications, and crucial transcriptionally regulatory network were changed in HS. In the present study, we found that FB-1, which was identified a major type of fibroblast and had the characteristics of myofibroblast, was significantly expanded in HS by integrative analysis of the single-cell and bulk RNA sequencing (RNA-seq) data. Moreover, the proportion of KC-2, which might be a differentiated type of keratinocyte (KC), was reduced in HS. To decipher the intercellular signaling, we conducted the cell-cell communication analysis between the cell types, and found the autocrine signaling of HB-1 through COL1A1/2-CD44 and CD99-CD99 and the intercellular contacts between FB-1/FB-5 and KC-2 through COL1A1/COL1A2/COL6A1/COL6A2-SDC4. Almost all the ligands and receptors involved in the autocrine signaling of HB-1 were upregulated in HS by both scRNA-seq and bulk RNA-seq data. In contrast, the receptor of KC-2, SDC4, which could bind to multiple ligands, was downregulated in HS, suggesting that the reduced proportion of KC-2 and apoptotic phenotype of KC-2 might be associated with the downregulation of SDC4. Furthermore, we also investigated the transcriptionally regulatory network involved in HS formation. The integrative analysis of the scRNA-seq and bulk RNA-seq data identified CREB3L1 and TWIST2 as the critical TFs involved in the myofibroblast of HS. In summary, the integrative analysis of the single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data greatly improved our understanding of the biological characteristics during the HS formation.

Abstract 15227: Egln1 Deficiency Induce Alveolar Macrophages Accumulation and Polarize Lung Interstitial Macrophages to a Pro-pah State Mediating Obliterative Pulmonary Vascular Remodeling and Severe PAH

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Jingbo Dai ◽  
Zhiyu Dai ◽  
Mengqi Zhu ◽  
Daoyin Dong ◽  
Youyang Zhao
Keyword(s):  
Mouse Model ◽  
Single Cell ◽  
Alveolar Macrophages ◽  
Vascular Remodeling ◽  
Vascular Occlusion ◽  
Right Heart Failure ◽  
Rna Seq ◽  
Pulmonary Vessel ◽  
Pulmonary Vascular Remodeling

Introduction: Previously we identified a mouse model (Tie2Cre-mediated disruption of Egln1 ) of Pulmonary arterial hypertension (PAH) with progressive obliterative vascular remodeling including vascular occlusion and plexiform-like lesions and right heart failure. Tie2Cre-meidated disruption of Egln1 in bone marrow contributes to the severity of PAH indicating the importance of the immune cells in the pathogenesis of PH. Hypothesis: Macrophage accumulation and polarization due to Egln1 deficiency contributes to obliterative pulmonary vascular remodeling and severe PAH in Egln1 Tie2Cre mice. Methods: Egln1 Tie2Cre mice with macrophage Fas-Induced apoptosis (MaFIA) transgene were generated (Egln1 Tie2Cre /MaFIA) and received AP20187 treatment to deplete the macrophages during the development of PAH afterwards the RVSP and RV/(LV+S) ratio were measured as the indicator of diseases severity. Flowcytometry and immunostaining were used to quantify different types of macrophages. Bulk RNA-seq and single cell RNA-seq were used to identify PAH-related pathway changes and population changes of lung macrophages in Egln1 Tie2Cre mice. BrdU staining was used to measure the smooth muscle cell (SMC) proliferation co-culturing with macrophages isolated from Egln1 Tie2Cre mice. Results: We observed that CD206+ Alternative Activated Macrophages (AAMs) are accumulated in the pulmonary vessel adventitia of IPAH patients as well as Egln1 Tie2Cre mice. These macrophages are Egln1 deficient and express elevated level of pro-PAH factors and thus promote SMC proliferation in vitro . Moreover, genetic depletion of total macrophages using the Egln1 Tie2Cre /MaFIA mouse model markedly inhibited obliterative pulmonary vascular remodeling and PAH. Single cell RNA-seq revealed that lung resident alveolar macrophages (Siglec-F+/Cd11c+) accumulated due to hyper-proliferation while recruited lung interstitial (Cx3cr1+/Aif1+) macrophages polarize to a pro-PAH state in Egln1 Tie2Cre mice. Conclusions: Egln1 deficiency in the HCs induced proliferation/accumulation of alveolar macrophages and polarized the recruited interstitial macrophages to AAM state which contributes to the vascular remodeling by secreting pro-PAH factors.

scholarly journals Single-cell RNA-seq profiling of mouse endothelial cells in response to pulmonary arterial hypertension

2021 ◽  
Author(s):  
Julie Rodor ◽  
Shiau-Haln Chen ◽  
Jessica P Scanlon ◽  
João P Monteiro ◽  
Axelle Caudrillier ◽  
...  
Keyword(s):  
Endothelial Cell ◽  
Pulmonary Arterial Hypertension ◽  
Arterial Hypertension ◽  
Single Cell ◽  
Lineage Tracing ◽  
Rna Seq ◽  
Cell Dysfunction ◽  
Pulmonary Arterial ◽  
Transcriptomic Changes

Abstract Aims Endothelial cell dysfunction drives the initiation and pathogenesis of pulmonary arterial hypertension (PAH). We aimed to characterise endothelial cell (EC) dynamics in PAH at single-cell resolution. Methods and Results We carried out single-cell RNA sequencing (scRNA-seq) of lung ECs isolated from an EC lineage-tracing mouse model in Control and SU5416/Hypoxia-induced PAH conditions. EC populations corresponding to distinct lung vessel types, including two discrete capillary populations, were identified in both Control and PAH mice. Differential gene expression analysis revealed global PAH-induced EC changes that were confirmed by bulk RNA-seq. This included upregulation of the major histocompatibility complex class II pathway, supporting a role for ECs in the inflammatory response in PAH. We also identified a PAH response specific to the second capillary EC population including upregulation of genes involved in cell death, cell motility and angiogenesis. Interestingly, four genes with genetic variants associated with PAH were dysregulated in mouse ECs in PAH. To compare relevance across PAH models and species, we performed a detailed analysis of EC heterogeneity and response to PAH in rats and humans through whole-lung PAH scRNA-seq datasets, revealing that 51% of up-regulated mouse genes were also up-regulated in rat or human PAH. We identified promising new candidates to target endothelial dysfunction including CD74, the knockdown of which regulates EC proliferation and barrier integrity in vitro. Finally, with an in silico cell ordering approach, we identified zonation-dependent changes across the arteriovenous axis in mouse PAH and showed upregulation of the Serine/threonine-protein kinase Sgk1 at the junction between the macro- and micro-vasculature. Conclusions This study uncovers PAH-induced EC transcriptomic changes at a high resolution, revealing novel targets for potential therapeutic candidate development.

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