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Nature Nov 2020Fibrosis can affect any organ and is responsible for up to 45% of all deaths in the industrialized world. It has long been thought to be relentlessly progressive and... (Review)
Review
Fibrosis can affect any organ and is responsible for up to 45% of all deaths in the industrialized world. It has long been thought to be relentlessly progressive and irreversible, but both preclinical models and clinical trials in various organ systems have shown that fibrosis is a highly dynamic process. This has clear implications for therapeutic interventions that are designed to capitalize on this inherent plasticity. However, despite substantial progress in our understanding of the pathobiology of fibrosis, a translational gap remains between the identification of putative antifibrotic targets and conversion of this knowledge into effective treatments in humans. Here we discuss the transformative experimental strategies that are being leveraged to dissect the key cellular and molecular mechanisms that regulate fibrosis, and the translational approaches that are enabling the emergence of precision medicine-based therapies for patients with fibrosis.
Topics: Cytokines; Fibroblasts; Fibrosis; Gastrointestinal Microbiome; Genome, Human; Humans; Integrins; Macrophages; Mesoderm; Precision Medicine; Single-Cell Analysis; Transforming Growth Factor beta; Translational Research, Biomedical
PubMed: 33239795
DOI: 10.1038/s41586-020-2938-9 -
Nature Jan 2021Kidney fibrosis is the hallmark of chronic kidney disease progression; however, at present no antifibrotic therapies exist. The origin, functional heterogeneity and...
Kidney fibrosis is the hallmark of chronic kidney disease progression; however, at present no antifibrotic therapies exist. The origin, functional heterogeneity and regulation of scar-forming cells that occur during human kidney fibrosis remain poorly understood. Here, using single-cell RNA sequencing, we profiled the transcriptomes of cells from the proximal and non-proximal tubules of healthy and fibrotic human kidneys to map the entire human kidney. This analysis enabled us to map all matrix-producing cells at high resolution, and to identify distinct subpopulations of pericytes and fibroblasts as the main cellular sources of scar-forming myofibroblasts during human kidney fibrosis. We used genetic fate-tracing, time-course single-cell RNA sequencing and ATAC-seq (assay for transposase-accessible chromatin using sequencing) experiments in mice, and spatial transcriptomics in human kidney fibrosis, to shed light on the cellular origins and differentiation of human kidney myofibroblasts and their precursors at high resolution. Finally, we used this strategy to detect potential therapeutic targets, and identified NKD2 as a myofibroblast-specific target in human kidney fibrosis.
Topics: Adaptor Proteins, Signal Transducing; Animals; Calcium-Binding Proteins; Case-Control Studies; Cell Differentiation; Cell Lineage; Extracellular Matrix; Female; Fibroblasts; Fibrosis; Humans; Kidney Tubules; Male; Mesoderm; Mice; Myofibroblasts; Pericytes; RNA-Seq; Receptor, Platelet-Derived Growth Factor alpha; Receptor, Platelet-Derived Growth Factor beta; Renal Insufficiency, Chronic; Single-Cell Analysis; Transcriptome
PubMed: 33176333
DOI: 10.1038/s41586-020-2941-1 -
Cell Feb 2021Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis...
Development of the human intestine is not well understood. Here, we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis, and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe diverse functions for these including as vascular niche cells. We pinpoint the origins of Peyer's patches and gut-associated lymphoid tissue (GALT) and describe location-specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders. We compile a publicly available online resource, spatio-temporal analysis resource of fetal intestinal development (STAR-FINDer), to facilitate further work.
Topics: Endothelial Cells; Enteric Nervous System; Fetus; Fibroblasts; Humans; Immunity; Intestinal Diseases; Intestinal Mucosa; Intestines; Ligands; Mesoderm; Neovascularization, Physiologic; Pericytes; Single-Cell Analysis; Stem Cells; Time Factors; Transcription Factors
PubMed: 33406409
DOI: 10.1016/j.cell.2020.12.016 -
Nature Dec 2022Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans,...
Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans, nonhuman primates are often used as surrogates to understand human development but currently suffer from a lack of in vivo datasets, especially from gastrulation to early organogenesis during which the major embryonic cell types are dynamically specified. To fill this gap, we collected six Carnegie stage 8-11 cynomolgus monkey (Macaca fascicularis) embryos and performed in-depth transcriptomic analyses of 56,636 single cells. Our analyses show transcriptomic features of major perigastrulation cell types, which help shed light on morphogenetic events including primitive streak development, somitogenesis, gut tube formation, neural tube patterning and neural crest differentiation in primates. In addition, comparative analyses with mouse embryos and human embryoids uncovered conserved and divergent features of perigastrulation development across species-for example, species-specific dependency on Hippo signalling during presomitic mesoderm differentiation-and provide an initial assessment of relevant stem cell models of human early organogenesis. This comprehensive single-cell transcriptome atlas not only fills the knowledge gap in the nonhuman primate research field but also serves as an invaluable resource for understanding human embryogenesis and developmental disorders.
Topics: Animals; Humans; Mice; Gastrulation; Macaca fascicularis; Organogenesis; Single-Cell Analysis; Embryoid Bodies; Gene Expression Profiling; Primitive Streak; Neural Tube; Neural Crest; Hippo Signaling Pathway; Mesoderm; Stem Cells
PubMed: 36517595
DOI: 10.1038/s41586-022-05526-y -
Nature Feb 2023Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks. Here we use gene-regulatory networks inferred from...
Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks. Here we use gene-regulatory networks inferred from single-cell multi-omics data to perform in silico transcription factor perturbations, simulating the consequent changes in cell identity using only unperturbed wild-type data. We apply this machine-learning-based approach, CellOracle, to well-established paradigms-mouse and human haematopoiesis, and zebrafish embryogenesis-and we correctly model reported changes in phenotype that occur as a result of transcription factor perturbation. Through systematic in silico transcription factor perturbation in the developing zebrafish, we simulate and experimentally validate a previously unreported phenotype that results from the loss of noto, an established notochord regulator. Furthermore, we identify an axial mesoderm regulator, lhx1a. Together, these results show that CellOracle can be used to analyse the regulation of cell identity by transcription factors, and can provide mechanistic insights into development and differentiation.
Topics: Animals; Humans; Mice; Cell Differentiation; Embryonic Development; Gene Regulatory Networks; Phenotype; Transcription Factors; Zebrafish; Computer Simulation; Mesoderm; Hematopoiesis
PubMed: 36755098
DOI: 10.1038/s41586-022-05688-9 -
Nature Dec 2019Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major...
Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.
Topics: Animals; Cell Differentiation; Cell Lineage; Chromatin; DNA Methylation; Demethylation; Embryoid Bodies; Endoderm; Enhancer Elements, Genetic; Epigenesis, Genetic; Epigenome; Erythropoiesis; Factor Analysis, Statistical; Gastrula; Gastrulation; Gene Expression Regulation, Developmental; Mesoderm; Mice; Pluripotent Stem Cells; RNA; Single-Cell Analysis; Time Factors; Zinc Fingers
PubMed: 31827285
DOI: 10.1038/s41586-019-1825-8 -
Nature Dec 2021Gastrulation is the fundamental process in all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity...
Gastrulation is the fundamental process in all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. In humans, gastrulation occurs in the third week after fertilization. Our understanding of this process in humans is relatively limited and based primarily on historical specimens, experimental models or, more recently, in vitro cultured samples. Here we characterize in a spatially resolved manner the single-cell transcriptional profile of an entire gastrulating human embryo, staged to be between 16 and 19 days after fertilization. We use these data to analyse the cell types present and to make comparisons with other model systems. In addition to pluripotent epiblast, we identified primordial germ cells, red blood cells and various mesodermal and endodermal cell types. This dataset offers a unique glimpse into a central but inaccessible stage of our development. This characterization provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.
Topics: Animals; Cell Differentiation; Datasets as Topic; Embryo, Mammalian; Endoderm; Erythrocytes; Female; Gastrula; Gastrulation; Gene Expression Profiling; Germ Cells; Humans; Male; Mesoderm; Mice; Single-Cell Analysis; Transcriptome
PubMed: 34789876
DOI: 10.1038/s41586-021-04158-y -
Developmental Cell Feb 2022The postnatal development and maturation of the liver, the major metabolic organ, are inadequately understood. We have analyzed 52,834 single-cell transcriptomes and...
The postnatal development and maturation of the liver, the major metabolic organ, are inadequately understood. We have analyzed 52,834 single-cell transcriptomes and identified 31 cell types or states in mouse livers at postnatal days 1, 3, 7, 21, and 56. We observe unexpectedly high levels of hepatocyte heterogeneity in the developing liver and the progressive construction of the zonated metabolic functions from pericentral to periportal hepatocytes, which is orchestrated with the development of sinusoid endothelial, stellate, and Kupffer cells. Trajectory and gene regulatory analyses capture 36 transcription factors, including a circadian regulator, Bhlhe40, in programming liver development. Remarkably, we identified a special group of macrophages enriched at day 7 with a hybrid phenotype of macrophages and endothelial cells, which may regulate sinusoidal construction and Treg-cell function. This study provides a comprehensive atlas that covers all hepatic cell types and is instrumental for further dissection of liver development, metabolism, and disease.
Topics: Animals; Animals, Newborn; Cell Communication; Endothelial Cells; Gene Expression Profiling; Hematopoiesis; Hepatocytes; Liver; Macrophages; Mesoderm; RNA-Seq; Single-Cell Analysis; Time Factors; Transcription Factors
PubMed: 35134346
DOI: 10.1016/j.devcel.2022.01.004 -
Nature Communications Jun 2021Fibrotic skin disease represents a major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix....
Fibrotic skin disease represents a major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix. Fibroblasts are found to be heterogeneous in multiple fibrotic diseases, but fibroblast heterogeneity in fibrotic skin diseases is not well characterized. In this study, we explore fibroblast heterogeneity in keloid, a paradigm of fibrotic skin diseases, by using single-cell RNA-seq. Our results indicate that keloid fibroblasts can be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory. Interestingly, the percentage of mesenchymal fibroblast subpopulation is significantly increased in keloid compared to normal scar. Functional studies indicate that mesenchymal fibroblasts are crucial for collagen overexpression in keloid. Increased mesenchymal fibroblast subpopulation is also found in another fibrotic skin disease, scleroderma, suggesting this is a broad mechanism for skin fibrosis. These findings will help us better understand skin fibrotic pathogenesis, and provide potential targets for fibrotic disease therapies.
Topics: Cell Adhesion Molecules; Collagen; Extracellular Matrix; Fibroblasts; Gene Expression Regulation; Gene Ontology; Humans; Keloid; Ligands; Mesoderm; RNA-Seq; Scleroderma, Systemic; Single-Cell Analysis; Skin Diseases
PubMed: 34140509
DOI: 10.1038/s41467-021-24110-y -
Cell Stem Cell Sep 2022A hallmark of primate postimplantation embryogenesis is the specification of extraembryonic mesoderm (EXM) before gastrulation, in contrast to rodents where this tissue...
A hallmark of primate postimplantation embryogenesis is the specification of extraembryonic mesoderm (EXM) before gastrulation, in contrast to rodents where this tissue is formed only after gastrulation. Here, we discover that naive human pluripotent stem cells (hPSCs) are competent to differentiate into EXM cells (EXMCs). EXMCs are specified by inhibition of Nodal signaling and GSK3B, are maintained by mTOR and BMP4 signaling activity, and their transcriptome and epigenome closely resemble that of human and monkey embryo EXM. EXMCs are mesenchymal, can arise from an epiblast intermediate, and are capable of self-renewal. Thus, EXMCs arising via primate-specific specification between implantation and gastrulation can be modeled in vitro. We also find that most of the rare off-target cells within human blastoids formed by triple inhibition (Kagawa et al., 2021) correspond to EXMCs. Our study impacts our ability to model and study the molecular mechanisms of early human embryogenesis and related defects.
Topics: Animals; Cell Differentiation; Embryo, Mammalian; Germ Layers; Humans; Mesoderm; Pluripotent Stem Cells; Primates
PubMed: 36055191
DOI: 10.1016/j.stem.2022.08.001