ABSTRACT
The processes that govern human haematopoietic stem cell (HSC) self-renewal and engraftment are poorly understood and challenging to recapitulate in culture to reliably expand functional HSCs1-3. Here we identify MYC target 1 (MYCT1; also known as MTLC) as a crucial human HSC regulator that moderates endocytosis and environmental sensing in HSCs. MYCT1 is selectively expressed in undifferentiated human haematopoietic stem and progenitor cells (HSPCs) and endothelial cells but becomes markedly downregulated during HSC culture. Lentivirus-mediated knockdown of MYCT1 prevented human fetal liver and cord blood (CB) HSPC expansion and engraftment. By contrast, restoring MYCT1 expression improved the expansion and engraftment of cultured CB HSPCs. Single-cell RNA sequencing of human CB HSPCs in which MYCT1 was knocked down or overexpressed revealed that MYCT1 governs important regulatory programmes and cellular properties essential for HSC stemness, such as ETS factor expression and low mitochondrial activity. MYCT1 is localized in the endosomal membrane in HSPCs and interacts with vesicle trafficking regulators and signalling machinery. MYCT1 loss in HSPCs led to excessive endocytosis and hyperactive signalling responses, whereas restoring MYCT1 expression balanced culture-induced endocytosis and dysregulated signalling. Moreover, sorting cultured CB HSPCs on the basis of lowest endocytosis rate identified HSPCs with preserved MYCT1 expression and MYCT1-regulated HSC stemness programmes. Our work identifies MYCT1-moderated endocytosis and environmental sensing as essential regulatory mechanisms required to preserve human HSC stemness. Our data also pinpoint silencing of MYCT1 as a cell-culture-induced vulnerability that compromises human HSC expansion.
Subject(s)
Cell Self Renewal , Hematopoietic Stem Cells , Nuclear Proteins , Animals , Female , Humans , Male , Mice , Cells, Cultured , Endocytosis , Endosomes/metabolism , Endothelial Cells/cytology , Endothelial Cells/metabolism , Fetal Blood/cytology , Gene Knockdown Techniques , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Liver/cytology , Liver/metabolism , Liver/embryology , Mitochondria/metabolism , Nuclear Proteins/metabolism , Signal Transduction , Proto-Oncogene Proteins c-ets/genetics , Proto-Oncogene Proteins c-ets/metabolism , Single-Cell Gene Expression AnalysisABSTRACT
The molecular events that initiate lymphoid-lineage specification remain unidentified because the stages of differentiation during which lineage commitment occurs are difficult to characterize. We isolated fetal liver progenitor cells undergoing restriction of their differentiation potential toward the T cell-innate lymphoid cell lineage or the B cell lineage. Transcripts that defined the molecular signatures of these two subsets were sequentially upregulated in lympho-myeloid precursor cells and in common lymphoid progenitor cells, respectively, and this preceded lineage restriction; this indicates that T cell-versus-B cell commitment is not a binary fate 'decision'. The T cell-bias and B cell-bias transcriptional programs were frequently co-expressed in common lymphoid progenitor cells and were segregated in subsets biased toward T cell differentiation or B cell differentiation, after interleukin 7 (IL-7) signaling that controlled the number of progenitor cells engaging in T cell differentiation versus B cell differentiation.
Subject(s)
B-Lymphocytes/cytology , Cell Lineage , Liver/cytology , Lymphopoiesis , T-Lymphocytes/cytology , Animals , B-Lymphocytes/metabolism , Biomarkers , Cell Differentiation/genetics , Cell Lineage/genetics , Cluster Analysis , Fetus , Gene Expression Profiling , Gene Expression Regulation, Developmental , Immunophenotyping , Interleukin-7/metabolism , Liver/embryology , Lymphoid Progenitor Cells/cytology , Lymphoid Progenitor Cells/metabolism , Lymphopoiesis/genetics , Mice , Mice, Transgenic , Signal Transduction , T-Lymphocytes/metabolism , TranscriptomeABSTRACT
Studies based on single cells have revealed vast cellular heterogeneity in stem cell and progenitor compartments, suggesting continuous differentiation trajectories with intermixing of cells at various states of lineage commitment and notable degrees of plasticity during organogenesis1-5. The hepato-pancreato-biliary organ system relies on a small endoderm progenitor compartment that gives rise to a variety of different adult tissues, including the liver, pancreas, gall bladder and extra-hepatic bile ducts6,7. Experimental manipulation of various developmental signals in the mouse embryo has underscored important cellular plasticity in this embryonic territory6. This is reflected in the existence of human genetic syndromes as well as congenital malformations featuring multi-organ phenotypes in liver, pancreas and gall bladder6. Nevertheless, the precise lineage hierarchy and succession of events leading to the segregation of an endoderm progenitor compartment into hepatic, biliary and pancreatic structures have not yet been established. Here we combine computational modelling approaches with genetic lineage tracing to accurately reconstruct the hepato-pancreato-biliary lineage tree. We show that a multipotent progenitor subpopulation persists in the pancreato-biliary organ rudiment, contributing cells not only to the pancreas and gall bladder but also to the liver. Moreover, using single-cell RNA sequencing and functional experiments we define a specialized niche that supports this subpopulation in a multipotent state for an extended time during development. Together these findings indicate sustained plasticity underlying hepato-pancreato-biliary development that might also explain the rapid expansion of the liver while attenuating pancreato-biliary growth.
Subject(s)
Biliary Tract/cytology , Cell Lineage , Liver/cytology , Pancreas/cytology , Stem Cell Niche , Animals , Biliary Tract/embryology , Biliary Tract/metabolism , Cell Lineage/genetics , Cell Tracking , Embryo, Mammalian/cytology , Embryo, Mammalian/metabolism , Female , Liver/embryology , Liver/metabolism , Male , Mice , Mice, Inbred C57BL , Models, Biological , Pancreas/embryology , Pancreas/metabolism , RNA-Seq , Signal Transduction , Single-Cell Analysis , Stem Cell Niche/geneticsABSTRACT
Hematopoietic stem cells (HSCs) develop from hemogenic endothelial cells (HECs) in vivo during mouse embryogenesis. When cultured in vitro, cells from the embryo phenotypically defined as pre-HSC-I and pre-HSC-II have the potential to differentiate into HSCs. However, minimal factors required for HSC induction from HECs have not yet been determined. In this study, we demonstrated that stem cell factor (SCF) and thrombopoietin (TPO) induced engrafting HSCs from embryonic day (E) 11.5 pre-HSC-I in a serum-free and feeder-free culture condition. In contrast, E10.5 pre-HSC-I and HECs required an endothelial cell layer in addition to SCF and TPO to differentiate into HSCs. A single-cell RNA sequencing analysis of E10.5 to 11.5 dorsal aortae with surrounding tissues and fetal livers detected TPO expression confined in hepatoblasts, while SCF was expressed in various tissues, including endothelial cells and hepatoblasts. Our results suggest a transition of signal requirement during HSC development from HECs. The differentiation of E10.5 HECs to E11.5 pre-HSC-I in the aorta-gonad-mesonephros region depends on SCF and endothelial cell-derived factors. Subsequently, SCF and TPO drive the differentiation of E11.5 pre-HSC-I to pre-HSC-II/HSCs in the fetal liver. The culture system established in this study provides a beneficial tool for exploring the molecular mechanisms underlying the development of HSCs from HECs.
Subject(s)
Cell Differentiation , Hemangioblasts , Hematopoietic Stem Cells , Stem Cell Factor , Thrombopoietin , Animals , Hematopoietic Stem Cells/metabolism , Hematopoietic Stem Cells/cytology , Mice , Thrombopoietin/metabolism , Stem Cell Factor/metabolism , Hemangioblasts/metabolism , Hemangioblasts/cytology , Endothelial Cells/metabolism , Endothelial Cells/cytology , Signal Transduction , Hematopoiesis/physiology , Embryonic Development , Embryo, Mammalian/metabolism , Embryo, Mammalian/cytology , Liver/embryology , Liver/metabolism , Liver/cytologyABSTRACT
Macrophages are the first cells of the nascent immune system to emerge during embryonic development. In mice, embryonic macrophages infiltrate developing organs, where they differentiate symbiotically into tissue-resident macrophages (TRMs)1. However, our understanding of the origins and specialization of macrophages in human embryos is limited. Here we isolated CD45+ haematopoietic cells from human embryos at Carnegie stages 11 to 23 and subjected them to transcriptomic profiling by single-cell RNA sequencing, followed by functional characterization of a population of CD45+CD34+CD44+ yolk sac-derived myeloid-biased progenitors (YSMPs) by single-cell culture. We also mapped macrophage heterogeneity across multiple anatomical sites and identified diverse subsets, including various types of embryonic TRM (in the head, liver, lung and skin). We further traced the specification trajectories of TRMs from either yolk sac-derived primitive macrophages or YSMP-derived embryonic liver monocytes using both transcriptomic and developmental staging information, with a focus on microglia. Finally, we evaluated the molecular similarities between embryonic TRMs and their adult counterparts. Our data represent a comprehensive characterization of the spatiotemporal dynamics of early macrophage development during human embryogenesis, providing a reference for future studies of the development and function of human TRMs.
Subject(s)
Macrophages/cytology , Single-Cell Analysis , Cell Lineage , Embryo, Mammalian/cytology , Head , Hematopoiesis , Humans , Leukocyte Common Antigens/metabolism , Liver/cytology , Liver/embryology , Lung/cytology , Macrophages/metabolism , Microglia/cytology , Myeloid Progenitor Cells/cytology , RNA-Seq , Skin/cytology , Spatio-Temporal Analysis , Transcriptome , Yolk Sac/cytologyABSTRACT
Tissue-resident macrophages can derive from yolk sac macrophages (YS-Macs), fetal liver monocytes (FL-MOs), or adult bone-marrow monocytes (BM-MOs). The relative capacity of these precursors to colonize a niche, self-maintain, and perform tissue-specific functions is unknown. We simultaneously transferred traceable YS-Macs, FL-MOs, and BM-MOs into the empty alveolar macrophage (AM) niche of neonatal Csf2rb(-/-) mice. All subsets produced AMs, but in competition preferential outgrowth of FL-MOs was observed, correlating with their superior granulocyte macrophage-colony stimulating factor (GM-CSF) reactivity and proliferation capacity. When transferred separately, however, all precursors efficiently colonized the alveolar niche and generated AMs that were transcriptionally almost identical, self-maintained, and durably prevented alveolar proteinosis. Mature liver, peritoneal, or colon macrophages could not efficiently colonize the empty AM niche, whereas mature AMs could. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages and the plasticity of the mononuclear phagocyte system is largest at the precursor stage.
Subject(s)
Bone Marrow Cells/cytology , Cell Differentiation/immunology , Granulocyte-Macrophage Colony-Stimulating Factor/immunology , Liver/cytology , Macrophages, Alveolar/cytology , Yolk Sac/cytology , Animals , Cell Proliferation , Cytokine Receptor Common beta Subunit/genetics , Liver/embryology , Liver/immunology , Macrophages, Alveolar/immunology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Knockout , Transcriptome/immunology , Yolk Sac/immunologyABSTRACT
Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.
Subject(s)
Fetus/cytology , Hematopoiesis , Liver/cytology , Liver/embryology , Blood Cells/cytology , Cellular Microenvironment , Female , Fetus/metabolism , Flow Cytometry , Gene Expression Profiling , Humans , Liver/metabolism , Lymphoid Tissue/cytology , Single-Cell Analysis , Stem Cells/metabolismABSTRACT
Organogenesis is a complex and interconnected process that is orchestrated by multiple boundary tissue interactions1-7. However, it remains unclear how individual, neighbouring components coordinate to establish an integral multi-organ structure. Here we report the continuous patterning and dynamic morphogenesis of hepatic, biliary and pancreatic structures, invaginating from a three-dimensional culture of human pluripotent stem cells. The boundary interactions between anterior and posterior gut spheroids differentiated from human pluripotent stem cells enables retinoic acid-dependent emergence of hepato-biliary-pancreatic organ domains specified at the foregut-midgut boundary organoids in the absence of extrinsic factors. Whereas transplant-derived tissues are dominated by midgut derivatives, long-term-cultured microdissected hepato-biliary-pancreatic organoids develop into segregated multi-organ anlages, which then recapitulate early morphogenetic events including the invagination and branching of three different and interconnected organ structures, reminiscent of tissues derived from mouse explanted foregut-midgut culture. Mis-segregation of multi-organ domains caused by a genetic mutation in HES1 abolishes the biliary specification potential in culture, as seen in vivo8,9. In sum, we demonstrate that the experimental multi-organ integrated model can be established by the juxtapositioning of foregut and midgut tissues, and potentially serves as a tractable, manipulatable and easily accessible model for the study of complex human endoderm organogenesis.
Subject(s)
Biliary Tract/embryology , Intestines/embryology , Liver/embryology , Models, Biological , Morphogenesis , Pancreas/embryology , Animals , Biliary Tract/cytology , Biomarkers/analysis , Biomarkers/metabolism , Body Patterning , Endoderm/cytology , Endoderm/embryology , Humans , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/metabolism , Intestines/cytology , Liver/cytology , Male , Mice , Organoids/cytology , Organoids/embryology , Pancreas/cytology , Spheroids, Cellular/cytology , Spheroids, Cellular/metabolism , Spheroids, Cellular/transplantation , Transcription Factor HES-1/analysis , Transcription Factor HES-1/metabolismABSTRACT
Centrosomes, the main microtubule-organizing centers in animal cells, are replicated exactly once during the cell division cycle to form the poles of the mitotic spindle. Supernumerary centrosomes can lead to aberrant cell division and have been causally linked to chromosomal instability and cancer. Here, we report that an increase in the number of mature centrosomes, generated by disrupting cytokinesis or forcing centrosome overduplication, triggers the activation of the PIDDosome multiprotein complex, leading to Caspase-2-mediated MDM2 cleavage, p53 stabilization, and p21-dependent cell cycle arrest. This pathway also restrains the extent of developmentally scheduled polyploidization by regulating p53 levels in hepatocytes during liver organogenesis. Taken together, the PIDDosome acts as a first barrier, engaging p53 to halt the proliferation of cells carrying more than one mature centrosome to maintain genome integrity.
Subject(s)
Centrosome/physiology , Genes, p53/genetics , Multiprotein Complexes/metabolism , Transcriptional Activation/genetics , A549 Cells , Animals , CRADD Signaling Adaptor Protein/metabolism , Caspase 2/metabolism , Cell Cycle Checkpoints/genetics , Cells, Cultured , Centrosome/pathology , Cytokinesis/genetics , Death Domain Receptor Signaling Adaptor Proteins/metabolism , Humans , Liver/cytology , Liver/embryology , Mice , Organogenesis/geneticsABSTRACT
BACKGROUND & AIMS: In the developing liver, bipotent epithelial progenitor cells undergo lineage segregation to form hepatocytes, which constitute the bulk of the liver parenchyma, and biliary epithelial cells (cholangiocytes), which comprise the bile duct (a complex tubular network that is critical for normal liver function). Notch and TGFß signalling promote the formation of a sheet of biliary epithelial cells, the ductal plate, that organises into discontinuous tubular structures. How these structures elongate and connect to form a continuous duct remains undefined. We aimed to define the mechanisms by which the ductal plate transitions from a simple sheet of epithelial cells into a complex and connected bile duct. METHODS: By combining single-cell RNA sequencing of embryonic mouse livers with genetic tools and organoid models we functionally dissected the role of planar cell polarity in duct patterning. RESULTS: We show that the planar cell polarity protein VANGL2 is expressed late in intrahepatic bile duct development and patterns the formation of cell-cell contacts between biliary cells. The patterning of these cell contacts regulates the normal polarisation of the actin cytoskeleton within biliary cells and loss of Vangl2 function results in the abnormal distribution of cortical actin remodelling, leading to the failure of bile duct formation. CONCLUSIONS: Planar cell polarity is a critical step in the post-specification sculpture of the bile duct and is essential for establishing normal tissue architecture. IMPACT AND IMPLICATIONS: Like other branched tissues, such as the lung and kidney, the bile ducts use planar cell polarity signalling to coordinate cell movements; however, how these biochemical signals are linked to ductular patterning remains unclear. Here we show that the core planar cell polarity protein VANGL2 patterns how cell-cell contacts form in the mammalian bile duct and how ductular cells transmit confluent mechanical changes along the length of a duct. This work sheds light on how biological tubes are patterned across mammalian tissues (including within the liver) and will be important in how we promote ductular growth in patients where the duct is mis-patterned or poorly formed.
Subject(s)
Cell Polarity , Nerve Tissue Proteins , Animals , Mice , Cell Polarity/physiology , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Epithelial Cells/metabolism , Epithelial Cells/cytology , Liver/embryology , Liver/cytology , Liver/metabolism , Bile Ducts, Intrahepatic/embryology , Bile Ducts, Intrahepatic/metabolism , Bile Ducts, Intrahepatic/cytology , Biliary Tract/embryology , Biliary Tract/cytology , Biliary Tract/metabolism , Signal Transduction/physiologyABSTRACT
Tissue-resident macrophages (MΦTR ) originate from at least two distinct waves of erythro-myeloid progenitors (EMP) arising in the yolk sac (YS) at E7.5 and E8.5 with the latter going through a liver monocyte intermediate. The relative potential of these precursors in determining development and functional capacity of MΦTR remains unclear. Here, we studied development of alveolar macrophages (AM) after single and competitive transplantation of different precursors from YS, fetal liver, and fetal lung into neonatal Csf2ra-/- mice, which lack endogenous AM. Fetal monocytes, promoted by Myb, outcompeted primitive MΦ (pMΦ) in empty AM niches and preferentially developed to mature AM, which is associated with enhanced mitochondrial respiratory and glycolytic capacity and repression of the transcription factors c-Maf and MafB. Interestingly, AM derived from pMΦ failed to efficiently clear alveolar proteinosis and protect from fatal lung failure following influenza virus infection. Thus, our data demonstrate superior developmental and functional capacity of fetal monocytes over pMΦ in AM development and underlying mechanisms explaining replacement of pMΦ in fetal tissues.
Subject(s)
Liver/embryology , Lung/embryology , Monocytes/cytology , Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Yolk Sac/embryology , Animals , Cells, Cultured , Female , Gene Expression Regulation, Developmental , Gene Knockout Techniques , Glycolysis , Liver/cytology , Liver/metabolism , Lung/cytology , Lung/metabolism , Macrophages, Alveolar , MafB Transcription Factor/metabolism , Mice , Monocytes/drug effects , Monocytes/metabolism , Proto-Oncogene Proteins c-maf/metabolism , Proto-Oncogene Proteins c-myb/pharmacology , Yolk Sac/cytology , Yolk Sac/metabolismABSTRACT
The earliest blood vessels in mammalian embryos are formed when endothelial cells differentiate from angioblasts and coalesce into tubular networks. Thereafter, the endothelium is thought to expand solely by proliferation of pre-existing endothelial cells. Here we show that a complementary source of endothelial cells is recruited into pre-existing vasculature after differentiation from the earliest precursors of erythrocytes, megakaryocytes and macrophages, the erythro-myeloid progenitors (EMPs) that are born in the yolk sac. A first wave of EMPs contributes endothelial cells to the yolk sac endothelium, and a second wave of EMPs colonizes the embryo and contributes endothelial cells to intraembryonic endothelium in multiple organs, where they persist into adulthood. By demonstrating that EMPs constitute a hitherto unrecognized source of endothelial cells, we reveal that embryonic blood vascular endothelium expands in a dual mechanism that involves both the proliferation of pre-existing endothelial cells and the incorporation of endothelial cells derived from haematopoietic precursors.
Subject(s)
Blood Vessels/cytology , Blood Vessels/embryology , Cell Lineage , Endothelial Cells/cytology , Erythrocytes/cytology , Myeloid Progenitor Cells/cytology , Aging , Animals , Cell Lineage/genetics , Cell Proliferation , Endothelial Cells/metabolism , Erythrocytes/metabolism , Gene Expression Profiling , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Humans , Integrases/genetics , Integrases/metabolism , Liver/cytology , Liver/embryology , Mice , Myeloid Progenitor Cells/metabolism , Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/genetics , Rhombencephalon/blood supply , Rhombencephalon/cytology , Rhombencephalon/embryology , Transcription, Genetic , Yolk Sac/cytology , Yolk Sac/embryologyABSTRACT
Single-cell genomics has transformed our ability to examine cell fate choice. Examining cells along a computationally ordered 'pseudotime' offers the potential to unpick subtle changes in variability and covariation among key genes. We describe an approach, scHOT-single-cell higher-order testing-which provides a flexible and statistically robust framework for identifying changes in higher-order interactions among genes. scHOT can be applied for cells along a continuous trajectory or across space and accommodates various higher-order measurements including variability or correlation. We demonstrate the use of scHOT by studying coordinated changes in higher-order interactions during embryonic development of the mouse liver. Additionally, scHOT identifies subtle changes in gene-gene correlations across space using spatially resolved transcriptomics data from the mouse olfactory bulb. scHOT meaningfully adds to first-order differential expression testing and provides a framework for interrogating higher-order interactions using single-cell data.
Subject(s)
Liver/embryology , Single-Cell Analysis/methods , Animals , Computational Biology , Databases, Nucleic Acid , Hepatocytes/physiology , Liver/cytology , Mice , Oligonucleotide Array Sequence Analysis , Sequence Analysis, RNA , SoftwareABSTRACT
BACKGROUND: Endothelial cells (ECs) play a critical role in angiogenesis and vascular remodeling. The heterogeneity of ECs has been reported at adult stages, yet it has not been fully investigated. This study aims to assess the transcriptional heterogeneity of developmental ECs at spatiotemporal level and to reveal the changes of embryonic ECs clustering when endothelium-enriched microRNA-126 (miR-126) was specifically knocked out. METHODS: C57BL/6J mice embryos at day 14.5 were harvested and digested, followed by fluorescence-activated cell sorting to enrich ECs. Then, single-cell RNA sequencing was applied to enriched embryonic ECs. Tie2 (Tek receptor tyrosine kinase)-cre-mediated ECs-specific miR-126 knockout mice were constructed, and ECs from Tie2-cre-mediated ECs-specific miR-126 knockout embryos were subjected to single-cell RNA sequencing. RESULTS: Embryonic ECs were clustered into 11 groups corresponding to anatomic characteristics. The vascular bed (arteries, capillaries, veins, lymphatics) exhibited transcriptomic similarity across the developmental stage. Embryonic ECs had higher proliferative potential than adult ECs. Integrating analysis showed that 3 ECs populations (hepatic, mesenchymal transition, and pulmonary ECs) were apparently disorganized after miR-126 being knocked out. Gene ontology analysis revealed that disrupted ECs were mainly related to hypoxia, glycometabolism, and vascular calcification. Additionally, in vivo experiment showed that Tie2-cre-mediated ECs-specific miR-126 knockout mice exhibited excessive intussusceptive angiogenesis; reductive glucose and pyruvate tolerance; and excessive accumulation of calcium. Agonist miR-126-3p agomir significantly rescued the phenotype of glucose metabolic dysfunction in Tie2-cre-mediated ECs-specific miR-126 knockout mice. CONCLUSIONS: The heterogeneity of ECs is established as early as the embryonic stage. The deficiency of miR-126 disrupts the differentiation and diversification of embryonic ECs, suggesting that miR-126 plays an essential role in the maintenance of ECs heterogeneity.
Subject(s)
Endothelial Cells/cytology , Endothelial Cells/metabolism , MicroRNAs/genetics , Mouse Embryonic Stem Cells/cytology , Mouse Embryonic Stem Cells/metabolism , Animals , Apoptosis/genetics , Cell Hypoxia/genetics , Cell Lineage/genetics , Cell Plasticity/genetics , Cell Proliferation/genetics , Endothelial Cells/classification , Gene Expression Profiling , Gene Expression Regulation, Developmental , Gestational Age , Glucose/metabolism , Liver/blood supply , Liver/embryology , Liver/metabolism , Metabolic Networks and Pathways/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , MicroRNAs/antagonists & inhibitors , MicroRNAs/metabolism , Mouse Embryonic Stem Cells/classification , Neovascularization, Physiologic/genetics , Single-Cell Analysis , Spatio-Temporal Analysis , Vascular Calcification/genetics , Vascular Calcification/metabolism , Vascular Calcification/pathologyABSTRACT
Conventional two-dimensional differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. Three-dimensional organoids generate complex organ-like tissues; however, it is unclear how heterotypic interactions affect lineage identity. Here we use single-cell RNA sequencing to reconstruct hepatocyte-like lineage progression from pluripotency in two-dimensional culture. We then derive three-dimensional liver bud organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during liver bud development. We find that liver bud hepatoblasts diverge from the two-dimensional lineage, and express epithelial migration signatures characteristic of organ budding. We benchmark three-dimensional liver buds against fetal and adult human liver single-cell RNA sequencing data, and find a striking correspondence between the three-dimensional liver bud and fetal liver cells. We use a receptor-ligand pairing analysis and a high-throughput inhibitor assay to interrogate signalling in liver buds, and show that vascular endothelial growth factor (VEGF) crosstalk potentiates endothelial network formation and hepatoblast differentiation. Our molecular dissection reveals interlineage communication regulating organoid development, and illuminates previously inaccessible aspects of human liver development.
Subject(s)
Cell Communication , Cell Differentiation , Cell Lineage , Liver/cytology , Liver/embryology , Organogenesis , Tissue Culture Techniques/methods , Aged , Cell Hypoxia , Cell Movement , Endothelium/cytology , Epithelial Cells/cytology , Extracellular Matrix/metabolism , Female , Fetus/cytology , Hepatocytes/cytology , Humans , Male , Middle Aged , Organoids/cytology , Pluripotent Stem Cells/cytology , Sequence Analysis, RNA , Signal Transduction , Single-Cell Analysis , Vascular Endothelial Growth Factor A/metabolism , Young AdultABSTRACT
Super-enhancers (SEs) mediate high transcription levels of target genes. Previous studies have shown that SEs recruit transcription complexes and generate enhancer RNAs (eRNAs). We characterized transcription at the human and murine ß-globin locus control region (LCR) SE. We found that the human LCR is capable of recruiting transcription complexes independently from linked globin genes in transgenic mice. Furthermore, LCR hypersensitive site 2 (HS2) initiates the formation of bidirectional transcripts in transgenic mice and in the endogenous ß-globin gene locus in murine erythroleukemia (MEL) cells. HS2 3'eRNA is relatively unstable and remains in close proximity to the globin gene locus. Reducing the abundance of HS2 3'eRNA leads to a reduction in ß-globin gene transcription and compromises RNA polymerase II (Pol II) recruitment at the promoter. The Integrator complex has been shown to terminate eRNA transcription. We demonstrate that Integrator interacts downstream of LCR HS2. Inducible ablation of Integrator function in MEL or differentiating primary human CD34+ cells causes a decrease in expression of the adult ß-globin gene and accumulation of Pol II and eRNA at the LCR. The data suggest that transcription complexes are assembled at the LCR and transferred to the globin genes by mechanisms that involve Integrator mediated release of Pol II and eRNA from the LCR.
Subject(s)
Enhancer Elements, Genetic , Gene Expression Regulation , RNA/metabolism , Transcription, Genetic , beta-Globins/genetics , Adult , Animals , Cell Line, Tumor , Endoribonucleases/genetics , Fetus , Humans , Liver/embryology , Liver/metabolism , Locus Control Region , Mice, Transgenic , RNA/physiology , RNA Polymerase II/metabolism , beta-Globins/biosynthesisABSTRACT
Yeast Rcl1 is a potential endonuclease that mediates pre-RNA cleavage at the A2-site to separate 18S rRNA from 5.8S and 25S rRNAs. However, the biological function of Rcl1 in opisthokonta is poorly defined. Moreover, there is no information regarding the exact positions of 18S pre-rRNA processing in zebrafish. Here, we report that zebrafish pre-rRNA harbours three major cleavage sites in the 5'ETS, namely -477nt (A'-site), -97nt (A0-site) and the 5'ETS and 18S rRNA link (A1-site), as well as two major cleavage regions within the ITS1, namely 208-218nt (site 2) and 20-33nt (site E). We also demonstrate that depletion of zebrafish Rcl1 mainly impairs cleavage at the A1-site. Phenotypically, rcl1-/- mutants exhibit a small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq analysis revealed that the most significant event in rcl1-/- mutants is the up-regulated expression of a cohort of genes related to ribosome biogenesis and tRNA production. Our data demonstrate that Rcl1 is essential for 18S rRNA maturation at the A1-site and for digestive organogenesis in zebrafish. Rcl1 deficiency, similar to deficiencies in other ribosome biogenesis factors, might trigger a common mechanism to upregulate the expression of genes responsible for ribosome biogenesis.
Subject(s)
Liver/metabolism , Organogenesis/genetics , Pancreas/metabolism , RNA Precursors/metabolism , RNA, Ribosomal, 18S/metabolism , Ribosomes/metabolism , Zebrafish/metabolism , Animals , Animals, Genetically Modified , Gene Knockout Techniques , Gene Ontology , In Situ Hybridization , Liver/embryology , Liver/pathology , Pancreas/embryology , Pancreas/pathology , RNA Precursors/genetics , RNA, Ribosomal, 18S/genetics , RNA, Transfer/metabolism , RNA-Seq , Real-Time Polymerase Chain Reaction , Ribosomes/genetics , Zebrafish/geneticsABSTRACT
Fibroblast growth factors (FGFs) are required to specify hepatic fate within the definitive endoderm through activation of the FGF receptors (FGFRs). While the signaling pathways involved in hepatic specification are well understood, the mechanisms through which FGFs induce hepatic character within the endoderm are ill defined. Here we report the identification of genes whose expression is directly regulated by FGFR activity during the transition from endoderm to hepatic progenitor cell. The FGFR immediate early genes that were identified include those encoding transcription factors, growth factors, and signaling molecules. One of these immediate early genes encodes naked cuticle homolog 1 (NKD1), which is a repressor of canonical WNT (wingless-type MMTV integration site) signaling. We show that loss of NKD1 suppresses the formation of hepatic progenitor cells from human induced pluripotent stem cells and that this phenotype can be rescued by using a pharmacological antagonist of canonical WNT signaling. We conclude that FGF specifies hepatic fate at least in large part by inducing expression of NKD1 to transiently suppress the canonical WNT pathway.
Subject(s)
Carrier Proteins/genetics , Cell Differentiation/genetics , Fibroblast Growth Factor 2/metabolism , Gene Expression Regulation, Developmental/genetics , Induced Pluripotent Stem Cells/cytology , Adaptor Proteins, Signal Transducing , Calcium-Binding Proteins , Carrier Proteins/metabolism , Endoderm/cytology , Humans , Liver/cytology , Liver/embryology , Wnt Signaling Pathway/physiologyABSTRACT
Retinol-binding protein 2 (RBP2; originally cellular retinol-binding protein, type II (CRBPII)) is a 16 kDa cytosolic protein that in the adult is localized predominantly to absorptive cells of the proximal small intestine. It is well established that RBP2 plays a central role in facilitating uptake of dietary retinoid, retinoid metabolism in enterocytes, and retinoid actions locally within the intestine. Studies of mice lacking Rbp2 establish that Rbp2 is not required in times of dietary retinoid-sufficiency. However, in times of dietary retinoid-insufficiency, the complete lack of Rbp2 gives rise to perinatal lethality owing to RBP2 absence in both placental (maternal) and neonatal tissues. Moreover, when maintained on a high-fat diet, Rbp2-knockout mice develop obesity, glucose intolerance and a fatty liver. Unexpectedly, recent investigations have demonstrated that RBP2 binds long-chain 2-monoacylglycerols (2-MAGs), including the canonical endocannabinoid 2-arachidonoylglycerol, with very high affinity, equivalent to that of retinol binding. Crystallographic studies establish that 2-MAGs bind to a site within RBP2 that fully overlaps with the retinol binding site. When challenged orally with fat, mucosal levels of 2-MAGs in Rbp2 null mice are significantly greater than those of matched controls establishing that RBP2 is a physiologically relevant MAG-binding protein. The rise in MAG levels is accompanied by elevations in circulating levels of the hormone glucose-dependent insulinotropic polypeptide (GIP). It is not understood how retinoid and/or MAG binding to RBP2 affects the functions of this protein, nor is it presently understood how these contribute to the metabolic and hormonal phenotypes observed for Rbp2-deficient mice.
Subject(s)
Retinol-Binding Proteins, Cellular/chemistry , Retinol-Binding Proteins, Cellular/metabolism , Adult , Animals , Embryonic Development/physiology , Female , Humans , Immunity, Innate , Intestine, Small/embryology , Intestine, Small/immunology , Intestine, Small/metabolism , Liver/embryology , Liver/metabolism , Male , Monoglycerides/metabolism , Obesity/metabolism , Pregnancy , Retinoids/metabolism , Retinol-Binding Proteins, Cellular/genetics , Vitamin A/metabolismABSTRACT
Fetal hypoxemia decreases insulin and increases cortisol and norepinephrine concentrations and may restrict growth by decreasing glucose utilization and altering substrate oxidation. Specifically, we hypothesized that hypoxemia would decrease fetal glucose oxidation and increase lactate and pyruvate production. We tested this by measuring whole body glucose oxidation and lactate production, and molecular pathways in liver, muscle, adipose, and pancreas tissues of fetuses exposed to maternal hypoxemia for 9 days (HOX) compared with control fetal sheep (CON) in late gestation. Fetuses with more severe hypoxemia had lower whole body glucose oxidation rates, and HOX fetuses had increased lactate production from glucose. In muscle and adipose tissue, expression of the glucose transporter GLUT4 was decreased. In muscle, pyruvate kinase (PKM) and lactate dehydrogenase B (LDHB) expression was decreased. In adipose tissue, LDHA and lactate transporter (MCT1) expression was increased. In liver, there was decreased gene expression of PKLR and MPC2 and phosphorylation of PDH, and increased LDHA gene and LDH protein abundance. LDH activity, however, was decreased only in HOX skeletal muscle. There were no differences in basal insulin signaling across tissues, nor differences in pancreatic tissue insulin content, ß-cell area, or genes regulating ß-cell function. Collectively, these results demonstrate coordinated metabolic responses across tissues in the hypoxemic fetus that limit glucose oxidation and increase lactate and pyruvate production. These responses may be mediated by hypoxemia-induced endocrine responses including increased norepinephrine and cortisol, which inhibit pancreatic insulin secretion resulting in lower insulin concentrations and decreased stimulation of glucose utilization.NEW & NOTEWORTHY Hypoxemia lowered fetal glucose oxidation rates, based on severity of hypoxemia, and increased lactate production. This was supported by tissue-specific metabolic responses that may result from increased norepinephrine and cortisol concentrations, which decrease pancreatic insulin secretion and insulin concentrations and decrease glucose utilization. This highlights the vulnerability of metabolic pathways in the fetus and demonstrates that constrained glucose oxidation may represent an early event in response to sustained hypoxemia and fetal growth restriction.