scholarly journals Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maciej Migdał ◽  
Eugeniusz Tralle ◽  
Karim Abu Nahia ◽  
Łukasz Bugajski ◽  
Katarzyna Zofia Kędzierska ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Liver Injury ◽  
Hepatic Stellate Cells ◽  
Tissue Injury ◽  
Early Stage ◽  
Stellate Cells ◽  
Cell Types ◽  
Cell Type ◽  
Cell Type Specific ◽  
Liver Endothelial Cells

Abstract Background Liver fibrosis is a wound-healing response to tissue injury and inflammation hallmarked by the extracellular matrix (ECM) protein deposition in the liver parenchyma and tissue remodelling. Different cell types of the liver are known to play distinct roles in liver injury response. Hepatocytes and liver endothelial cells receive molecular signals indicating tissue injury and activate hepatic stellate cells which produce ECM proteins upon their activation. Despite the growing knowledge on the molecular mechanism underlying hepatic fibrosis in general, the cell-type-specific gene regulatory network associated with the initial response to hepatotoxic injury is still poorly characterized. Results In this study, we used thioacetamide (TAA) to induce hepatic injury in adult zebrafish. We isolated three major liver cell types - hepatocytes, endothelial cells and hepatic stellate cells - and identified cell-type-specific chromatin accessibility and transcriptional changes in an early stage of liver injury. We found that TAA induced transcriptional shifts in all three cell types hallmarked by significant alterations in the expression of genes related to fatty acid and carbohydrate metabolism, as well as immune response-associated and vascular-specific genes. Interestingly, liver endothelial cells exhibit the most pronounced response to liver injury at the transcriptome and chromatin level, hallmarked by the loss of their angiogenic phenotype. Conclusion Our results uncovered cell-type-specific transcriptome and epigenome responses to early stage liver injury, which provide valuable insights into understanding the molecular mechanism implicated in the early response of the liver to pro-fibrotic signals.

Identification of Multi-Omics Cell Signatures of Early Liver Injury

2021 ◽  
Author(s):  
Maciej Migdał ◽  
Eugeniusz Tralle ◽  
Karim Abu Nahia ◽  
Łukasz Bugajski ◽  
Katarzyna Zofia Kędzierska ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Liver Injury ◽  
Hepatic Stellate Cells ◽  
Tissue Injury ◽  
Early Stage ◽  
Stellate Cells ◽  
Cell Types ◽  
Cell Type ◽  
Cell Type Specific ◽  
Liver Endothelial Cells

Abstract Background Liver fibrosis is a wound-healing response to tissue injury and inflammation hallmarked by the extracellular matrix (ECM) protein deposition in the liver parenchyma and tissue remodelling. Different cell types of the liver are known to play distinct roles in liver injury response. Hepatocytes and liver endothelial cells receive molecular signals indicating tissue injury and activate hepatic stellate cells which produce ECM proteins upon their activation. Despite the growing knowledge on the molecular mechanism underlying hepatic fibrosis in general, the cell-type-specific gene regulatory network associated with the initial response to hepatotoxic injury is still poorly characterized. Results In this study, we used thioacetamide (TAA) to induce hepatic injury in adult zebrafish. We isolated three major liver cell types - hepatocytes, endothelial cells and hepatic stellate cells - and identified cell-type-specific chromatin accessibility and transcriptional changes in an early stage of liver injury. We found that TAA induced transcriptional shifts in all three cell types hallmarked by significant alterations in the expression of genes related to fatty acid and carbohydrate metabolism, as well as immune response-associated and vascular-specific genes. Interestingly, liver endothelial cells exhibit the most pronounced response to liver injury at the transcriptome and chromatin level, hallmarked by the loss of their angiogenic phenotype. Conclusion Our results uncovered cell-type-specific transcriptome and epigenome responses to early stage liver injury, which provide valuable insights into understanding the molecular mechanism implicated in the early response of the liver to pro-fibrotic signals.

scholarly journals HMGB1 recruits hepatic stellate cells and liver endothelial cells to sites of ethanol-induced parenchymal cell injury

2013 ◽  
Vol 305 (11) ◽  
pp. G838-G848 ◽  
Author(s):  
Yeon S. Seo ◽  
Jung H. Kwon ◽  
Usman Yaqoob ◽  
Liu Yang ◽  
Thiago M. De Assuncao ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Liver Injury ◽  
Hepatic Stellate Cells ◽  
Hepg2 Cells ◽  
Cell Injury ◽  
Parenchymal Cell ◽  
Stellate Cells ◽  
Hmgb1 Protein ◽  
Liver Endothelial Cells ◽  
Stimulation Of

Hepatic stellate cells (HSC) and liver endothelial cells (LEC) migrate to sites of injury and perpetuate alcohol-induced liver injury. High-mobility group box 1 (HMGB1) is a protein released from the nucleus of injured cells that has been implicated as a proinflammatory mediator. We hypothesized that HMGB1 may be released from ethanol-stimulated liver parenchymal cells and contribute to HSC and LEC recruitment. Ethanol stimulation of rat hepatocytes and HepG2 cells resulted in translocation of HMGB1 from the nucleus as assessed by Western blot. HMGB1 protein levels were increased in the supernatant of ethanol-treated hepatocytes compared with vehicle-treated cells. Migration of both HSC and LEC was increased in response to conditioned medium for ethanol-stimulated hepatocytes (CMEtOH) compared with vehicle-stimulated hepatocytes (CMVEH) ( P < 0.05). However, the effect of CMEtOH on migration was almost entirely reversed by treatment with HMGB1-neutralizing antibody or when HepG2 cells were pretransfected with HMGB1-siRNA compared with control siRNA-transfected HepG2 cells ( P < 0.05). Recombinant HMGB1 (100 ng/ml) also stimulated migration of HSC and LEC compared with vehicle stimulation ( P < 0.05 for both HSC and LEC). HMGB1 stimulation of HSC increased the phosphorylation of Src and Erk and HMGB1-induced HSC migration was blocked by the Src inhibitor PP2 and the Erk inhibitor U0126. Hepatocytes release HMGB1 in response to ethanol with subsequent recruitment of HSC and LEC. This pathway has implications for HSC and LEC recruitment to sites of ethanol-induced liver injury.

scholarly journals Cell type-specific biogenesis of novel vesicles containing viral products in human cytomegalovirus infection

2020 ◽  
Author(s):  
Samina Momtaz ◽  
Belen Molina ◽  
Luwanika Mlera ◽  
Felicia Goodrum ◽  
Jean M. Wilson
Keyword(s):  
Endothelial Cells ◽  
Human Cytomegalovirus ◽  
Biosynthetic Pathway ◽  
Cell Types ◽  
Endocytic Pathway ◽  
Specific Cell ◽  
Cell Type ◽  
Subcellular Compartment ◽  
Increased Risk ◽  
Cell Type Specific

AbstractHuman cytomegalovirus (HCMV), while highly restricted for the human species, infects an unlimited array of cell types in the host. Patterns of infection are dictated by the cell type infected, but cell type-specific factors and how they impact tropism for specific cell types is poorly understood. Previous studies in primary endothelial cells showed that HCMV infection induces large multivesicular-like bodies that incorporate viral products including dense bodies and virions. Here we define the nature of these large vesicles using a recombinant virus where UL32, encoding the pp150 tegument protein, is fused in frame with green fluorescent protein (GFP, TB40/E-UL32-GFP). Cells were fixed and labeled with antibodies against subcellular compartment markers and imaged using confocal and super-resolution microscopy. In fibroblasts, UL32-GFP-positive vesicles were marked with classical markers of MVBs, including CD63 and lysobisphosphatidic acid (LBPA), both classical MVB markers, as well as the clathrin and LAMP1. Unexpectedly, UL32-GFP-positive vesicles in endothelial cells were not labeled by CD63, and LBPA was completely lost from infected cells. We defined these UL32-positive vesicles in endothelial cells using markers for the cis-Golgi (GM130), lysosome (LAMP1), and autophagy (LC3B). These findings suggest that virus-containing MVBs in fibroblasts are derived from the canonical endocytic pathway and takeover classical exosomal release pathway. Virus containing MVBs in HMVECs are derived from the early biosynthetic pathway and exploit a less characterized early Golgi-LAMP1-associated non-canonical secretory autophagy pathway. These results reveal striking cell-type specific membrane trafficking differences in host pathways that are exploited by HCMV.ImportanceHuman cytomegalovirus (HCMV) is a herpesvirus that, like all herpesvirus, that establishes a life long infection. HCMV remains a significant cause of morbidity and mortality in the immunocompromised and HCMV seropositivity is associated with increased risk vascular disease. HCMV infects many cells in the human and the biology underlying the different patterns of infection in different cell types is poorly understood. Endothelial cells are important target of infection that contribute to hematogenous spread of the virus to tissues. Here we define striking differences in the biogenesis of large vesicles that incorporate virions in fibroblasts and endothelial cells. In fibroblasts, HCMV is incorporated into canonical MVBs derived from an endocytic pathway, whereas HCMV matures through vesicles derived from the biosynthetic pathway in endothelial cells. This work defines basic biological differences between these cell types that may impact the outcome of infection.

scholarly journals Rickettsia rickettsii Infection of Human Macrovascular and Microvascular Endothelial Cells Reveals Activation of Both Common and Cell Type-Specific Host Response Mechanisms

2010 ◽  
Vol 78 (6) ◽  
pp. 2599-2606 ◽  
Author(s):  
Elena Rydkina ◽  
Loel C. Turpin ◽  
Sanjeev K. Sahni
Keyword(s):  
Endothelial Cells ◽  
Host Response ◽  
Cell Types ◽  
Microvascular Endothelial Cells ◽  
Cell Type ◽  
Rickettsia Rickettsii ◽  
Specific Host ◽  
Cell Type Specific ◽  
Cox 2 ◽  
Microvascular Endothelial

ABSTRACT Although inflammation and altered barrier functions of the vasculature, due predominantly to the infection of endothelial cell lining of small and medium-sized blood vessels, represent salient pathological features of human rickettsioses, the interactions between pathogenic rickettsiae and microvascular endothelial cells remain poorly understood. We have investigated the activation of nuclear transcription factor-kappa B (NF-κB) and p38 mitogen-activated protein (MAP) kinase, expression of heme oxygenase 1 (HO-1) and cyclooxygenase 2 (COX-2), and secretion of chemokines and prostaglandins after Rickettsia rickettsii infection of human cerebral, dermal, and pulmonary microvascular endothelial cells in comparison with pulmonary artery cells of macrovascular origin. NF-κB and p38 kinase activation and increased HO-1 mRNA expression were clearly evident in all cell types, along with relatively similar susceptibility to R. rickettsii infection in vitro but considerable variations in the intensities/kinetics of the aforementioned host responses. As expected, the overall activation profiles of macrovascular endothelial cells derived from human pulmonary artery and umbilical vein were nearly identical. Interestingly, cerebral endothelial cells displayed a marked refractoriness in chemokine production and secretion, while all other cell types secreted various levels of interleukin-8 (IL-8) and monocyte chemoattractant protein 1 (MCP-1) in response to infection. A unique feature of all microvascular endothelial cells was the lack of induced COX-2 expression and resultant inability to secrete prostaglandin E2 after R. rickettsii infection. Comparative evaluation thus yields the first experimental evidence for the activation of both common and unique cell type-specific host response mechanisms in macrovascular and microvascular endothelial cells infected with R. rickettsii, a prototypical species known to cause Rocky Mountain spotted fever in humans.

scholarly journals Profiling of Primary and Mature miRNA Expression in Atherosclerosis Associated Cell Types

2021 ◽  
Author(s):  
Pierre R. Moreau ◽  
Vanesa Tomas Bosch ◽  
Maria Bouvy-Liivrand ◽  
Kadri Õunap ◽  
Tiit Örd ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Smooth Muscle ◽  
Molecular Mechanisms ◽  
Umbilical Vein ◽  
Cell Types ◽  
Integrative Approach ◽  
Dependent Manner ◽  
Cell Type ◽  
A Cell ◽  
Cell Type Specific

Objective: Atherosclerosis is the underlying cause of most cardiovascular diseases. The main cell types associated with disease progression in the vascular wall are endothelial cells, smooth muscle cells, and macrophages. Although their role in atherogenesis has been extensively described, molecular mechanisms underlying gene expression changes remain unknown. The objective of this study was to characterize microRNA (miRNA)-related regulatory mechanisms taking place in the aorta during atherosclerosis: Approach and Results: We analyzed the changes in primary human aortic endothelial cells and human umbilical vein endothelial cell, human aortic smooth muscle cell, and macrophages (CD14+) under various proatherogenic stimuli by integrating GRO-seq, miRNA-seq, and RNA-seq data. Despite the highly cell-type-specific expression of multi-variant pri-miRNAs, the majority of mature miRNAs were found to be common to all cell types and dominated by 2 to 5 abundant miRNA species. We demonstrate that transcription contributes significantly to the mature miRNA levels although this is dependent on miRNA stability. An analysis of miRNA effects in relation to target mRNA pools highlighted pathways and targets through which miRNAs could affect atherogenesis in a cell-type-dependent manner. Finally, we validate miR-100-5p as a cell-type specific regulator of inflammatory and HIPPO-YAP/TAZ-pathways. Conclusions: This integrative approach allowed us to characterize miRNA dynamics in response to a proatherogenic stimulus and identify potential mechanisms by which miRNAs affect atherogenesis in a cell-type-specific manner.

scholarly journals Cell type-specific biogenesis of novel vesicles containing viral products in human cytomegalovirus infection

2021 ◽  
Author(s):  
Samina Momtaz ◽  
Belen Molina ◽  
Luwanika Mlera ◽  
Felicia Goodrum ◽  
Jean M. Wilson
Keyword(s):  
Endothelial Cells ◽  
Human Cytomegalovirus ◽  
Biosynthetic Pathway ◽  
Cell Types ◽  
Endocytic Pathway ◽  
Progeny Virus ◽  
Specific Cell ◽  
Cell Type ◽  
Infected Cells ◽  
Cell Type Specific

Human cytomegalovirus (HCMV), while highly restricted for the human species, infects an diverse array of cell types in the host. Patterns of infection are dictated by the cell type infected, but cell type-specific factors and how they impact tropism for specific cell types is poorly understood. Previous studies in primary endothelial cells showed that HCMV infection induces large multivesicular-like bodies (MVBs) that incorporate viral products, including dense bodies (DBs) and virions. Here we define the nature of these large vesicles using a recombinant virus where UL32, encoding the pp150 tegument protein, is fused in frame with green fluorescent protein (GFP, TB40/E-UL32-GFP). In fibroblasts, UL32-GFP-positive vesicles were marked with classical markers of MVBs, including CD63 and lysobisphosphatidic acid (LBPA), both classical MVB markers, as well as the clathrin and LAMP1. Unexpectedly, UL32-GFP-positive vesicles in primary human microvascular endothelial cells (HMVECs) were not labeled by CD63, and LBPA was completely lost from infected cells. We defined these UL32-positive vesicles in endothelial cells using markers for the cis-Golgi (GM130), lysosome (LAMP1), and autophagy (LC3B). These findings suggest that UL32-GFP containing MVBs in fibroblasts are derived from the canonical endocytic pathway and takeover classical exosomal release pathway. However, UL32-GFP containing MVBs in HMVECs are derived from the early biosynthetic pathway and exploit a less characterized early Golgi-LAMP1-associated non- canonical secretory autophagy pathway. These results reveal striking cell-type specific membrane trafficking differences in host pathways that are exploited by HCMV, which may reflect distinct pathways for virus egress. Importance Human cytomegalovirus (HCMV) is a herpesvirus that, like all herpesvirus, that establishes a life-long infection. HCMV remains a significant cause of morbidity and mortality in the immunocompromised and HCMV seropositivity is associated with age-related pathology. HCMV infects many cells in the human host and the biology underlying the different patterns of infection in different cell types is poorly understood. Endothelial cells are important target of infection that contribute to hematogenous spread of the virus to tissues. Here we define striking differences in the biogenesis of large vesicles that incorporate virions in fibroblasts and endothelial cells. In fibroblasts, HCMV is incorporated into canonical MVBs derived from an endocytic pathway, whereas HCMV matures through vesicles derived from the biosynthetic pathway in endothelial cells. This work defines basic biological differences between these cell types that may impact how progeny virus is trafficked out of infected cells.

Characterization and subcellular localization of a bacterial flotillin homologue

Microbiology ◽  
2009 ◽  
Vol 155 (6) ◽  
pp. 1786-1799 ◽  
Author(s):  
Catriona Donovan ◽  
Marc Bramkamp
Keyword(s):  
Early Stage ◽  
Model Organism ◽  
Cell Types ◽  
Specific Gene ◽  
Cell Type ◽  
Distinct Cell ◽  
Sporulation Efficiency ◽  
Cell Type Specific ◽  
Detergent Resistant Membranes

The process of endospore formation in Bacillus subtilis is complex, requiring the generation of two distinct cell types, a forespore and larger mother cell. The development of these cell types is controlled and regulated by cell type-specific gene expression, activated by a σ-factor cascade. Activation of these cell type-specific sigma factors is coupled with the completion of polar septation. Here, we describe a novel protein, YuaG, a eukaryotic reggie/flotillin homologue that is involved in the early stages of sporulation of the Gram-positive model organism B. subtilis. YuaG localizes in discrete foci in the membrane and is highly dynamic. Purification of detergent-resistant membranes revealed that YuaG is associated with negatively charged phospholipids, e.g. phosphatidylglycerol (PG) or cardiolipin (CL). However, localization of YuaG is not always dependent on PG/CL in vivo. A yuaG disruption strain shows a delay in the onset of sporulation along with reduced sporulation efficiency, where the spores develop to a certain stage and then appear to be trapped at this stage. Our results indicate that YuaG is involved in the early stage of spore development, probably playing a role in the signalling cascade at the onset of sporulation.

scholarly journals In vivo characterisation of endogenous cardiovascular extracellular vesicles in larval and adult zebrafish

2019 ◽  
Author(s):  
Aaron Scott ◽  
Lorena Sueiro Ballesteros ◽  
Marston Bradshaw ◽  
Ann Power ◽  
James Lorriman ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Extracellular Vesicles ◽  
Cell Types ◽  
Live Imaging ◽  
Adult Zebrafish ◽  
Cell Type ◽  
Spatiotemporal Resolution ◽  
Zebrafish Model ◽  
Cell Type Specific

AbstractObjectiveExtracellular vesicles (EVs) facilitate molecular transport across extracellular space, allowing local and systemic signalling during homeostasis and in disease. Extensive studies have described functional roles for EV populations, including during cardiovascular disease, but the in vivo characterisation of endogenously produced EVs is still in its infancy. Due to their genetic tractability and opportunities for live imaging, zebrafish represent an ideal but under-used model to investigate endogenous EVs. The overall aim of this study was to establish a transgenic zebrafish model to allow the in vivo identification, tracking and extraction of endogenous EVs produced by different cell types.Approach and ResultsUsing a membrane-tethered fluorophore reporter system, we show that EVs can be fluorescently labelled in larval and adult zebrafish and demonstrate that multiple cell types including endothelial cells and cardiomyocytes actively produce EVs in vivo. Cell-type specific EVs can be tracked by high spatiotemporal resolution light-sheet live imaging and modified flow cytometry methods allow these EVs to be further evaluated. Importantly, we demonstrate the utility of this model by showing that cardiomyocytes, endothelial cells and macrophages exchange EVs in the adult heart and that ischaemic injury models dynamically alter EV production.ConclusionsWe have developed a powerful in vivo zebrafish model for the investigation of endogenous EVs in all aspects of cardiovascular biology and pathology. A cell membrane fluorophore labelling approach allows cell type-specific tracing of EV origin without bias towards the expression of individual protein markers and will allow detailed future examination of their function.

Altered ADAMTS-13 Expression in Human Umbilical Vein Endothelial Cells.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2709-2709
Author(s):  
Stephen J. Kling ◽  
Cambria A. Judd ◽  
Keith Warner ◽  
George M. Rodgers
Keyword(s):  
Endothelial Cells ◽  
Vascular Injury ◽  
Hepatic Stellate Cells ◽  
Time Course ◽  
Umbilical Vein ◽  
Stellate Cells ◽  
Cell Types ◽  
Cellular Protein ◽  
Intense Staining ◽  
Human Umbilical Vein

Abstract von Willebrand factor (vWF), as secreted by endothelial cells (ECs), is a highly thrombogenic, ultra-large multimeric protein which promotes platelet adhesion and clot formation. This ultra-large vWF would lead to platelet aggregation even without vascular injury if not for the activity of a plasma vWF-cleaving protease, ADAMTS-13, which cleaves the ultra-large vWF multimers upon secretion into the more moderately-sized, less thrombogenic multimers commonly found circulating in normal plasma. The production of ADAMTS-13 was first described in hepatic stellate cells, but has since been found to be produced in a variety of tissues and cell types including ECs. Production of ADAMTS-13 by ECs is of interest as the newly secreted ultra-large vWF is immediately cleaved on the surface of ECs by ADAMTS-13. Quiescent ECs normally exist as a confluent non-thrombogenic monolayer lining the lumen of the vasculature. Damage to the EC monolayer results in cell activation, stimulating not only thrombosis but proliferation as the ECs attempt to prevent blood loss and repair vascular wall damage. To assess the production of ADAMTS-13 by human umbilical vein ECs, as measured by a commercially-available ELISA (American Diagnostica Inc., Stamford, CT), cellular supernatants were collected and cellular proteins extracted from either confluent ECs (EC monolayers), damaged confluent ECs (EC monolayers which had narrow strips of cells removed with a sterile pipette tip), or subconfluent ECs (50% confluence). After four hours, supernatants from subconfluent ECs contained 2.5X as much ADAMTS-13 (161.5±29.1 pg/ml/μg cellular protein; p<0.002) as compared with either confluent or damaged confluent ECs (60.2±22.5 and 56.0±19.2 pg/ml/μg cellular protein, respectively). Similarly, cell lysates from subconfluent ECs contained ∼2.5X as much ADAMTS-13 (645.1±73.1 pg/ml/μg cellular protein; p<0.002) as compared with either confluent or damaged confluent ECs (257.8±32.8 and 311.3±29.3 pg/ml/μg cellular protein, respectively). In time-course experiments, confluent, damaged confluent, and subconfluent ECs were fixed 4, 24, 48, 72, or 96 hours following injury (producing the damaged confluent ECs). ADAMTS-13 expression was subsequently detected by immunohistochemistry using a rabbit polyclonal anti-human ADAMTS-13 antibody directed against the metalloproteinase domain (Abcam Inc., Cambridge, MA) and a fluorescent secondary antibody. Subconfluent ECs expressed more intense staining for ADAMTS-13 throughout the time course when compared with the confluent ECs. By 72 hours, the damaged confluent ECs began expressing comparable intense staining, particularly in regions where the ECs were reestablishing the monolayer. Previous work has suggested that the hepatic stellate cells, as well as the other cell types which express ADAMTS-13, produce this protease constitutively and that this production is not otherwise regulated. The data presented herein demonstrate that ADAMTS-13 production, at least in ECs, is affected by the growth state of the ECs. This enhanced production of ADAMTS-13 may limit the extent of platelet thrombosis at sites of vascular injury.

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