Gene expression profiling of sorted primary human bronchial epithelial cell populations
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE263356 | GEO | 2024/06/26
REPOSITORIES: GEO
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Project description:Influenza viruses pose a significant burden on global human health. Influenza has a broad cellular tropism in the airway, but how infection of different epithelial cell types impacts replication kinetics and burden in the airways is not fully understood. Using primary human airway cultures, which recapitulate the diverse epithelial cell landscape of the human airways, we investigated the impact of cell type composition on virus tropism and replication kinetics. Cultures were highly diverse across multiple donors and 30 independent differentiation conditions and supported a range of influenza replication. Although many cell types were susceptible to influenza, ciliated and secretory cells were predominantly infected. Despite the strong tropism preference for secretory and ciliated cells, which consistently make up 75% or more of infected cells, only ciliated cells were associated with increased virus production. Surprisingly, infected secretory cells were associated with overall reduced virus output. These data highlight the heterogeneous outcomes of influenza virus infections in primary human airway cultures and the disparate impacts of infected cell identity on burst size, even among preferentially infected cell types.
2024-06-25 | GSE247979 | GEO
Project description:The epithelium of the pulmonary airway is specially differentiated to provide defense against environmental insults, but also subject to dysregulated differentiation that results in lung disease. The current paradigm for airway epithelial differentiation is a one-step program whereby a p63+ basal epithelial progenitor cell generates a ciliated or secretory cell lineage, but the cue for this transition and whether there are intermediate steps is poorly defined. Here we identify transcription factor Myb as a key regulator that permits early multilineage differentiation of airway epithelial cells. Myb+ cells were identified as p63– and therefore distinct from basal progenitor cells, but were still negative for markers of differentiation. Myb RNAi treatment of primary-culture airway epithelial cells and Myb gene deletion in mice resulted in a p63– population with failed maturation of Foxj1+ ciliated cells, as well as Scbg1a1+ and Muc5ac+ secretory cells. Consistent with these findings, analysis of whole genome expression of Myb-deficient cells identified Myb-dependent programs for ciliated and secretory cell differentiation. Myb+ cells were rare in human airways but were increased in regions of ciliated cells and mucous cell hyperplasia in samples from subjects with chronic obstructive pulmonary disease. Together, the results show that a p63– Myb+ population of airway epithelial cells represents a distinct intermediate stage of differentiation that is required under normal conditions and may be heightened in airway disease. 12 samples, 2x2 factorial design, factor 1: time (days post-ALI), factor 2:shRNA (Myb vs Scrambled Control), performed in triplicate (biological replicates)
2014-08-12 | E-GEOD-60365 | biostudies-arrayexpress
Project description:Exosomes are extracellular vesicles secreted by cells that have an important biological function in intercellular communication by transferring biologically active proteins, lipids, and RNAs to neighbouring or distant cells. While a role for exosomes in antimicrobial defence has recently emerged, currently very little is known regarding the nature and functional relevance of exosomes generated in vivo, particularly during an active viral infection. Here, we characterised exosomes released into the airways during influenza virus infection. We show that these vesicles dynamically change in protein composition over the course of infection, increasing expression of host proteins with known anti-influenza activity, and viral proteins with the potential to trigger host immune responses. We show that exosomes released into the airways during influenza virus infection trigger pulmonary inflammation and carry viral antigen that can be utilized by antigen presenting cells to drive the induction of a cellular immune response. Moreover, we show that attachment factors for influenza virus, namely α2,3 and α2,6-linked sialic acids, are present on the surface of airway exosomes and these vesicles have the ability to neutralize influenza virus, thereby preventing the virus from binding and entering target cells. These data reveal a novel role for airway exosomes in the antiviral innate immune defence against influenza virus infection.
2020-06-03 | PXD018389 | Pride
Project description:The epithelium of the pulmonary airway is specially differentiated to provide defense against environmental insults, but also subject to dysregulated differentiation that results in lung disease. The current paradigm for airway epithelial differentiation is a one-step program whereby a p63+ basal epithelial progenitor cell generates a ciliated or secretory cell lineage, but the cue for this transition and whether there are intermediate steps is poorly defined. Here we identify transcription factor Myb as a key regulator that permits early multilineage differentiation of airway epithelial cells. Myb+ cells were identified as p63– and therefore distinct from basal progenitor cells, but were still negative for markers of differentiation. Myb RNAi treatment of primary-culture airway epithelial cells and Myb gene deletion in mice resulted in a p63– population with failed maturation of Foxj1+ ciliated cells, as well as Scbg1a1+ and Muc5ac+ secretory cells. Consistent with these findings, analysis of whole genome expression of Myb-deficient cells identified Myb-dependent programs for ciliated and secretory cell differentiation. Myb+ cells were rare in human airways but were increased in regions of ciliated cells and mucous cell hyperplasia in samples from subjects with chronic obstructive pulmonary disease. Together, the results show that a p63– Myb+ population of airway epithelial cells represents a distinct intermediate stage of differentiation that is required under normal conditions and may be heightened in airway disease.
2014-08-12 | GSE60365 | GEO
Project description:Influenza A virus has a broad cellular tropism in the respiratory tract. Infected epithelial cells sense the infection and initiate an antiviral response. To define the antiviral response at the earliest stages of infection we used two different single cycle replication reporter viruses. These tools demonstrated heterogeneity in virus replication levels in vivo. Transcriptional profiling demonstrated tiers of interferon stimulated gene responses that were dependent on the magnitude of virus replication. Uninfected cells and cells with blunted replication expressed a distinct and potentially protective ISG signature. Finally, we used these single cycle reporter viruses to determine the antiviral landscape during virus spread, which unveiled disparate protection mediated by IFN. Together these results highlight the complexity of virus-host interactions within the infected lung and suggest that magnitude and round of replication tune the antiviral response.
2018-09-20 | GSE112794 | GEO
Project description:Influenza B virus (IBV) is an acute respiratory pathogen that induces phenotypic alterations to the lung epithelium, such as the denudation of the respiratory cilium, during and after IBV infection. It has been assumed that these epithelial changes are non-adaptive, and simply the result of cellular death following lytic virus infection. However, previous reports have shown that not all infected cells are killed after viral infection; some cells can completely clear viral RNA and protein and persist in the host long-term. In this study, we utilized a novel recombinant virus in combination with a Cre recombinase-responsive transgenic mouse model to demonstrate that IBV infection leads to the formation of a population of survivor ciliated cells in the proximal airways of infected mice. We then performed transcriptional profiling on infected and surviving ciliated cell populations to determine how surviving viral infection affected these cells. To specifically profile ciliated cells, we digested mouse lungs and sorted cells based on their expression of CD24 with tdTomato as a marker of infection. We sorted cell populations from the lungs of animals mock infected with PBS (Mock), during active infection (2 DPI), and matched ciliated cell populations at 14 days post-infection that had either experienced direct viral infection (14 DPI Survivor Cell) or those that had never been infected (14 DPI). The resulting data indicate that after surviving infection and clearing the virus, survivor ciliated cells undergo significant transcriptional reprogramming.
2019-02-04 | GSE115952 | GEO
Project description:Influenza B virus (IBV) is an acute respiratory pathogen that induces phenotypic alterations to the lung epithelium, such as the denudation of the respiratory cilium, during and after IBV infection. It has been assumed that these epithelial changes are non-adaptive, and simply the result of cellular death following lytic virus infection. However, previous reports have shown that not all infected cells are killed after viral infection; some cells can completely clear viral RNA and protein and persist in the host long-term. In this study, we utilized a novel recombinant virus in combination with a Cre recombinase-responsive transgenic mouse model to demonstrate that IBV infection leads to the formation of a population of survivor ciliated cells in the proximal airways of infected mice. To ensure that we were studying ciliated cells with markers that were maintained during viral infection in vivo, we performed single-cell transcriptional profiling on infected and surviving ciliated cell populations. We digested mouse lungs and sorted cells using tdTomato as a marker of infection. We sorted cell populations from the lungs of animals mock infected with PBS (Mock) and during active infection (2 DPI). The resulting data revealed that the marker CD24 is consistently expressed on ciliated cells before and during viral infection.
2018-12-05 | GSE116031 | GEO
Project description:Airway basal cells (BC) function as progenitor cells capable of differentiating into ciliated and secretory cells to replenish the airway epithelium during physiological turnover and repair. The objective of this study was to define the role of Notch signaling in regulating human airway BC differentiation into a pseudostratified mucociliated epithelium. Notch inhibition with γ-secretase inhibitors demonstrated Notch activation is essential for BC differentiation into secre-tory cells and ciliated cells, but more so for the secretory lineage. Sustained Notch activation via lentivirus expression of the intracellular domain of each Notch receptor (NICD1-4) demonstrated that the Notch 2 and 4 pathways have little effect on BC differentiation, while activation of the Notch1 or 3 pathways has a major influence, with persistent expression of NICD1 or 3 resulting in a skewing toward secretory cell differentiation with a parallel decrease in ciliated cell differentiation. These observations provide insights into the control of the balance of BC differentiation into the secretory vs ciliated cell lineage, a balance that is critical for maintaining the normal function of the airway epithelium in barrier defense against the inhaled environment. Array-based expression profiling of the Notch signaling pathway genes specifically in human airway basal cells.
2015-04-13 | E-GEOD-53537 | biostudies-arrayexpress
Project description:Functional properties of mucosal surfaces are dependent on establishing the correct proportions of specialized epithelial cell types. In the mammalian airway, the proportions of ciliated and secretory cells types are tightly regulated to ensure efficient mucociliary clearance. Ciliated cells are one of the first mature cell types to be specified by differentiation of multipotent endodermal progenitors of the developing lung and can be replaced postnatally by differentiation of secretory progenitors. In each case, cell cycle exit is a necessary, early step that precedes differentiation. However, the relationship between cell cycle exit and cell fate determination is poorly understood. We show that the serine-threonine kinase Stk11 controls the cell cycle exit in airway stem/progenitor cells via phosphorylation and activation of the AMPK-related kinase Mark3, which directly suppresses Erk1/2 mediated Rb inactivation. Our study demonstrates that Stk11-dependent cell cycle exit accounts for the normal program of ciliated cell differentiation in developing and postnatal airways.
2018-07-06 | GSE116690 | GEO
Project description:BACKGROUND: The type 2 cytokine-high asthma endotype (T2H) is characterized by IL-13-driven mucus obstruction of the airways. To investigate this poorly understood pathobiology, we characterized IL-13 effects on human airway epithelial cultures using single cell RNA-sequencing, finding that IL-13 generated a novel transcriptional state for each cell type. Specifically, we discovered a mucus secretory program induced by IL-13 in all cell types which converted both mucus and defense secretory cells into a metaplastic state with emergent mucin production and secretion, while leading to ER stress and cell death in ciliated cells. The IL-13-remodeled epithelium secreted a pathologic, mucin-imbalanced, and innate immunity-depleted proteome that arrested mucociliary motion. Signatures of IL-13-induced cellular remodeling were mirrored by transcriptional signatures characteristic of the nasal airway epithelium within T2H versus T2-low asthmatic children. Our results reveal the epithelium-wide scope of T2H asthma and present novel therapeutic targets for restoring normal epithelial function.
2020-07-13 | GSE145013 | GEO