RNA-seq Transcriptome Analysis of Chronic Injured Lung Epithelial Cells Reveals Similar Features of IPF Lung Epithelium

Cellular senescence is a biological process by which cells lose their capacity to proliferate yet remain metabolically active. Although originally considered a protective mechanism to limit the formation of cancer, it is now appreciated that cellular senescence also contributes to the development of disease, including common respiratory ailments such as chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. While many factors have been linked to the development of cellular senescence, mitochondrial dysfunction has emerged as an important causative factor. In this study, we uncovered that the mitochondrial biogenesis pathway driven by the mammalian target of rapamycin/peroxisome proliferator-activated receptor-γ complex 1α/β (mTOR/PGC-1α/β) axis is markedly upregulated in senescent lung epithelial cells. Using two different models, we show that activation of this pathway is associated with other features characteristic of enhanced mitochondrial biogenesis, including elevated number of mitochondrion per cell, increased oxidative phosphorylation, and augmented mitochondrial reactive oxygen species (ROS) production. Furthermore, we found that pharmacological inhibition of the mTORC1 complex with rapamycin not only restored mitochondrial homeostasis but also reduced cellular senescence to bleomycin in lung epithelial cells. Likewise, mitochondrial-specific antioxidant therapy also effectively inhibited mTORC1 activation in these cells while concomitantly reducing mitochondrial biogenesis and cellular senescence. In summary, this study provides a mechanistic link between mitochondrial biogenesis and cellular senescence in lung epithelium and suggests that strategies aimed at blocking the mTORC1/PGC-1α/β axis or reducing ROS-induced molecular damage could be effective in the treatment of senescence-associated lung diseases.

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Time-resolved dual RNA-Seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection

10.1101/048959 ◽

2016 ◽

Author(s):

Rieza Aprianto ◽

Jelle Slager ◽

Siger Holsappel ◽

Jan-Willem Veening

Keyword(s):

Epithelial Cells ◽

Pneumococcal Infection ◽

Alveolar Epithelial Cells ◽

Lung Epithelial Cells ◽

Infection Model ◽

Rna Seq ◽

Time Resolved ◽

Alveolar Epithelial ◽

Lung Epithelial ◽

Host Microbe Interactions

AbstractStreptococcus pneumoniae(pneumococcus) is the main etiological agent of pneumonia. Pneumococcal pneumonia is initiated by bacterial adherence to lung epithelial cells. Infection to the epithelium is a disruptive interspecies interaction involving numerous transcription-mediated processes. Revealing transcriptional changes may provide valuable insights into pneumococcal disease. Dual RNA-Seq allows simultaneous monitoring of the transcriptomes of both host and pathogen. Here, we developed a time-resolved infection model of human lung alveolar epithelial cells byS. pneumoniaeand assessed transcriptome changes by dual RNA-Seq. Our data provide new insights into host-microbe interactions and show that the epithelial glutathione-detoxification pathway is activated by bacterial presence. We observed that adherent pneumococci, not free-floating bacteria, access host-associated carbohydrates and repress innate immune responses. In conclusion, we provide a dynamic dual-transcriptomics overview of early pneumococcal infection with easy online access (http://dualrnaseq.molgenrug.nl). Further database exploration may expand our understanding of epithelial-pneumococcal interaction, leading to novel antimicrobial strategies.Graphical Abstract

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Lung epithelial cells interact with immune cells and bacteria to shape the microenvironment in tuberculosis

Thorax ◽

10.1136/thoraxjnl-2021-217997 ◽

2022 ◽

pp. thoraxjnl-2021-217997

Author(s):

Amy M de Waal ◽

Pieter S Hiemstra ◽

Tom HM Ottenhoff ◽

Simone A Joosten ◽

Anne M van der Does

Keyword(s):

Epithelial Cells ◽

Immune Cells ◽

Lung Epithelial Cells ◽

Lung Epithelium ◽

Adaptive Immune ◽

Adaptive Immune Cells ◽

Essential Components ◽

Lung Epithelial ◽

Sense And Respond ◽

Tuberculosis Disease

The lung epithelium has long been overlooked as a key player in tuberculosis disease. In addition to acting as a direct barrier to Mycobacterium tuberculosis (Mtb), epithelial cells (EC) of the airways and alveoli act as first responders during Mtb infections; they directly sense and respond to Mtb by producing mediators such as cytokines, chemokines and antimicrobials. Interactions of EC with innate and adaptive immune cells further shape the immune response against Mtb. These three essential components, epithelium, immune cells and Mtb, are rarely studied in conjunction, owing in part to difficulties in coculturing them. Recent advances in cell culture technologies offer the opportunity to model the lung microenvironment more closely. Herein, we discuss the interplay between lung EC, immune cells and Mtb and argue that modelling these interactions is of key importance to unravel early events during Mtb infection.

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Mesenchymal maintenance of distal epithelial cell phenotype during late fetal lung development

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00221.2006 ◽

2007 ◽

Vol 292 (3) ◽

pp. L725-L741 ◽

Cited By ~ 22

Author(s):

Julie Deimling ◽

Kate Thompson ◽

Irene Tseu ◽

Jinxia Wang ◽

Richard Keijzer ◽

...

Keyword(s):

Epithelial Cells ◽

Notch Pathway ◽

Secretory Protein ◽

Lung Epithelial Cells ◽

Clara Cell ◽

Cell Phenotype ◽

Lung Epithelium ◽

Morphological Pattern ◽

Lung Epithelial ◽

Distal Lung

Classical tissue recombination experiments have reported that at early gestation both tracheal and distal lung epithelium have the plasticity to respond to mesenchymal signals. Herein we examined the role of epithelial-mesenchymal interactions in maintaining epithelial differentiation at late (E19–E21, term = 22 days) fetal gestation in the rat. Isolated distal lung epithelial cells were recombined with mesenchymal cells from lung, skin, and intestine, and the homotypic or heterotypic recombinant cell aggregates were cultured for up to 5 days. Recombining lung epithelial cells with mesenchyme from various sources induced a morphological pattern that was specific to the type of inducing mesenchyme. In situ analysis of surfactant protein (SP)-C, SP-B, and Clara cell secretory protein (CCSP) expression, as well as SP-C and CCSP promoter transactivation experiments, revealed that distal lung epithelium requires lung mesenchyme to maintain the alveolar, but not bronchiolar, phenotype. Incubation of lung recombinants with an anti-FGF7 antibody resulted in a partial inhibition of mesenchyme-induced SP-C promoter transactivation. Immunoreactivity for Delta and Lunatic fringe, components of the Notch pathway that regulates cell differentiation, was downregulated in the heterotypic recombinants. In contrast, Hes1 mRNA expression was increased in these recombinants. Cumulatively, these results suggest that at late fetal gestation, distal lung epithelial cells are not fully committed to a specific phenotype and still have the plasticity to respond to various signals. Their alveolar phenotype is likely maintained by Notch/Notch ligand interactions and mesenchymal factors, including FGF7.

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Profiling of the silica-induced molecular events in lung epithelial cells using the RNA-Seq approach

Journal of Applied Toxicology ◽

10.1002/jat.3471 ◽

2017 ◽

Vol 37 (10) ◽

pp. 1162-1173 ◽

Cited By ~ 6

Author(s):

Judy Y. W. Chan ◽

Joseph C. C. Tsui ◽

Patrick T. W. Law ◽

Winnie K. W. So ◽

Doris Y. P. Leung ◽

...

Keyword(s):

Epithelial Cells ◽

Lung Epithelial Cells ◽

Rna Seq ◽

Molecular Events ◽

Lung Epithelial

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Transcriptome Profiles of Human Lung Epithelial Cells A549 Interacting with Aspergillus fumigatus by RNA-Seq

PLoS ONE ◽

10.1371/journal.pone.0135720 ◽

2015 ◽

Vol 10 (8) ◽

pp. e0135720 ◽

Cited By ~ 28

Author(s):

Fangyan Chen ◽

Changjian Zhang ◽

Xiaodong Jia ◽

Shuo Wang ◽

Jing Wang ◽

...

Keyword(s):

Epithelial Cells ◽

Aspergillus Fumigatus ◽

Human Lung ◽

Lung Epithelial Cells ◽

Rna Seq ◽

Lung Epithelial ◽

Human Lung Epithelial Cells

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Induction of Fibrinogen Expression in the Lung Epithelium during Pneumocystis carinii Pneumonia

Infection and Immunity ◽

10.1128/iai.66.9.4431-4439.1998 ◽

1998 ◽

Vol 66 (9) ◽

pp. 4431-4439 ◽

Cited By ~ 39

Author(s):

Patricia J. Simpson-Haidaris ◽

Mary-Anne Courtney ◽

Terry W. Wright ◽

Rachel Goss ◽

Allen Harmsen ◽

...

Keyword(s):

Epithelial Cells ◽

Immunoelectron Microscopy ◽

Pneumocystis Carinii ◽

The Body ◽

Alveolar Epithelial Cells ◽

Lung Epithelial Cells ◽

Northern Hybridization ◽

Lung Epithelium ◽

Lung Epithelial

ABSTRACT Pneumocystis carinii is an important pulmonary pathogen responsible for morbidity and mortality in patients with AIDS. The acute-phase response (APR), the primary mechanism used by the body to restore homeostasis following infection, is characterized by increased levels of circulating fibrinogen (FBG). Although the liver is the primary site of increased FBG synthesis during the APR, we unexpectedly discovered that FBG is synthesized and secreted by lung alveolar epithelial cells in vitro during an inflammatory stimulus. Therefore, we sought to determine whether lung epithelial cells produce FBG in vivo using animal models of P. cariniipneumonia (PCP). Inflammation was noted by an influx of macrophages to P. carinii-infected alveoli. Northern hybridization revealed that γ-FBG mRNA increased two- to fivefold in P. carinii-infected lung tissue, while RNA in situ hybridization demonstrated increased levels of γ-FBG mRNA in the lung epithelium. Immunoelectron microscopy detected lung epithelial cell-specific production of FBG, suggesting induction of a localized inflammatory response resembling the APR. A systemic APR was confirmed by a two- to fivefold upregulation of the levels of hepatic γ-FBG mRNA in animals with PCP, resulting in a corresponding increase in levels of FBG in plasma. Furthermore, immunoelectron microscopy revealed the presence of FBG at the junction of cell membranes of trophic forms of P. carinii organisms aggregated along the alveolar epithelium. These results implicate FBG in the pathogenesis of PCP in a manner similar to that of the adhesive glycoproteins fibronectin and vitronectin, which are known to participate in intra-alveolar aggregation of organisms and adherence ofP. carinii to the lung epithelium.

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Role of β-catenin-regulated CCN matricellular proteins in epithelial repair after inflammatory lung injury

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00180.2012 ◽

2013 ◽

Vol 304 (6) ◽

pp. L415-L427 ◽

Cited By ~ 40

Author(s):

Rachel L. Zemans ◽

Jazalle McClendon ◽

Yael Aschner ◽

Natalie Briones ◽

Scott K. Young ◽

...

Keyword(s):

Epithelial Cells ◽

Target Genes ◽

Lung Epithelial Cells ◽

Human Neutrophils ◽

Albumin Concentration ◽

Lung Epithelium ◽

Inflammatory Injury ◽

Epithelial Repair ◽

Lung Epithelial

Repair of the lung epithelium after injury is integral to the pathogenesis and outcomes of diverse inflammatory lung diseases. We previously reported that β-catenin signaling promotes epithelial repair after inflammatory injury, but the β-catenin target genes that mediate this effect are unknown. Herein, we examined which β-catenin transcriptional coactivators and target genes promote epithelial repair after inflammatory injury. Transmigration of human neutrophils across cultured monolayers of human lung epithelial cells resulted in a fall in transepithelial resistance and the formation of discrete areas of epithelial denudation (“microinjury”), which repaired via cell spreading by 96 h. In mice treated with intratracheal (i.t.) LPS or keratinocyte chemokine, neutrophil emigration was associated with increased permeability of the lung epithelium, as determined by increased bronchoalveolar lavage (BAL) fluid albumin concentration, which decreased over 3–6 days. Activation of β-catenin/p300-dependent gene expression using the compound ICG-001 accelerated epithelial repair in vitro and in murine models. Neutrophil transmigration induced epithelial expression of the β-catenin/p300 target genes Wnt-induced secreted protein (WISP) 1 and cysteine-rich (Cyr) 61, as determined by real-time PCR (qPCR) and immunostaining. Purified neutrophil elastase induced WISP1 upregulation in lung epithelial cells, as determined by qPCR. WISP1 expression increased in murine lungs after i.t. LPS, as determined by ELISA of the BAL fluid and qPCR of whole lung extracts. Finally, recombinant WISP1 and Cyr61 accelerated repair, and Cyr61-neutralizing antibodies delayed repair of the injured epithelium in vitro. We conclude that β-catenin/p300-dependent expression of WISP1 and Cyr61 is critical for epithelial repair and represents a potential therapeutic target to promote epithelial repair after inflammatory injury.

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Differential effects of the Akt pathway on the internalization of Klebsiella by lung epithelium and macrophages

Innate Immunity ◽

10.1177/1753425920942582 ◽

2020 ◽

Vol 26 (7) ◽

pp. 618-626

Author(s):

De Chang ◽

Jingjing Feng ◽

Hongbo Liu ◽

Wei Liu ◽

Lokesh Sharma ◽

...

Keyword(s):

Epithelial Cells ◽

Bacterial Infection ◽

Cell Types ◽

Lung Epithelial Cells ◽

Akt Pathway ◽

Lung Epithelium ◽

Akt Inhibitor ◽

Phagocytic Ability ◽

Relative Contribution ◽

Lung Epithelial

Host response to lung infection includes coordinated efforts of multiple cell types, including the lung epithelium and macrophages. Importantly, both the lung epithelium and macrophages can internalize and clear invading pathogens. However, the mechanisms and their ability to internalize or phagocytose differ. Akt is a key cellular pathway that controls cell proliferation and survival, in addition to its role in host defense. The role of the Akt pathway was assessed using pharmacological Akt modulators in lung epithelial (A549) and macrophage (RAW 264.7) cell lines during Klebsiella bacterial infection. Our data show that the inhibition of the Akt pathway using specific Akt inhibitor MK2206 increased the phagocytic ability of lung epithelial cells but not of macrophages. In contrast, the activation of Akt using specific activator SC-79 decreased the phagocytic ability of epithelial cells, while it increased the phagocytic ability of macrophages. The altered phagocytic ability in both cell types using Akt modulators was not due to changes in bacterial adhesion to the host cell. The clinical usefulness of these Akt modulators may vary based on the type of infection and on the relative contribution of epithelial cells and macrophages in clearing the particular bacterial infection. The Akt pathway has differential roles in the internalization of Klebsiella bacteria by respiratory epithelial cells and immune cells.

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Gene therapy-emulating small molecule treatments in cystic fibrosis airway epithelial cells and patients

Respiratory Research ◽

10.1186/s12931-019-1214-8 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Q. Yang ◽

A. R. Soltis ◽

G. Sukumar ◽

X. Zhang ◽

H. Caohuy ◽

...

Keyword(s):

Gene Expression ◽

Cystic Fibrosis ◽

Gene Therapy ◽

Epithelial Cells ◽

Small Molecule ◽

Gene Signature ◽

Lung Epithelial Cells ◽

Rna Seq ◽

Transcriptional Responses ◽

Lung Epithelial

Abstract Background Several small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy. Methods IB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared in vitro gene expression signatures with in vivo data from biopsied nasal epithelial cells from digitoxin-treated CF patients. Results CF cells exposed to digitoxin exhibited significant suppression of both TNFα/NFκB signaling and downstream secretion of IL-8, IL-6 and GM-CSF, with or without co-treatment with VX drugs. No evidence of drug-drug interference was observed. RNA-seq analysis showed that gene therapy-treated CF lung cells induced changes in 3134 genes. Among these, 32.6% were altered by digitoxin treatment in the same direction. Shared functional gene ontology themes for genes suppressed by both digitoxin and gene therapy included inflammation (84 gene signature), and cell-cell interactions and fibrosis (49 gene signature), while genes elevated by both were enriched for epithelial differentiation (82 gene signature). A new analysis of mRNA data from digitoxin-treated CF patients showed consistent trends in expression for genes in these signatures. Conclusions Adjuvant gene therapy-emulating activities of digitoxin may contribute to enhancing the efficacy of currently licensed correctors and potentiators in CF patients.

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