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Global transcriptomic changes in alveolar epithelial type II (ATII) cells upon GRK6 depletion based on RNA-seq

ABSTRACT: G protein coupled receptor kinase 6 (GRK6) is a member of the GRKs family, which is expressed in various tissues and involved in the development of several diseases, including lung adenocarcinoma. Our previous study suggested that GRK6 expression was significantly down-regulated in lung adenocarcinoma patients, and its level was an independent prognostic factor for overall survival. Here, by performing RNA-sequencing (RNA-seq) in alveolar epithelial type II (ATII) cells transfected with either short interfering RNA (siRNA) oligos against GRK6 or control siRNAs, several disease related alterations were identified.

ORGANISM(S): Homo sapiens

PROVIDER: GSE164921 | GEO | 2021/04/24

REPOSITORIES: GEO

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LKB1 inhibition in alveolar epithelial cells induces fibroblast activation in pulmonary fibrosis [RNA-seq in 2D-cultured ATII]

Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, and lethal lung disease. The initiation of IPF involves microinjuries to and/or dysfunction of the alveolar epithelium, but factors that determine fibrosis progression or normal tissue repair are largely unknown. We previously demonstrated that autophagy inhibition-mediated epithelial-mesenchymal transition (EMT) in human alveolar epithelial type II (ATII) cells augments local myofibroblast differentiation in pulmonary fibrosis by paracrine signalling. Here, we report that liver kinase B1 (LKB1) inactivation in ATII cells induces autophagy inhibition and EMT as a consequence. In IPF lungs, this is caused by a downregulation of CAB39L, a key subunit within the LKB1 complex. 3D co-cultures of ATII cells and lung fibroblast MRC5 coupled with RNA sequencing (RNA-seq) confirmed that paracrine signalling between LKB1-depleted ATII cells and fibroblasts augmented myofibroblast differentiation. Together these data suggest that reduced autophagy caused by LKB1 inhibition can induce EMT in ATII cells and contribute to fibrosis via aberrant epithelial–fibroblast crosstalk.

2023-08-09 | GSE205969 | GEO

LKB1 inhibition in alveolar epithelial cells induces fibroblast activation in pulmonary fibrosis [RNA-seq in 3D co-cultured ATII+MRC5]

2023-08-09 | GSE205965 | GEO

Exogenous BAPN administration does not regulate gene expression in primary murine lung fibroblasts and alveolar epithelial type II (ATII) cells.

Project description:Primary murine lung fibroblasts or ATII cells were either treated with vehicle or 1mM BAPN for 24 h. Overall, only one change in gene expression was found in the corrected p values in fibroblasts group in this microarray study.

2016-10-25 | GSE89119 | GEO

Transcriptome in alveolar epithelial type II-like cells differentiated from human lung progenitor cells

Project description:Resident stem/progenitor cells in lungs are important for tissue homeostasis and repair. We isolated human lung progenitor cells and named alveolar epithelial progenitor cells (AEPCs)(Fujino N, et al. 2011. Lab Invest. 91:363). AEPCs have phenotypes of both alveolar epithelial type II (ATII) cells and mesenchymal stem cells. AEPCs had the potential to generate ATII-like cells in vitro. ATII-like cells derived from AEPCs expressed protein and mRNA of pulmonary surfactant, and displayed lamellar bodies containing the surfactants. However, it has not been evaluated whether global gene expression of the ATII-like cells from AEPCs was similar to that of mature ATII cells isolated from human lung tissues. This study demonstrated gene expression profiles of ATII-like cells from AEPCs. In addition, transcriptomes in AEPCs and mature ATII cells were deposited in the GEO website (GSE21095 and GSE29133, respectively). We isolated AEPCs from tissue samples obtained from patients who underwent lung resection at Department of Thoracic Surgery, Tohoku University Hospital. We induced differentiation of AEPCs to ATII-like cells on extracellular matrix with medium containing KGF, cAMP and IBMX, as previously described (Fujino N, et al. 2011. Lab Invest. 91:363). We profiled the gene expression in three different batches of the ATII-like cells. We extracted total RNA from the differentiated cells. This study was approved by the Ethics Committee at Tohoku University School of Medicine. All subjects gave informed consent.

2012-10-11 | E-GEOD-33825 | biostudies-arrayexpress

RNA quantitative sequencing in bleomycin-treated p300 knockout primary ATII cells

Project description:p300 was knockout in ATII cells of murine lung, and then treated with 4mg/kg bleomycin for 2 weeks.

2023-09-06 | GSE190157 | GEO

Long Term Culture of the A549 Cell Line Promotes Differentiation Towards an Alveolar Type II (ATII) Phenotype; Comparison of A549 cells with Primary ATII Cells

Project description:Pulmonary research requires models that represent the physiology of alveolar epithelium but concerns with reproducibility, consistency and the technical and ethical challenges of using primary or stem cells has resulted in widespread use of continuous cancer or other immortalized cell lines. The A549 ‘alveolar’ cell line has been available for over four decades but there is an inconsistent view as to its suitability as an appropriate model for primary alveolar type II (ATII) cells. Since most work with A549 cells involves short term culture of proliferating cells, we postulated that culture conditions that reduced proliferation of the cancer cells would promote a more differentiated ATII cell phenotype. We examined A549 cell growth in different media over long term culture and then used microarray analysis to investigate temporal regulation of pathways involved in cell cycle and ATII differentiation; we also made comparisons with gene expression in freshly isolated human ATII cells. Analyses indicated that long term culture in Ham’s F12 resulted in substantial modulation of cell cycle genes to result in a quiescent population of cells with significant up-regulation of autophagic, differentiation and lipidogenic pathways. There were also increased numbers of up- and down-regulated genes shared with primary cells suggesting adoption of ATII characteristics and multilamellar body (MLB) development. Subsequent Oil Red-O staining and Transmission Electron Microscopy confirmed MLB expression in the differentiated A549 cells. This work defines a set of conditions for promoting ATII differentiation characteristics in A549 cells that may be advantageous for studies with this cell line.

2016-10-19 | GSE88880 | GEO

Global transcriptomic changes in human lung fibroblasts MRC5 exposed to conditioned media from RAS-activated alveolar epithelial type II (ATII) cells based on RNA-seq.

Project description:IPF (idiopathic pulmonary fibrosis), a progressive lung disease with an unmet need for treatment, causes increased morbidity and mortality worldwide. Abnormal wound healing is strongly implicated in IPF, but the underlying mechanisms remain poorly understood. Here we reported that aberrant epithelial-mesenchymal crosstalk provides self-sustaining pro-fibrotic signals in IPF. By performing RNA-sequencing (RNA-seq) in human lung fibroblasts MRC5 treated with either conditioned media (CM) from control or 4-OHT (4-hydroxytamoxifen) - treated ATIIER:KRASV12 cells (kindly provided by Prof Julian Downward, The Francis Crick Institute, UK), in which addition of 4-OHT acutely activates RAS pathway (Yao et al. Cell Death & Differentiation 2019), we identify several IPF-related pathological alterations. These include increases in GO terms related to extracellular matrix (ECM) and collagen, cell migration, and inflammatory response. Our data suggest that RAS-activated ATII cells crosstalk to MRC5 lung fibroblasts to augment their activation and migration.

2021-08-09 | GSE163908 | GEO

Long Term Culture of the A549 Cell Line Promotes Differentiation Towards an Alveolar Type II (ATII) Phenotype; A549 Time course.

2016-10-19 | GSE88879 | GEO

Gene expression in ATII cells transduced with adenovirus expressing constitutively active mutant HIF1a

Project description:To determine HIF1a target genes in ATII cells, we transduced freshly isolated rat ATII cells with an adenoviral vector expressing either GFP or a constitutively active mutant HIF1a construct. After 24 hours, RNA was extracted and subjected to microarray.

2017-05-01 | GSE87555 | GEO

Transcriptome in alveolar epithelial type II-like cells differentiated from human lung progenitor cells

2012-10-11 | GSE33825 | GEO

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