Candidate Genes as Biomarkers in Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome Based on mRNA Expression Profile by Next-Generation RNA-Seq Analysis

Wan, Qiquan; Wu, Di; Ye, Qifa

doi:10.1155/2018/4384797

Cited by 6 publications

(6 citation statements)

References 63 publications

(48 reference statements)

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“…It is interesting that, Na, K-ATPase β1 promotes the expression of key proteins such as ZO-1, ZO-2, occludin and claudin-18 in tight junction complex and reduces the production of lung water [ 21 ]. In our study, the level of ZO-1 mRNA in lung tissue of ARDS rats induced by LPS was significantly lower than that in control group [ 22 ]. Accordingly, we speculate that increasing the level of Na, K-ATPase α1/β1 may enhance the tight junction of lung epithelium and reduce the production of lung water.…”

Section: Discussionmentioning

confidence: 93%

Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis

et al. 2022

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Background Acute respiratory distress syndrome (ARDS) is characterized by refractory hypoxemia caused by accumulation of pulmonary fluid, which is related to inflammatory cell infiltration, impaired tight junction of pulmonary epithelium and impaired Na, K-ATPase function, especially Na, K-ATPase α1 subunit. Up until now, the pathogenic mechanism at the level of protein during lipopolysaccharide- (LPS-) induced ARDS remains unclear. Methods Using an unbiased, discovery and quantitative proteomic approach, we discovered the differentially expressed proteins binding to Na, K-ATPase α1 between LPS-A549 cells and Control-A549 cells. These Na, K-ATPase α1 interacting proteins were screened by co-immunoprecipitation (Co-IP) technology. Among them, some of the differentially expressed proteins with significant performance were identified and quantified by liquid chromatography-tandem mass spectrometry (LC–MS/MS). Data are available via ProteomeXchange with identifier PXD032209. The protein interaction network was constructed by the related Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Several differentially expressed proteins were validated by Western blot. Results Of identified 1598 proteins, 89 were differentially expressed proteins between LPS-A549 cells and Control-A549 cells. Intriguingly, protein–protein interaction network showed that there were 244 significantly enriched co-expression among 60 proteins in the group control-A549. while the group LPS-A549 showed 43 significant enriched interactions among 29 proteins. The related GO and KEGG analysis found evident phenomena of ubiquitination and deubiquitination, as well as the pathways related to autophagy. Among proteins with rich abundance, there were several intriguing ones, including the deubiquitinase (OTUB1), the tight junction protein zonula occludens-1 (ZO-1), the scaffold protein in CUL4B-RING ubiquitin ligase (CRL4B) complexes (CUL4B) and the autophagy-related protein sequestosome-1 (SQSTM1). Conclusions In conclusion, our proteomic approach revealed targets related to the occurrence and development of ARDS, being the first study to investigate significant differences in Na, K-ATPase α1 interacting proteins between LPS-induced ARDS cell model and control-A549 cell. These proteins may help the clinical diagnosis and facilitate the personalized treatment of ARDS. Graphical Abstract

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Section: Discussionmentioning

confidence: 93%

Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis

et al. 2022

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“…As previously reported ( 25 ), image analysis and base calling were performed using the Off-Line Base Caller software v1.8 (Illumina, Inc.). Sequence quality was examined using FastQC software v0.11.7 ( 26 ).…”

Section: Methodsmentioning

confidence: 99%

Cardiac‑specific deletion of natriuretic peptide receptor A induces differential myocardial expression of circular RNA and mRNA molecules involved in metabolism in mice

Chen¹,

Pan

Shen³

et al. 2020

Mol Med Rep

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Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are important biological markers and regulators of cardiac function. The natriuretic peptide receptor A (NPRA), also known as NPR1 or guanylyl cyclase A, binds ANP and BNP to initiate transmembrane signal transduction by elevating the intracellular levels of cyclic guanosine monophosphate. However, the effects and mechanisms downstream of NPRA are largely unknown. The aim of the present study was to evaluate the changes in the global pattern of mRNA and circular RNA (circRNA) expression in NPRA −/− and NPRA +/+ myocardium. Differentially expressed mRNA molecules were characterised using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis and were found to be primarily related to metabolic processes. Moreover, circRNA expression was also examined, and a possible competing endogenous RNA network consisting of circRNA, microRNA (miRNA), and mRNA molecules was constructed. The results of this study indicated that NPRA may play a role in cardiac metabolism, which could be mediated by circRNA through endogenous competition mechanisms. These findings may provide insight into future characterisation of various ceRNA network pathways.

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“…Data from NGS not only confirm the upregulation of cytokine- and chemokine-related genes in response to lipopolysaccharides (LPS) [52], but also reveal alterations in genes related to other pathological signaling pathways. In the ventilator-induced lung injury animal model, RNA sequencing of lung tissue showed that activation of the mechanistic target of rapamycin pathway and Janus kinase-signal transducer and activator of transcription (JAK/STAT) signaling were implicated in early inflammation, while the hypoxia inducible factor-1 (HIF-1) and nuclear factor κB (NF-κB) signaling pathways were activated in the late stage, which might be related to subsequent fibrosis [53].…”

Section: Introductionmentioning

confidence: 99%

Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing

Fan

2019

Military Med Res

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The lung plays a vital role in maintaining homeostasis, as it is responsible for the exchange of oxygen and carbon dioxide. Pulmonary homeostasis is maintained by a network of tissue-resident cells, including epithelial cells, endothelial cells and leukocytes. Myeloid cells of the innate immune system and epithelial cells form a critical barrier in the lung. Recently developed unbiased next generation sequencing (NGS) has revealed cell heterogeneity in the lung with respect to physiology and pathology and has reshaped our knowledge. New phenotypes and distinct gene signatures have been identified, and these new findings enhance the diagnosis and treatment of lung diseases. Here, we present a review of the new NGS findings on myeloid cells in lung development, homeostasis, and lung diseases, including acute lung injury (ALI), lung fibrosis, chronic obstructive pulmonary disease (COPD), and lung cancer.

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Candidate Genes as Biomarkers in Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome Based on mRNA Expression Profile by Next-Generation RNA-Seq Analysis

Cited by 6 publications

References 63 publications

Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis

Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis

Cardiac‑specific deletion of natriuretic peptide receptor A induces differential myocardial expression of circular RNA and mRNA molecules involved in metabolism in mice

Discovering myeloid cell heterogeneity in the lung by means of next generation sequencing

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