Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium

Abstract

Background: Posttranscriptional gene regulation (PTGR) contributes to inflammation through alterations in messenger RNA (mRNA) turnover and translation rates. RNA-binding proteins (RBPs) coordinate these processes but their role in lung inflammatory diseases is ill-defined. We evaluated the expression of a curated list of mRNA-binding RBPs (mRBPs) in selected Gene Expression Omnibus (GEO) transcriptomic databases of airway epithelium isolated from chronic obstructive pulmonary disease (COPD), severe asthma (SA) and matched control subjects, hypothesizing that global changes in mRBPs expression could be used to infer their pathogenetic roles and identify novel disease-related regulatory networks. Methods: A published list of 692 mRBPs [Nat Rev Genet 2014] was searched in GEO datasets originated from bronchial brushings of stable COPD patients (C), smokers (S), non-smokers (NS) controls with normal lung function (n = 6/12/12) (GEO ID: GSE5058) and of (SA) and healthy control (HC) (n = 6/12) (GSE63142). Fluorescence intensity data were extracted and normalized on the medians for fold change (FC) comparisons. FCs were set at ≥ |1.5| with a false discovery rate (FDR) of ≤ 0.05. Pearson correlation maps and heatmaps were generated using tMEV tools v4_9_0.45. DNA sequence motifs were searched using PScan-ChIP. Gene Ontology (GO) was performed with Ingenuity Pathway Analysis (IPA) tool. Results: Significant mRBP expression changes were detected for S/NS, COPD/NS and COPD/S (n = 41, 391, 382, respectively). Of those, 32% of genes changed by FC ≥ |1.5| in S/NS but more than 60% in COPD/NS and COPD/S (n = 13, 267, 257, respectively). Genes were predominantly downregulated in COPD/NS (n = 194, 73%) and COPD/S (n = 202, 79%), less so in S/NS (n = 4, 31%). Unsupervised cluster analysis identified in 4 out of 12 S the same mRBP pattern seen in C, postulating subclinical COPD. Significant DNA motifs enrichment for transcriptional regulation Ricciardi et al. Airway Epithelial RNA-Binding Protein Profiling was found for downregulated RBPs. Correlation analysis identified five clusters of co-expressed mRBPs. GO analysis revealed significant enrichments in canonical pathways both specific and shared among comparisons. Unexpectedly, no significant mRBPs modulation was found in SA compared to controls. Conclusions: Airway epithelial mRBPs profiling reveals a COPD-specific global downregulation of RBPs shared by a subset of control smokers, the potential of functional cooperation by coexpressed RBPs and significant impact on relevant pathogenetic pathways in COPD. Elucidation of PTGR in COPD could identify disease biomarkers or pathways for therapeutic targeting.

Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation

“…Recent studies are increasingly reporting the loss of several RBPs in in vitro and mouse models of cellular senescence, such as HuD (197), fragile X-related protein 1 (FXR1) (198), and cold shock domain containing E1 (CSDE1)/upstream of N-Ras (UNR) (199). The identification of a global RBP downregulation in two COPD bronchiolar epithelium transcriptomic databases (50) further connects these evidence to a role of AUF-1 in inflammaging through mechanisms yet to be uncovered, likely also related to its extracellular transfer in exosomes. Epithelial-derived exosomes and MV -which were detected, measured and then visualized by TEM in this studycontribute to lung inflammatory disease pathogenesis and the ensuing systemic component through multiple mechanisms (200)(201)(202)(203)(204).…”

“…This finding was specific for the epithelium, as neither other structural cells (endothelium, fibroblasts) or immune cells (macrophages, infiltrating leukocytes) displayed this difference, nor the levels of the RNA binding proteins Tristetraprolin (TTP) and HuR were changed in the ex vivo and in vitro models (48). We again documented changes in AUF-1 expression in COPD in silico within the identification of a global downregulation for a curated list of 600 RBPs (49) in two COPD bronchiolar epithelium transcriptomic databases (50). The downregulated RBP expression pattern was significantly represented for several pathogenic COPD pathways by Genome Ontology (GO) analysis, expanding relevance of RBP biology in chronic lung inflammation beyond a single member.…”

“…Our current study and previous investigations (48) are the first providing evidence that the striking similarities between the accelerated senescence phenotype of AUF1 -/mouse and cellular models and key features of COPD pathogenesispremature aging, tissue senescence, inflammation, increased cancer riskindicate that AUF-1 plays a role in this human lung disease. Our experimental design was shaped upon the initial finding of diminished expression of AUF-1 in broncho-epithelium both ex vivo and in vitro (48,50). This is a challenging experimental system to interrogate in vitro, with several drawbacks for results' interpretation.…”

Endotyping Eosinophilic Inflammation in COPD with ELAVL1, ZfP36 and HNRNPD mRNA Genes

“…Furthermore, in silico analysis has documented alterations in AUF-1 expression in COPD [25]. This was observed in the context of a global downregulation trend across a curated list of 600 RNA-binding proteins (RBPs) in two transcriptomic databases focusing on the COPD bronchiolar epithelium [26]. The identified downregulated expression pattern of RBPs, including AUF-1, holds significance as it was found to be notably associated with various pathogenic pathways implicated in COPD [27].…”

Aberrant Post-Transcriptional Regulation of Protein Expression in the Development of Chronic Obstructive Pulmonary Disease

“…Although this suggests that AUF1 may regulate the expression of inflammatory genes involved in COPD, direct regulation by AUF1 of these downstream mRNA, and its implications for the pathogenesis of COPD, remain to be investigated. Recently, a mapping profile of RBPs indicated that most RBP genes are downregulated in the small airway epithelium of those with COPD, comparing to non-smokers and smokers [ 147 ]. Overall, these studies raise the possibility that RBPs may be involved in the development of COPD.…”