Analysis of competing endogenous RNA (ceRNA) crosstalk in eosinophilic chronic rhinosinusitis with nasal polyps

Abstract

Background Chronic rhinosinusitis with nasal polyps (CRSwNP) is one of the most common chronic inflammatory diseases, and has various phenotypes. Although its pathophysiology remains obscure, evidence has shown that dysregulation of noncoding RNAs (ncRNAs) is associated with CRSwNP. ncRNAs in the cytoplasm can act as competing endogenous RNAs (ceRNAs), which are involved in many inflammatory processes. However, the ceRNA crosstalk in CRSwNP is still unclear Methods We investigated expression profiles of messenger RNA (mRNA), microRNAs (miRNAs), and long noncoding RNAs (lncRNAs) in eosinophilic CRSwNP and constructed a global triple ceRNA network. Results As a result, 964 differentially expressed mRNAs (DEmRs), 207 differentially expressed miRNAs (DEmiRs), and 15 differentially expressed lncRNAs (DElncRs) were identified, and a ceRNA network containing 598 miRNA‐mRNA pairs and 70 lncRNA‐miRNA pairs was finally constructed. Gene set enrichment analysis (GSEA) results indicated these DEmRs were mainly enriched in “cytokine‐cytokine receptor interaction,” “salivary secretion,” “hematopoietic cell lineage,” and “chemokine signaling pathway.” Moreover, we also predicted the subcellular localization of the DElncRs identified in the network via bioinformatics approaches Conclusion In summary, the present study provided the first comprehensive assessment of the ceRNA crosstalk in eosinophilic CRSwNP. These findings will be of interest to the understanding of the potential pathophysiology of this disease.

Insights into the epigenetics of chronic rhinosinusitis with and without nasal polyps: a systematic review

“…Out of the 44 studies investigating the role of non-coding RNAs, most studies investigated miRNAs, and only a few investigated other RNA types such as lncRNAs (40)(41)(42)(43)(44), siRNAs (45), and circRNAs (46,47). Six studies used pre-existing GEO data sets to identify transcriptome-wide miRNA or lncRNA profiles of CRSwNP vs. controls, either exclusively or in conjunction with in vivo studies on CRS subjects (40-42, 44, 46, 48).…”

“…The presence of co-morbid conditions like asthma and allergic rhinitis may influence results of studies, and this may limit our understanding of CRSwNP-specific epigenetic changes. Bioinformatic analyses on pre-existing GEO data sets need to be consistent in including studies that have used the same disease and control tissue, and this has not been done uniformly across these studies (40)(41)(42). In a recent review on epigenetics in CRS, authors have elaborated that several miRNA studies have shown controversial results in whether a specific miRNA was upregulated or downregulated in CRS (18).…”

Epigenetic modifications in chronic rhinosinusitis with and without nasal polyps

“…Furthermore, its expression displays no statistical difference between ECRSwNP and non-ECRSwNP ( Yu et al, 2021b ). Recently, Li and Liu (2022) have found 207 lowly expressed miRNAs and constructed 598 miRNA-mRNA pairs in ECRSwNP. The level of miR-124 decreases in CRSwNP, and is negatively correlated with the expression of aryl hydrocarbon receptor (AHR) and TNF-α, suggesting that miR-124 can influence the differentiation of Th1 and Th17 cells by inhibiting STAT1 and STAT3 activation in the presence of protein inhibitor cytokine signaling 5 (SOCS5) ( Liu et al, 2018 ).…”

“…This network showcases six hub differently expressed lncRNAs (MIAT, HOTAIRM1, TSPOAP1-AS1, MSC-AS1, LBX2-AS1, and CARD8-AS1), which interact with miRNAs to regulate the expression of mRNAs in ECRSwNP patients. Among these lncRNAs, CARD8-AS1 and MSC-AS1 can act as ceRNA ( Li and Liu, 2022 ). Recently, Chen et al (2022) have constructed another lncRNA-miRNA-mRNA ceRNA network of CRSwNP, which contains 21 lncRNAs, 8 miRNAs and 8 mRNAs; they proved that the MIAT/miR-125a/IRF4 axis drives the progression of CRSwNP.…”