A Global Analysis of Tandem 3′UTRs in Eosinophilic Chronic Rhinosinusitis with Nasal Polyps

Abstract

BackgroundAlternative polyadenylation (APA) is emerging as a widespread mechanism of gene regulation. The usage of APA sites allows a single gene to encode multiple mRNA transcripts with different 3′-untranslated region (3′UTR) lengths. Many disease processes reflect the importance of the regulation of APA site switching. The objective of this study was to explore the profiling of tandem APA sites in nasal polyps compared with nasal uncinate process mucosa.MethodsSequencing of APA sites (SAPAS) based on second-generation sequencing technology was undertaken to investigate the use of tandem APA sites and identify gene expression patterns in samples from the nasal polyps and nasal uncinate process mucosa of two patients with chronic rhinosinusitis with nasal polyps. The findings of the SAPAS analysis were validated via quantitative reverse-transcription polymerase chain reaction (qRT-PCR).ResultsFirst, the results showed a switching of 3′UTR lengths in nasal polyps compared with nasal uncinate process mucosa. From the two patients, 105 genes that were detected in both patients in the nasal polyps were switched to distal poly(A) sites, and 90 such genes were switched to proximal poly(A) sites. Several Gene Ontology terms were enriched in the list of genes with switched APA sites, including transcription regulation, cell cycle, apoptosis, and metabolism. Second, we detected genes that showed differential expression with at least a 3-fold difference between nasal polyp tissue and nasal uncinate process mucosa. Between the two sample types, 627 genes exhibited differential expression. The qRT-PCR results confirmed our SAPAS results.ConclusionAPA site-switching events of 3′UTRs are prevalent in nasal polyp tissue, and the regulation of gene expression mediated by APA may play an important role in the formation and persistence of nasal polyps. Our results may provide new insights into the possible pathophysiologic processes involved in nasal polyps.

Canonical Wnt Signaling Drives Tumor-Like Lesions from Sox2-Positive Precursors of the Murine Olfactory Epithelium

“…Also, inflammatory nasal polyps are not likely to arise from the olfactory mucosa [40]. However, an upregulation of Wnt pathway genes in nasal polyposis has been reported [41]. …”

Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method

“…Each cleavage cluster with more than one read was assigned as a poly(A) site. In order to annotate the poly(A) sites, a dataset of all known 3′UTR regions was extracted from the Known Genes database of the UCSC table browser, the detailed procedures were as in the study by Tian et al ( 21 ), except that the non-coding gene items were kept. With UCSC Known Genes ( 19 ) and polyA_DB2 ( 22 ), all the poly(A) sites were annotated as known and novel sites.…”

“…The tandem poly(A) site was defined with the same conditions as in the study by Tian et al ( 21 ). The poly(A) sites that overlapped with multiple known 3′UTR regions were not taken into consideration.…”

“…For each sample, 1,000 ng of total RNA was then used in reverse transcription reactions using random hexamers and SuperScript ® II Reverse Transcriptase (Invitrogen). For each gene, two gene-specific primer sets were designed according to Tian et al ( 21 ). RT-qPCR was performed using the LightCycler 480 Instrument (Roche Biochemicals, Indianapolis, IN, USA) according to the manufacturer’s instructions.…”

Study on 3′-UTR length polymorphism in peripheral blood mononuclear cells of uremia patient

“…16 Changes in 3 0 -UTR lengths mediated by APA sites are a coordinated mechanism for regulating the expression of genes in various physiological and pathological processes, such as T cell activation, cellular transformation, and immune responses. 17 In our study, the genes that were identified to undergo APA site-switching events included genes involved in ubiquitin-mediated proteolysis, B cell receptor signaling pathway, apoptosis and many other functions. The conversion of normal cells into cells with failed function is a progressive and dynamic process that is driven by changes of some genes under various environmental forces.…”