High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome

Abstract

Background: Psoriasis is a chronic inflammatory skin disease characterized by hyperproliferation and abnormal differentiation of keratinocytes. It is one of the most prevalent chronic inflammatory skin condition in adults worldwide, with a considerable negative impact on quality of life. Circular RNAs (circRNAs) are a recently identified type of non-coding RNA with diverse cellular functions related to their exceptional stability. In particular, some circRNAs can bind and regulate microRNAs (miRNAs), a group of RNAs that play a role in the pathogenesis of psoriasis. The aim of this study was to characterize the circRNAome in psoriasis and to assess potential correlations to miRNA expression patterns. Results:Using high-throughput RNA-sequencing (RNA-seq) and NanoString nCounter technology, we found a substantial down-regulation of circRNA expression in lesional skin compared to non-lesional skin from psoriasis patients. We saw that this mainly applies to the epidermis by analyzing laser capture microdissected tissues and by RNA chromogenic in situ hybridization (CISH). We also found that the majority of the circRNAs were downregulated independent of their corresponding linear host genes. The observed downregulation of circRNAs in psoriasis was not due to altered expression levels of factors known to affect circRNA biogenesis, nor because lesional skin contained an increased number of inflammatory cells such as lymphocytes. Finally, we saw that the overall differences in available miRNA binding sites on the circRNAs between lesional and non-lesional skin did not correlate with differences in miRNA expression patterns. Conclusions:We have performed the first genome-wide circRNA profiling of paired lesional and non-lesional skin from psoriasis patients and revealed that circRNAs are much less abundant in the lesional samples. Whether this is a cause or a consequence of the disease remains to be revealed, 3 however, we found no evidence that the loss of miRNA binding sites on the circRNAs could explain differences in miRNA expression reported between lesional and non-lesional skin. BackgroundPsoriasis is one of the most common chronic inflammatory skin conditions, with 1-3% of the adult population affected worldwide [1]. It is defined by a pronounced hyperproliferation and deficient terminal differentiation of the keratinocytes. Moreover, a complex interplay between different cell types (e.g. T cells and dendritic cells) and a variety of cytokines are known to contribute in the development of psoriasis. The pathogenesis is also based on a complex synergy between genetic predisposition, major histocompatibility alleles, and a variety of environmental triggers [2]. From the molecular point of view, however, the mechanisms responsible for the interactions between keratinocytes and inflammatory cells infiltrating the epidermis are still not fully understood. The analysis of the molecular backdrop of psoriasis has described numerous disease-associated genes and proteins with abnormal expression patterns [3], but little is...

The eminent roles of ncRNAs in the pathogenesis of psoriasis

“…Factors that influence circRNA biogenesis or the amounts inflammatory cells in the lesion did not affect the levels of circRNAs. Down-regulation of circRNAs might be due to high proliferation and turnover rates of the keratinocytes in the affected skin and lower differentiation status of these cells [ 57 ], since expressions of circRNAs are mostly increased during differentiation [ 58 ].…”

Spatial expression analyses of the putative oncogene ciRS-7 in cancer reshape the microRNA sponge theory

“…The clinicopathological patient characteristics are shown in Table 1 . When applying a recently developed, sensitive, and specific RNA chromogenic in situ hybridization (CISH) assay for spatial visualization of ciRS-7 expression 24 to analyze samples from 16 representative patients, surprisingly, we found that ciRS-7 was not expressed in colon cancer cells in any of the samples. On the other hand, we observed a strong staining in stromal cells within the tumors (Fig.…”

“…The vast majority of these studies did not investigate the spatial relationship between the putative circular ceRNA and the potentially post-transcriptionally regulated genes. Moreover, circRNAs are often less abundant in rapidly proliferating cells 24 , 41 , 42 possibly due to their slow production rate 43 and extreme stability 1 preventing them from reaching steady state levels. This likely results in major expression differences among cell populations with different proliferation rates within a tumor.…”

“…The cellular localization of ciRS-7 was investigated by chromogenic in situ hybridization (CISH) using a modified version of the RNAScope 2.5 high-definition procedure (Advanced Cell Diagnostics [ACD], Hayward, CA, USA) 24 . In brief, 3.5-µm thick paraffin sections from colon cancer samples, TMAs and formalin-fixed and paraffin-embedded cell pellets from ciRS-7 knockout and wild-type cells were pretreated and hybridized with 12 ZZ-pairs (Probe-Hs-CDR1-AS-No-XMm, 510711, ACD) targeting ciRS-7 overnight.…”

hsa_circ_0003738 Inhibits the Suppressive Function of Tregs by Targeting miR-562/IL-17A and miR-490-5p/IFN-γ Signaling Pathway

“…11 In the other study, which used RNA sequencing, a substantial downregulation of circRNAs was characterized in psoriatic lesional skin compared with non-lesional skin (128 versus 285). 19 The other two studies focused on the role of circRNAs in mesenchymal stem cells (MSCs) in psoriatic lesions. 20,21 Different from other investigations, we are the first to identify the role of circRNAs in Tregs in the pathogenesis of psoriasis.…”