A comprehensive evaluation of skin aging-related circular RNA expression profiles

Abstract

Background: Circular RNAs (circRNAs) have been shown to play important regulatory roles in a range of both pathological and physiological contexts, but their functions in the context of skin aging remain to be clarified. In the present study, we therefore, profiled circRNA expression profiles in four pairs of aged and non-aged skin samples to identify identifying differentially expressed circRNAs that may offer clinical value as biomarkers of the skin aging process.

Methods: We utilized an RNA-seq to profile the levels of circRNAs in eyelid tissue samples, with qRT-PCR being used to confirm these RNA-seq results, and with bioinformatics approaches being used to predict downstream target miRNAs for differentially expressed circRNAs.

Results: In total, we identified 571 circRNAs with 348 and 223 circRNAs being up and downregulated that were differentially expressed in aged skin samples compared to young skin samples. The top 10 upregulated circRNAs in aged skin sample were hsa_circ_0123543, hsa_circ_0057742, hsa_circ_0088179, hsa_circ_0132428, hsa_circ_0094423, hsa_circ_0008166, hsa_circ_0138184, hsa_circ_0135743, hsa_circ_0114119, and hsa_circ_0131421. The top 10 reduced circRNAs were hsa_circ_0101479, hsa_circ_0003650, hsa_circ_0004249, hsa_circ_0030345, hsa_circ_0047367, hsa_circ_0055629, hsa_circ_0062955, hsa_circ_0005305, hsa_circ_0001627, and hsa_circ_0008531. Functional enrichment analyses revealed the potential functionality of these differentially expressed circRNAs. The top 3 enriched gene ontology (GO) terms of the host genes of differentially expressed circRNAs are regulation of GTPase activity, positive regulation of GTPase activity and autophagy. The top 3 enriched KEGG pathway ID are Lysine degradation, Fatty acid degradation and Inositol phosphate metabolism. The top 3 enriched reactome pathway ID are RAB GEFs exchange GTP for GDP on RABs, Regulation of TP53 Degradation and Regulation of TP53 Expression and Degradation. Six circRNAs were selected for qRT-PCR verification, of which 5 verification results were consistent with the sequencing results. Moreover, targeted miRNAs, such as hsa-miR-588, hsa-miR-612, hsa-miR-4487, hsa-miR-149-5p, hsa-miR-494-5p were predicted for circRna-miRna interaction networks.

Conclusion: Overall, these results offer new insights into circRNA expression profiles, potentially highlighting future avenues for research regarding the roles of these circRNAs in the context of skin aging.

Keywords: NGS; biomarker; circRNA; skin aging.

FIGURE 1

Profiling of skin aging‐related circRNAs. A, Those circRNAs that were up or downregulated (red and green, respectively) in aged skin tissue samples relative to young tissues samples were arranged in a heat map, with rows corresponding to individual circRNAs and columns corresponding to individual samples. B, Differentially regulated circRNAs were arranged in a Volcano plot, with blue dots corresponding to a lack of statistical significance, whereas red and green correspond to up and downregulated circRNAs, respectively (Fold change >1.5 and p < 0.05). C, Locations of DECs on human chromosomes are represented by circos plots, with chromosomes being represented by the outermost circle, whereas circRNAs are indicated in the middle circle, and DECs are shown in the innermost circle. Up and downregulated circRNAs are represented by red and blue lines, respectively

FIGURE 2

GO analysis of DEC host genes associated with aging

FIGURE 3

KEGG and Reactome pathway analyses in aged and young skin sample groups. A, The top 15 enriched KEGG pathways. B, The top 15 enriched Reactome pathways

FIGURE 4

qRT‐PCR validation of 6 differentially expressed circRNAs in 20 young and 20 aged skin samples

FIGURE 5

Predicted circRNA‐miRNA interaction networks. Yellow and red rectangles correspond to circRNAs and target miRNAs, respectively