Genome-Wide RNA Sequencing Analysis in Human Dermal Fibroblasts Exposed to Low-Dose Ultraviolet A Radiation

Abstract

Ultraviolet A (UVA) radiation can pass through the epidermis and reach the dermal skin layer, contributing to photoaging, DNA damage, and photocarcinogenesis in dermal fibroblasts. High-dose UVA exposure induces erythema, whereas low-dose, long-term UVA exposure causes skin damage and cell senescence. Biomarkers for evaluating damage caused by low-dose UVA in fibroblasts are lacking, making it difficult to develop therapeutic agents for skin aging and aging-associated diseases. We performed RNA-sequencing to investigate gene and pathway alterations in low-dose UVA-irradiated human skin-derived NB1RGB primary fibroblasts. Differentially expressed genes were identified and subjected to Gene Ontology and reactome pathway analysis, which revealed enrichment in genes in the senescence-associated secretory phenotype, apoptosis, respiratory electron transport, and transcriptional regulation by tumor suppressor p53 pathways. Insulin-like growth factor binding protein 7 (IGFBP7) showed the lowest p-value in RNA-sequencing analysis and was associated with the senescence-associated secretory phenotype. Protein-protein interaction analysis revealed that Fos proto-oncogene had a high-confidence network with IGFBP7 as transcription factor of the IGFBP7 gene among SASP hit genes, which were validated using RT-qPCR. Because of their high sensitivity to low-dose UVA radiation, Fos and IGFBP7 show potential as biomarkers for evaluating the effect of low-dose UVA radiation on dermal fibroblasts.

Keywords: Fos; IGFBP7; biomarker; differentially expressed gene; low-dose UVA; senescence-associated secretory phenotype; ultraviolet A.

Figure 1

Mechanism of UVA damage to the skin. (A) UVA penetration into the skin dermis layers. (B) UVA-induced damage to cellular DNA, protein, and membrane via ROS production in skin fibroblasts. (C) Schematic diagram of this study.

Figure 2

(A) Morphological characteristics of NB1RGB fibroblasts irradiated with 5, 10, or 20 J/cm² ultraviolet A (UVA). Inset scale bar, 50 μm. (B) Optical density of NB1RGB fibroblasts irradiated with 5, 10, or 20 J/cm² UVA. The mean ± SEM of a representative result from independent experiments performed in quadruplicate. Asterisks indicate significant differences analyzed with Student’s t-test, ** p < 0.01 vs. UVA non-irradiation group as a control at different UVA doses.

Figure 3

(A) Volcano map of 771 differentially expressed genes (DEGs) (p < 0.05, log₂ fold-change > 0.8). Significantly upregulated and downregulated DEGs are represented as blue and red dots, respectively. (B) Distribution of DEGs.

Figure 4

Bubble diagram of Gene Ontology (GO) enrichment analysis. Bubble size represents the number of differentially expressed genes.

Figure 5

(A) Bubble diagram of top eight enriched reactomes. Bubble size indicates the number of differentially expressed genes. Bubble color indicates the p-value. (B) Cluster diagram of enriched pathways.

Figure 6

(A) Top eight annotated differentially expressed genes. Bar color represents the log₂ fold-change value. Bar length represents the p-value. (B) Schematic of protein–protein interactions. Solid lines represent proven relationships. Dotted lines indicate putative associations.

Figure 7

IGFBP7 and Fos mRNA expression in cells treated with 5 J/cm² UVA radiation. (A) Fos mRNA levels. (B) IGFBP7 mRNA levels. Data represent the mean ± SEM of three biological independent experiments performed in triplicate. Asterisks indicate significant difference analyzed using Student’s t-test, * p < 0.05, *** p < 0.001 vs. control, UVA non-irradiation group.