Transcription analysis of primary dermal fibroblasts with different genotypes for CTGF rs9399005 SNP after irradiation or sham irradiation

After data trimming with Trimmomatic, pseudo- alignment with Kallisto and data normalization (voom function, limma), differential gene expression (DGE) analysis was carried out using the limma package (FDR<0.05). Pathway enrichment analysis was conducted using the ReactomePA package in R. Results: Few differentially expressed genes (DEGs) were identified at baseline (day-0) between the genotypes (TT vs CC: n=5; TT vs CT: n=2; CT vs CC: n=1).

Transcriptome changes on day-2 were assessed by comparing irradiated and untreated samples of each genotype to the untreated CC genotype at baseline (day-0) as a common control. Significant differences in the number of DEGs were observed between fibroblasts of different genotypes (p<0.001, Chi-squared test). The highest number of DEGs on day-2 was found in CC fibroblasts (0 Gy: n=2372, 4 Gy: n=9576), while fibroblasts with the TT genotype showed significantly fewer DEGs (0 Gy: n=523, 4 Gy: n=3538), with CT fibroblasts showing intermediate levels (0 Gy: n=788, 4 Gy: n=5471).

Pathway analysis after irradiation revealed similar expected responses across all genotypes, consistent with previous reports. However, pathways related to cell cycle regulation, metabolism, and signal transduction were underrepresented in TT fibroblasts at baseline but overrepresented on day-2 post-irradiation, compared to CC fibroblasts. Distinct genes were leading these under- and over-representations.

A significant influence of the candidate SNP on fibroblast responses to irradiation was demonstrated, primarily through the modulation of pathways related to growth and stress regulation. Personalized approaches to managing fibrosis risk may be guided by these findings.