Computation and comparison of gene expression variability in fibroblasts of long-term survivors of childhood cancer and cancer-free controls in response to ionizing and sham-irradiation: the KiKme study

Abstract

Abstract Background: Differential expression analysis is usually adjusted for variation. However, most studies that examined the expression variability (EV) have used computations affected by low expression levels and did not examine healthy tissue. This study aims to calculate and characterize an unbiased EV in primary fibroblasts of childhood cancer survivors and cancer-free controls (N0) in response to ionizing radiation. Methods: Human skin fibroblasts of 52 donors with a first primary neoplasm in childhood (N1), 52 donors with at least one second primary neoplasm (N2+), as well as 52 N0 were obtained from the KiKme case-control study and exposed to a high (2 Gray) and a low dose (0.05 Gray) of X-rays and sham- irradiation (0 Gray). Genes were then classified as hypo-, non-, or hyper-variable per donor group and radiation treatment, and subsequently examined for enriched functional signatures. Results: We found 22 genes with considerable EV differences between donor groups, of which 11 genes were associated with response to ionizing radiation, stress, and DNA repair. The largest number of genes exclusive to one donor group and variability classification combination were all detected in N0: hypo-variable genes after 0 Gray (n=49), 0.05 Gray (n=41), and 2 Gray (n=38), as well as hyper-variable genes after any dose (n=43). After 2 Gray GO term groups contained the Notch signalling pathway, subsuming cellular response to oxidative stress, cell death in response to hydrogen peroxide, DNA damage response, and detection of DNA damage. In N2+, 30 genes were uniquely classified as hyper-variable after the low dose, and were associated with inflammatory functions. For N1, no exclusive gene sets with functions related to the radiation response were detected in our data. Conclusion: Only in N0, the handling of genotoxic and oxidative stress after a high dose of ionizing radiation may be tightly regulated and thus more efficient, whereas, after a low dose, only N2+ showed high degrees of variability in inflammatory pathways that can be a result of radiation-induced reactive oxygen species, potentially leading to a higher vulnerability towards side effects of exposure to high doses of ionizing radiation.