Long-term global gene expression patterns in irradiated human lymphocytes

Abstract

Radiation-induced chromosomal instability has many features in common with genomic instability of cancer cells. In order to understand the delayed cellular response to ionizing radiation we have studied variations in the patterns of gene expression in primary human lymphocytes at various time points after gamma irradiation in vitro. Cells either exposed to 3 Gy of gamma rays in vitro or unexposed were subjected to long-term growth in bulk culture or as individual T-cell clones. Samples were taken at days 7, 17 or 55 from bulk cultures. The T-cell clones were harvested after 22-46 days. Total RNA was used to generate cDNA probes for hybridization to oligonucleotide arrays containing 12,625 gene templates (Affymetrix). The results showed that: (i) irradiation as well as culture time influence the gene expression patterns, (ii) the number of genes with increased or decreased expression in irradiated cells increases dramatically with increasing culture time, (iii) the changes of gene expression showed a significantly more diversified pattern in the irradiated T-cell clones than in non-irradiated clones. We conclude that the diversification of the transcriptome associated with radiation exposure reflects subtle changes of expression in many genes, rather than being the result of major changes in a few genes. Finally, (iv) we sorted out a set of genes whose change of expression correlates with radiation exposure in both bulk cultures and T-cell clones. Very few of these genes overlap with genes that change during the acute response to radiation. This set of genes may be regarded as a starting point for further studies of the cellular phenotype associated with radiation-induced genomic instability.

Studies of the in vivo radiosensitivity of human skin fibroblasts

“…In addition, no decrease in background MN burden was observed when five strains of the fibroblasts were cultivated for four passages (up to 4-6.5 weeks of culture) without irradiation (data not shown). These results suggest that genomic damage is persisting during culture consistent with studies by others of surviving descendants of irradiated cells in vitro and in vivo [13,15,33,34,38,49,50], even after a dose as low as 0.5 Gy [43], although only a fraction of the cell progeny (about 30-60%, depending on cell type and dose) may carry this damage [21,32]. Such persistent instability is also consistent with work on the bystander effect and could be due to factors released into the medium during culturing.…”

A class comparison method with filtering‐enhanced variable selection for high‐dimensional data sets

“…In the simulation studies, the expression of 50,000 variables for two groups of 5,20 or 50 samples each was simulated independently from a multivariate Gaussian distribution. Variances for each variable were drawn from an inverse gamma distribution with shape parameter a= 3 and scale parameter b=1, as in [14].…”

Delayed effects of exposure to a moderate radiation dose on transcription profiles in human primary fibroblasts

“…However, studies performed on delayed IR effects demonstrate that irradiated cells present persistent biological alterations [Jamali and Trott, 1996;Lyng et al, 1996;Manti et al, 1997]. These findings raise questions about long-term, delayed, or late consequences due to persistent DNA lesions or mutations, and the extent to which transcriptional alterations may impose a risk to humans [Falt et al, 2003;Snyder and Morgan, 2004].…”