Genome wide screen identifies microsatellite markers associated with acute adverse effects following radiotherapy in cancer patients

Abstract

Background: The response of normal tissues in cancer patients undergoing radiotherapy varies, possibly due to genetic differences underlying variation in radiosensitivity.

Methods: Cancer patients (n = 360) were selected retrospectively from the RadGenomics project. Adverse effects within 3 months of radiotherapy completion were graded using the National Cancer Institute Common Toxicity Criteria; high grade group were grade 3 or more (n = 180), low grade group were grade 1 or less (n = 180). Pooled genomic DNA (gDNA) (n = 90 from each group) was screened using 23,244 microsatellites. Markers with different inter-group frequencies (Fisher exact test P < 0.05) were analyzed using the remaining pooled gDNA. Silencing RNA treatment was performed in cultured normal human skin fibroblasts.

Results: Forty-seven markers had positive association values; including one in the SEMA3A promoter region (P = 1.24 x 10(-5)). SEMA3A knockdown enhanced radiation resistance.

Conclusions: This study identified 47 putative radiosensitivity markers, and suggested a role for SEMA3A in radiosensitivity.

Figure 1

Results of two rounds of screening of microsatellite markers for association with radiosensitivity. (A) Results of the screen of the entire genome using 23,244 microsatellite markers and the HGG-1 and LGG-1 pooled DNAs. (B) Results of screening 3,052 markers of interest identified in the preceding genome scan and using the HGG-2 and LGG-2 pooled DNAs. P values calculated using Fisher's exact test and 2 × 2 contingency tables are shown. The level of significance (P < 0.05) is shown as a horizontal broken line.

Figure 2

In vitro radiosensitivity assay on human skin fibroblast cells treated with SEMA3A gene-directed siRNA. The relative clonogenic survival rate of cells at the indicated X-ray dose (Gy) is plotted. Open box: mock control. Closed triangle: SEMA3A siRNA1. Closed circle: SEMA3A siRNA2. The linear-quadratic model [27] of cell survival as a function of irradiated dose was fitted to the data. The asterisk indicates significant difference between the siRNA transfected cells and the control cells (P value < 0.05).