Classification of sensitivity or resistance of cervical cancers to ionizing radiation according to expression profiles of 62 genes selected by cDNA microarray analysis

Abstract

To identify a set of genes related to radiosensitivity of cervical squamous cell carcinomas and to establish a predictive method, we compared expression profiles of 9 radiosensitive and 10 radioresistant tumors obtained by biopsy before treatment, on a cDNA microarray consisting of 23,040 human genes. We identified 121 genes whose expression was significantly greater in radiosensitive cells than in radioresistant cells, and 50 genes that showed higher levels of expression in radioresistant cells than in radiosensitive cells. Some of these genes had already known to be associated with the radiation response, such as aldehyde dehydrogenase 1 (ALDH1) and X-ray repair cross-complementing 5 (XRCC5) (P<.05, Mann-Whitney test). The validity of the total of 171 genes as radiosensitivity related genes were certified by permutation test (P<.05). Furthermore, we selected 62 genes on the basis of a clustering analysis, and confirmed the validity of these genes with cross-validation test. The cross-validation test also indicates the possibility of making prediction of radiosensitivity for discriminating radiation-sensitive from radiation resistant biopsy samples by predicting score (PS) values calculated from expression values of 62 genes in 19 samples, because the prediction successfully and unequivocally discriminated the radiosensitive phenotype from the radioresistant phenotype in our test panel of 19 cervical carcinomas. The extensive list of genes identified in these experiments provides a large body of potentially valuable information for studying the mechanism(s) of radiosensitivity, and selected 62 genes opens the possibility of providing appropriate and effective radiotherapy to cancer patients.

Figure 1

Differential gene expression between the radiosensitive group (CR; 9 samples) and the radioresistant group (NC; 10 samples) with significant difference (P<.05). U indicates the Mann-Whitney test statistic. Expression levels (Ex=Cy5 signal intensity from cancer sample/Cy3 signal intensity from control), of two genes are plotted here. Median Ex values for each group of tumors are denoted by horizontal lines. (A) Retinol-binding protein 1 (RBP1; U=19); (B) X-ray repair cross-complementing 5 (XRCC5; U= 73).

Figure 2

Expression patterns of 62 genes across 19 samples of cervical squamous cell carcinoma. Red or green colors indicate higher or lower expression, respectively, relative to the mean signal intensity of a given gene across 19 tumor samples; black, same expression level with mean value; gray, no expression detected (intensities of both Cy3 and Cy5 were below cut-off values). Each row represents each gene and each column a cervical squamous cell carcinoma sample. Single and double triangles indicate the gene-expression profiles of TCF4 and BAK1, respectively.

Figure 3

Predictive score (PS) for radiosensitive and radioresistant groups by cross-validation test. Details of the calculation method were noted in the Materials and Methods section. A dashed line indicates the threshold.