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

<p>Abstract</p> <p>Background</p> <p>The response of normal tissues in cancer patients undergoing radiotherapy varies, possibly due to genetic differences underlying variation in radiosensitivity.</p> <p>Methods</p> <p>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 <it>P </it>< 0.05) were analyzed using the remaining pooled gDNA. Silencing RNA treatment was performed in cultured normal human skin fibroblasts.</p> <p>Results</p> <p>Forty-seven markers had positive association values; including one in the <it>SEMA3A </it>promoter region (P = 1.24 × 10^-5). <it>SEMA3A </it>knockdown enhanced radiation resistance.</p> <p>Conclusions</p> <p>This study identified 47 putative radiosensitivity markers, and suggested a role for <it>SEMA3A </it>in radiosensitivity.</p

Comet assay, a possible screening assay to classify subgroups of individuals with different radiosensitivity using high throughput scanning system for multiple samples of human blood lymphocytes

This research was designed to identify the correlation between clinical radiosensitivity among breast cancer patients and in vitro radiosensitivity measured by alkaline comet assay in high throughput fashion. In 62 patients with breast cancer and age-matched 41 healthy volunteers, acute adverse effects on skin after radiotherapy were clinically scored according to RTOG grading system. Maximum score during 6 months after radiotherapy was grade 0 for 9 patients, grade 1 for 25 patients, grade 2 for 24 patients, and grade 3 for 4 patients. The parameters of alkaline comet assay were initial damage, which was mean tail moment (MTM) values in irradiated cells in vitro immediately after irradiation with 5 Gy, and % residual damage (RD) at 15 min after irradiation. Correlation between initial damage and skin reaction was found in breast cancer patients with grade 1 and grade 2, 3 (p=0.017). There was no correlation between RD and skin reaction (p=0.056), while large inter-individual variation of RD was revealed among breast cancer patients with grade 0 (17.04 +13.31 %), or grade 2, 3 (16.86 +11.09 %). By introducing a new analyzer, throughput of the comet assay data was highly improved. Our data suggests that the comet assay might be one of supportive assays to classify subpopulation of patients who have different radiosensitivity from normal responders with a fair-poor discriminating capacity of the test to identify the patients with higher risk of developing a severe acute reaction.The 12th International Congress of Radiation Research(ICRR

Correlation between single nucleotide polymorphisms and jejunal crypt cell apoptosis after whole body irradiation

PURPOSE: To identify loci concerned with radiosensitivity in a mouse model using single nucleotide polymorphism (SNP) markers. MATERIALS AND METHODS: We subjected 276 second filial generation (F2) mice descended from two inbred mouse strains, radiation-induced apoptosis sensitive C57BL/6JNrs (B6) and radiation-induced apoptosis resistant C3H/HeNrs (C3H), to 2.5 Gy whole-body irradiation. We quantified jejunal crypt apoptosis, performed a genome-wide survey, and identified quantitative trait loci (QTL) associated with radiation sensitivity. We expressed apoptosis levels as an apoptotic score (AS), which was equal to the number of apoptotic bodies divided by the number of crypts. We genotyped the mice for 109 SNP markers. RESULTS: AS values were 97.7+/-32.9 in B6 mice and 49.0+/-24.9 in C3H mice (p < 0.01). Genome-wide analysis revealed 8 markers (2 on chromosome 9, 4 on 15, 1 on 17, and 1 on 18) affecting radiation-induced jejunal apoptosis with log odds (LOD) scores ranging from 2.11+/-3.91. We found a significant locus on chromosome 15, which was previously reported by Weil and colleagues. CONCLUSION: These findings support the view that the radiosensitivity of clinically normal tissue depends on variations in several genes

Possible influence of multiple SNP markers to urological morbidity induced by radiotherapy with carbon-ions among 133 prostate cancer patients

Purpose: To develop efficient predictive method for risk of dysuria after radiotherapy (RT). Patients and Methods: A total of 197 prostate cancer patients who underwent C-ion RT at a total dose of 64.4 +/- 2.7 GyE and evaluated for urinary morbidity (dysuria) according to the Late Effects of Normal Tissue/Subjective, Objective, Management, and Analytic scoring system (LENTSOMA). Three hundred seventy-three SNPs in 109 candidate genes were genotyped by MassARRAY system. Patients were categorized into control (grade 0) and case (grade >1) groups. First, association between the genotype at each SNP site and dysuria were assessed using the Fisher exact test (P ) had 3 or more risk genotypes. Conclusions: Although more patients are required to validate the results, this study supports the assumptions that radiosensitivity is caused by multigenetic factors and that the number of high-risk genotypes on SNPs might predict radiosensitivity.The 13th International Congress of Radiation Researc

Risk estimation of radiation-induced normal tissue injury on cancer patients by convenient analysis of marker SNPs

It has been increasingly recognized that cancer patient\u27s genetic information significantly influences therapeutic outcomes. In this study, a novel experimental system was developed for estimating risk of radiation-induced normal tissue injury on individual cancer patients based on analysis of marker SNP genotypes, which had been screened by a large association study on genes involved in DNA damage repair, cell cycle control, redox regulation, inflammation and so on. These marker SNPs were analyzed simultaneously using patient\u27s blood-derived genomic DNA by a novel DNA chip method that provided optical detection of typing results. The resulting spot images on the DNA chips were captured by a digital camera and processed by computerized tool to call genotype of SNPs. The genotype information was then referred a database made by the foregoing large association study to statistically calculate risk of radiation-induced normal tissue injury. This system does not require specific instruments and can be easily operated in a short time. It is suitable to be used at laboratory of clinical hospitals.Cancer Models & Mechanism

Prediction of radiation morbidity from polymorphisms in candidate genes among prostate cancer patients treated with carbon ion therapy.

Heavy ion beams possess high linear energy transfer components and a prominent Bragg peak in the human body. These properties promote higher relative biological effectiveness and a favorable dose distribution. Some patients, however, develop adverse effects in the rectum and /or bladder/urethra. Using DNA samples collected from 95 Japanese prostate cancer patients who underwent radiotherapy with the Heavy Ion Medical Accelerator in Chiba, 905 SNPs were genotyped from 127 candidate genes for radiation susceptibility. These genes were selected from our previous gene expression analyses of cultured human cell lines and mouse strains that had exhibited variable radiosensitivities. The SNPs in the candidate genes were selected from jSNP and dbSNP databases and their allele frequencies were examined using 133 healthy controls. The acute and late radiation morbidities were scored using Late Effects of Normal Tissues-subjective, objective, management, and analytic criteria. Significant differences were observed of genotype frequencies for SNPs in candidate gene loci. Area under the curve of the Receiver Operating Characteristic Curve (ROC) was estimated for each SNP marker for radiation morbidity to construct a predictive score. The top 7 markers were used in constructing predictive scores for dysuria within 3 months, and the top 5 markers at 6 months after starting radiotherapy. The top 10 markers were used in constructing predictive scores for polyuria within 3 months, and the top 11 markers at 6 months after starting radiotherapy. The distribution of ten predictive scores according to response values showed the potential discriminating power of these analyses.ASHG 55th Annual Meetin

Influence of Multiple Genetic Polymorphisms on Genitourinary Morbidity After Carbon Ion Radiotherapy for Prostate Cancer

Purpose: To investigate the genetic risk of late urinary morbidity after carbon ion radiotherapy in prostate cancer patients.Methods and Materials: A total of 197 prostate cancer patients who had undergone carbon ion radiotherapy were evaluated for urinary morbidity. The distribution of patients with dysuria was as follows: Grade 0, 165; Grade 1, 28; and Grade 2, 4 patients. The patients were divided (2:1) consecutively into the training and test sets and then categorized into control (Grade 0) and case (Grade 1 or greater) groups. First, 450 single nucleotide polymorphisms (SNPs) in 118 candidate genes were genotyped in the training set. The associations between the SNP genotypes and urinary morbidity were assessed using Fisher\u27s exact test. Then, various combinations of the markers were tested for their ability to maximize the area under the receiver operating characteristics (AUC-ROC) curve analysis results. Finally, the test set was validated for the selected markers.Results: When the SNP markers in the SART1, ID3, EPDR1, PAH, and XRCC6 genes in the training set were subjected to AUC-ROC curve analysis, the AUC-ROC curve reached a maximum of 0.86. The AUC-ROC curve of these markers in the test set was 0.77. The SNPs in these five genes were defined as "risk genotypes." Approximately 90% of patients in the case group (Grade 1 or greater) had three or more risk genotypes.Conclusions: Our results have shown that patients with late urinary morbidity after carbon ion radiotherapy can be stratified according to the total number of risk genotypes they harbor