Genetic locus copy number variation level and minimally invasive assessment of radiation therapy efficiency in rectal cancer patients

Abstract

Aim. The screening of molecular genetic markers for a minimally invasive assessment of the radiation therapy effectiveness for rectum malignant tumors.Materials and methods. The study was carried out in 4 stages: 1) bioinformatic analysis of TCGA (The Cancer Ge- nome Atlas) databases using the GISTIC algorithm; 2) validation of bioinformatics analysis data in a model experiment on cell culture; 3) study of genes copy number features validated in a model experiment in patients with different responses to radiation therapy; 4) determination of the gene copy number in cell-free DNA in patientswith different responses to radiation therapy. 100 patients with rectum adenocarcinoma (G1–2), as well as 30 apparently healthy individuals, took part in the work. Radiotherapy was carried out according to the standard protocol (single focal dose 2.4 Gy, total focal dose 54 Gy) on a Novalis TX linear accelerator. The relative copy number of genetic loci was determined by real-time quantitative polymerase chain reaction.Results. Bioinformatic analysis revealed 32 candidate genetic loci. Validation of these markers on irradiated HT-29 cells showed that the copy number of BRCA2, H2AX, CASP9 and RBBP8 genes was increased, while the copy number of BCL2 gene was reduced relative to intact cells. In 74 patients with a partial response to radiation therapy, an increase in the copy number of BRCA2, H2AX, RBBP8 and BCL2 was found, which positively correlated with the copy number of these genes in blood plasma cell-free DNA.Conclusion. The application of an integrated approach based on TCGA database bioinformatic analysis, radiation therapy modeling in cell culture and validation of the identified markers on tissue and blood samples of patients with rectal adenocarcinoma revealed RBBP8, BRCA2, H2AX and BCL2 genes copy number association with the preoperative radiation therapy effectiveness.