Displaying the expression of selected cancer associated genes from RNA-seq data of mouse mamary tumor virus-transforming growth factor-α mice in thymus tissue

Breast cancer is a type of cancer that has high mortality rates. Mouse mammary tumor virus transforming growth factor-α (MMTV-TGF-α) transgenic mice are experimental animals that are used in breast cancer researches. They are organisms that develop breast cancer from the second year of their lives. Changes in the expression of genes play a critical role in cancer formation. RNA-seq is a widely used method in determining gene expression changes. Caloric restriction is a potent nutritional intervention. It is known as limiting the calorie intake without causing malnutrition. It has been reported effects on organisms such as increasing life span, inhibiting tumor formation and strengthening immunological function. The thymus and other lymphoid organs respond quickly to nutritional restriction. The cancer-related genes that are altered expressions in thymus tissue by caloric restriction are the focal point of this study. The aim of the study is to compare the "differentially expressed genes" (DEGs) identified by RNA-seq with Real Time PCR results and validation of the RNA-seq data and follow up expression amount of these genes in the following weeks. In this study, RNA-seq data obtained from an earlier study were used as reference. It has been reported that RNAs used in RNA-seq were isolated from thymus tissues of MMTV-TGF-a mice, which have been sacrificed at 17th -18th week, divided into Ad Libitum diet, chronic caloric restricted diet and intermittent caloric restricted diet groups from 10th week of the life. RNAs used in this study were isolated from thymus tissues of mice, which have been sacrificed at 17th – 18th, 49th -50th and 80th – 81st week, grown by the same protocol. In total 6091 statistically significant "differentially expressed genes" (DEGs) (p < 0.05) were detected in RNA-seq data that obtained from caloric restricted mice. The selected 21 breast cancer-directed genes were screened in DEGs data. It was found that changes in the expression of 6 genes were statistically significant. Changes in expression rates of 3 genes of these were validated by Real Time PCR. It was noted that there were differences in gene expression in the same amount of energy input and in different caloric restriction. Thus, it is thought that besides calorie restriction, nutrition type is also effective in preventing tumor formation.