Investigation of system biology analysis of colorectal cancer (CRC) patients and evaluating the expression of obtained differentially expressed genes in CRC cell line treated with common chemo-drugs

Abstract

Colorectal cancer is one of the most common types of cancer in the world and its incidence increases with age. Most colon cancers with or without lymph node metastases. Surgery is the treatment of choice for nonmetastatic colorectal cancer, and adjuvant chemotherapy is usually recommended for patients with lymph node metastases. However, factors such as late diagnosis and resistance to current treatment methods cause failure in patients. Therefore, it is necessary to identify new targets and molecular pathways to explain new and targeted treatment methods. Therefore, in this study, we used bioinformatics to identify the genes involved in the occurrence of colorectal cancer and the effect of common chemotherapy drugs on their expression. Materials and Methods: In this study, firstly, the raw data available in GEO bank, including the gene expression profile related to the tumor samples of patients with colorectal cancer compared to the normal samples, were examined and then using packages under the R program. Identification of genes with significant expression differences were identified, which are also called DEGs. The identified DEGs were analyzed using Cytoscape software and co-expression network and Gene Ontology including (Biological Process) BP and Molecular Function. Finally, by reviewing and summarizing the data obtained in the KEGG pathway signaling database, the location of predicted target genes and related pathways in colorectal cancer induction were investigated. After bioinformatic investigations and reaching the genes related to cancer induction, in order to confirm them, the HT-29 colorectal cancer cell line was treated with conventional drugs in the treatment of this cancer, including paclitaxel and 5-FU, and the samples obtained for RNA extraction and gene expression analysis were used. In order to measure the relative changes in the mRNA expression level of the target genes identified from the bioinformatics analysis, Real-Time PCR technique was used. Results: Bioinformatics analyzes using the GSE110224 dataset showed that TACSTD2, CXCL1, SERPINB5 and CXCL8 genes are among the genes whose significant expression changes can play a role in the development and progression of colorectal cancer and probably to They act as oncogenes. Also, the results of Real-Time PCR showed that the expression of TACSTD2 gene significantly decreases after treatment with paclitaxel, while the decrease in the expression of this gene was not significant due to treatment with 5-FU. In addition, both chemotherapy drugs led to a significant decrease in the expression of CXCL1 and SERPINB5 genes in the treatment samples compared to the control samples. Also, the change in CXCL8 gene expression was not significant with the mentioned treatments.