The Prognostic Value Of Blood RNA Expression Profile In Colorectal Cancer Patients

PurposeUse microarray technology to compare the blood expression profile between healthy volunteers and confirmed colorectal cancer patients. Identify prognosis genes related to patients’ survival, confirm the candidate genes expression with real-time PCR method, and understand the feasibility of gene expression signature to predict the prognosis of colorectal cancer patients.Patients and MethodsPart1:Whole blood samples were collected into PAXgene tube, from healthy volunteers and confirmed colorectal cancer patient. The extracted RNA samples were examined with Affymetrix Human Genome GeneChip U1332.0plus Array. Differential expression genes were analyzed with Significance Analysis of Microarrays (SAM) method. Functional enrichment analysis of Gene Ontology and the Panther pathway were carried out. The selected gene expression was further confirmed by real-time PCR method.Part2:Whole blood samples were collected into PAXgene tube, from confirmed colorectal cancer patient. The extracted RNA samples were examined with Affymetrix Human Genome GeneChip U1332.0plus Array. Prognosis-related genes were identified with Significance Analysis of Microarrays (SAM) survival method. Functional enrichment analysis was also performed.Part3:The top31genes were further selected according to their significance, using real-time PCR method to check the RNA expression. A colorectal cancer patient prognosis prediction model was established by forward stepwise selection method of cox regression analysis. Overall survival was estimated by the methods of Kaplan-Meier and log-rank test to determine the significance of the prediction model. ResultsPart1:We identified1,469genes that were differentially expressed between the healthy controls and cancer patients. Gene annotation and functional enrichment analysis revealed that those genes are mainly related to immune functions. Particularly, a set of genes belonging to the Toll-Like Receptor pathways was up-regulated in the colorectal cancer patients. These findings provide a new understanding of blood gene expression profiles in colorectal cancer.Part2:It showed significant different expression levels for968genes between dead patients and survival patients using Significance Analysis of Microarrays (SAM), including773risky genes and195protected genes. The Panther pathway analysis revealed a list of12canonical pathways that were significantly enriched in candidate gene list. As expected, pathways associated with specific immune functions were well represented and highly significant. Particularly, Toll-Like Receptor pathway and T cell activation were significantly changed. GO analysis shows that the biological processes of response to wounding and T cell differentiation are very important for CRC prognosis. Part3:From candidate genes, we identified a5-gene (SRA1, RCAN3, HP, BST1and MGST1) signature that showed a promising prognostic accuracy from training set of colorectal patients. In test set, it showed the tendency to predict prognosis for stage II patients, but not for stage III patients.Conclusion1. These findings provide a new understanding of blood gene expression profiles in colorectal cancer. Our result may serve as the basis for further development of blood biomarkers for the diagnosis and prognosis of colorectal cancer.2. Peripheral blood gene expression profiling study by microarray technique was a prospective method for prognosis of colorectal cancer. It may be useful in predicting the outcome of CRC patients and can provide the candidate genes for the further study.3. A set of genes belonging to the Toll-Like Receptor pathways was up-regulated in the colorectal cancer patients. In addition, Toll-Like Receptor pathways were also associated with the prognosis of colorectal cancer patients. And9risky genes belonging to the Toll-Like Receptor pathways were identified. T cell activation pathways were closely related to the clinical outcome of CRC patients.9protective genes and4risky genes belonging to the T cell activation pathways were identified.4. A blood based biomarker panel to predict the prognosis of colorectal patients is still needed to be studied.