ABSTRACT
Objective To analyze the immune genome environment of colon adenocarcinoma (COAD), find the immune genes related to the prognosis of COAD patients, and construct a prognostic risk score model to provide a basis for prognosis evaluation and individual diagnosis and treatment of COAD patients. Methods The RNA-seq data and clinical data of COAD patients were downloaded from TCGA (The Cancer Genome Atlas) database. Samples were divided into Tumor group and Normal group according to the type of tissues, and the differentially expressed immune genes were screened by R language. The immune genes related to the prognosis of COAD patients were screened by Cox regression analysis, and the prognostic risk score model was constructed. The COAD patients were divided into high-risk group and low-risk group according to their median risk score. The predictive efficiency of the immune gene prognosis model was evaluated by Kaplan-Meier analysis and Receiver Operating Characteristic (ROC) curve, and the correlation between immune gene prognostic risk model and the immune cell infiltration was analyzed. Results A total of 220 differentially expressed immune genes existed in Tumor group and Normal group. By Cox univariate and multivariate regression analysis, seven prognosis-related immune genes were screened, i.e. CXCL5 (C-X-C motif Chemokine Ligand 5), IGHV5-51 (Immunoglobulin Heavy Variable 5-51), IGKV1-33 (Immunoglobulin Kappa Variable 1-33), CHGA (Chromogranin A), UCN (Urocortin), VIP (Vasoactive Intestinal Peptide) and NR3C2 (Nuclear Receptor subfamily 3 group C member 2). The overall survival rate of COAD patients was higher in low-risk group than in high-risk group (P<0.001). The overall 5-year survival rate in high-risk group and low-risk group were 49.4% and 75.8%, respectively. ROC curve showed that AUC was 0.741, suggesting that the immune gene prognosis model had a good predictive efficiency, and was associated with immune cell infiltration of B cells, CD4+ T cells, CD8+ T cells, dendritic cells, macrophages and natural killer cells. Conclusions An immune gene risk score model has been constructed, The importance of such a prognostic model is systematically evaluated and verified in individualized treatment of patients with colon adenocarcinoma, so as to provide a direction for finding new immunotherapy targets.
ABSTRACT
Genome of an extreme thermophile, Thermus caldophilus GK24 has been analyzed to construct the genomic map. The genomic DNAs encapsulated in agarose gel were digested with SspI, EcoRI, SpeI, and HpaI restriction endonucleases, and then the resulting genomic DNA fragments were analyzed by pulsed-field gel electrophoresis. Its restriction map has been constructed by analyzing sizes of the restriction fragments obtained from both complete and partial digestions. The circular form of its genome was composed of about 1.98 Mbp and a megaplasmid. The genomic loci for the genes of xylose isomerase, thioredoxin, tRNA-16S rRNA, 23S rRNA, L5 ribosomal protein, ADP-glucose pyrophosphorylase, DNA-ligase, and Tca DNA polymerase were determined by both Southern hybridization and PCR.