ABSTRACT
Objective:To analyze the alternative splicing (AS) events of patients with thyroid carcinoma (THYC) and explore the correlation between AS events and the prognosis of THYC.Methods:The clinical data and the Percent Splice In (PSI) value of AS events of THYC were downloaded from The Cancer Gene Atlas (TCGA) database and the TCGA SpliceSeq database respectively. The occurrence of seven kinds of AS events including AA, AD, AF, AP, ME, ES and RI in THYC was investigated and the matrix of AS events and survival data was constructed. Univariate Cox regression analysis was used to screen AS events related to prognosis of THYC. To avoid over-fitting, the least absolute shrinkage and selection operator (LASSO) regression analysis was performed. Then Multivariate Cox regression analysis was used to construct prognosis model. Kaplan-Meier curve and receiver operating characteristic (ROC) curve were performed to evaluate the prognosis ability of the risk model. We also used Pearson correlation analysis to select splicing factors (SF) which were correlated with survival associated AS events. Above SF genes were enrolled to gene ontology (GO) enrichment and KEGG pathway analysis.Results:A total of 10 447 genes and 45 150 AS events in 507 THYC patients were found in the present study. Among them, ES was the main type (38.84%) and ME was the type with the least frequency (0.51%). Totally 1 842 AS events associated with prognosis of THYC patients were identified. Three AS events including USHBP1-48249-AA、CACNB1-40626-AT and BEX5-89679-AP were selected to construct the prognosis model. The risk score of 0.807 was indicated as the best cut-off value of prognosis model. The patients were divided into high-risk group (240 cases) and low-risk group (241 cases) based on the risk score. The results demonstrated that the risk model could be used as a valuable prognostic factor for THYC ( P<0.001, AUC=0.929). The SF-AS network was constructed and several SF genes, including CDK12, RBM25, DDX39B, SRRM2 and DDX46 were identified as hub genes. Conclusions:The risk model based on 3-AS events was valuable prognosis predictor of THYC. The SF-AS network provided new insight for the exploration of tumorigenesis and development of THYC.
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Objective To establish a direct reverse transcription real-time fluorescence quantitative polymerase chain reaction ( RT-qPCR-D ) method for detecting serum circulating B cell-specific moloney murine leukemia virus integration site-1 (Bmi-1) mRNA, and analyze the levels of serum circulating Bmi-1 mRNA in colorectal cancer patients by using of this method for exploring its diagnosis value in colorectal cancer.Methods Methodology establishment.RNA was extracted from colorectal cancer HT 29 cell line, and detection standard curves of Bmi-1, ubiquitin C ( UBC), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH) mRNAs were established , then the amplification efficiencies were calculated.Bmi-1 mRNA level was directly detected in serum and preparation buffer mixture , then the specificity of assay was evaluated by melting curve, and detection limit was observed through diluted serum samples.The serum circulating Bmi-1 mRNA levels were detected by ELISA in 158 cases with colorectal cancer , of which there were 26 cases of tumor node metastasis ( TNM)Ⅰstage, 53 cases of TNMⅡ, 47 cases of TNMⅢ, 32 cases of TNMⅣand 53 cases of controls with normal colonoscopy collected from January 2008 to January 2009 in Qilu Hospital of Shandong University.Comparisons of groups were determined by applying Mann-Whitney U test or Kruskal-Wallis test, and receiver operating characteristic ( ROC) curves were established to illustrate the diagnostic performance.Results The log values of Bmi-1, UBC and GAPDH showed good linear correlations with quantification cycle (Cq) values(R2 =0.990, 0.990, 0.991, all P 0.05).ROC curve analysis showed area under the ROC curve ( AUC) for serum circulating Bmi-1 mRNA was 0.921(95%CI=0.876-0.953), which was significantly superior to the AUC of CEA (0.745, 95%CI=0.680-0.802, Z=4.697, P0.05).Conclusions The study establishes a higher sensitive, specific for detecting serum circulating Bmi-1 mRNA. Based on this method , serum circulating Bmi-1 mRNA is found to be increased in colorectal cancer , and is superior to traditional tumor marker CEA in diagnosis of colorectal cancer, which may become a potential detection index for early detection of colorectal cancer.
ABSTRACT
Objective To detect biomarker proteins in relation to metastasis by comparing serum protein profiles of primary colorectal cancer patients with or without metastasis. Methods A total of 219 serum samples were analyzed using surface enhanced laser desorption ionization time of flight mass spectrometry(SELDI-TOF-MS).The samples were divided into two groups:the training group consisting of 57 primary colorectal cancer patients、63 metastatic colorectal cancer patients and 42 healthy controls,and the test group consisting of 26 primary colorectal cancer patients and 31 metastatic colorectal cancer patients.Samples in training group were analyzed to identify serum biomarker proteins which could differentiate colorectal cancer patients with or without metastasis.The sensitivity and specificity of biomarker proteins were examined by results from blind test group. Results In the m/z region of 2000～30000,31 proteins had statistically significant difference between primary colorectal cancer patients and healthy controls.The m/z of difierentiated proteins were respectively 3240.7、9289.3、5334.4、4596.1 and 4792.4 according to P value.38 proteins had statistically significant diffefence between metastatic colorectal cancer patients and healthy controls.The m/z of differentiated proteins were respectively 3240.7、9289.3、9184.4、3191.5 and 9340.9 according to P value.Only two protein peaks(9184.4 and 9340.9)were found of statistical difference between primary eolorectal cancer patients and metastatic colorectal cancer patients.The sensitivity and specificity of the combination use of the two biomarkers were respectively 90.3% and 88.5% in the test group. Conclusion SELDI-TOF-MS was helpful to find protein biomarkers with relation to metastasis in colorectal carcinoma patients.