Gene expression profile of peripheral blood in colorectal cancer

AIM:Optimal molecular markers for detecting colorectal cancer(CRC)in a blood-based assay were evaluated.METHODS:A matched(by variables of age and sex)case-control design(111 CRC and 227 non-cancer samples)was applied.Total RNAs isolated from the338 blood samples were reverse-transcribed,and the relative transcript levels of candidate genes were analyzed.The training set was made of 162 random samples of the total 338 samples.A logistic regression analysis was performed,and odds ratios for each gene were determined between CRC and non-cancer.The samples(n=176)in the testing set were used to validate the logistic model,and an inferred performance(generality)was verified.By pooling 12 public microarray datasets(GSE 4107,4183,8671,9348,10961,13067,13294,13471,14333,15960,17538,and 18105),which included 519 cases of adenocarcinoma and 88 controls of normal mucosa,we were able to verify the selected genes from logistic models and estimate their external generality.RESULTS:The logistic regression analysis resulted in the selection of five significant genes(P<0.05;MDM2,DUSP6,CPEB4,MMD,and EIF2S3),with odds ratios of 2.978,6.029,3.776,0.538 and 0.138,respectively.The five-gene model performed stably for the discrimination of CRC cases from controls in the training set,with accuracies ranging from 73.9%to 87.0%,a sensitivity of 95%and a specificity of 95%.In addition,a good performance in the test set was obtained using the discrimination model,providing 83.5%ac-curacy,66.0%sensitivity,92.0%specificity,a positive predictive value of 89.2%and a negative predictive value of 73.0%.Multivariate logistic regressions analyzed 12 pooled public microarray data sets as an external validation.Models that provided similar expected and observed event rates in subgroups were termed well calibrated.A model in which MDM2,DUSP6,CPEB4,MMD,and EIF2S3 were selected showed the result in logistic regression analysis(H-L P=0.460,R2=0.853,AUC=0.978,accuracy=0.949,specificity=0.818 and sensitivity=0.971).CONCLUSION:A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.

Verification of gene expression profiles for colorectal cancer using 12 internet public microarray datasets

AIM:To verify gene expression profiles for colorectal cancer using 12 internet public microarray datasets.METHODS:Logistic regression analysis was performed,and odds ratios for each gene were determined between colorectal cancer(CRC)and controls.Twelvepublic microarray datasets of GSE 4107,4183,8671,9348,10961,13067,13294,13471,14333,15960,17538,and 18105,which included 519 cases of adenocarcinoma and 88 normal mucosa controls,were pooled and used to verify 17 selective genes from 3 published studies and estimate the external generality.RESULTS:We validated the 17 CRC-associated genes from studies by Chang et al(Model 1:5 genes),Marshall et al(Model 2:7 genes)and Han et al(Model 3:5genes)and performed the multivariate logistic regression analysis using the pooled 12 public microarray datasets as well as the external validation.The goodnessof-fit test of Hosmer-Lemeshow(H-L)showed statistical significance(P=0.044)for Model 2 of Marshall et al in which observed event rates did not match expected event rates in subgroups of the model population.Expected and observed event rates in subgroups were similar,which are called well calibrated,in Models 1,3and 4 with non-significant P values of 0.460,0.194 and1.000 for H-L tests,respectively.A 7-gene model of CPEB4,EIF2S3,MGC20553,MS4A1,ANXA3,TNFAIP6and IL2RB was pairwise selected,which showed the best results in logistic regression analysis(H-L P=1.000,R2=0.951,areas under the curve=0.999,accuracy=0.968,specificity=0.966 and sensitivity=0.994).CONCLUSION:A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.