In silico validation of a new classifier, PCSCGier , for predicting recurrence-free survival in prostate cancer patients: Evidence from multiple datasets.
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SUBMITTER: Zhang M
PROVIDER: S-EPMC9841121 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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In silico validation of a new classifier, PCSCG<sub>ier</sub> , for predicting recurrence-free survival in prostate cancer patients: Evidence from multiple datasets.
Zhang Meng M Bian Zichen Z Chen Jia J Chen Lei L Zhou Jun J Niu Qingsong Q Hao Zongyao Z Meng Jialin J Liang Chaozhao C
Clinical and translational medicine 20230101 1
Similar Datasets
Project description:To identify prostate cancer (PCa) patients with a high risk of recurrence is critical before delivering adjuvant treatment. We developed a classifier based on the Enzalutamide treatment resistance-related genes to assist the currently available staging system in predicting the recurrence-free survival (RFS) prognosis of PCa patients. We overlapped the DEGs from two datasets to obtain a more convincing Enzalutamide-resistance-related-gene (ERRG) cluster. The five-ERRG-based classifier obtained good predictive values in both the training and validation cohorts. The classifier precisely predicted RFS of patients in four cohorts, independent of patient age, pathological tumour stage, Gleason score and PSA levels. The classifier and the clinicopathological factors were combined to construct a nomogram, which had an increased predictive accuracy than that of each variable alone. Besides, we also compared the differences between high- and low-risk subgroups and found their differences were enriched in cancer progression-related pathways. The five-ERRG-based classifier is a practical and reliable predictor, which adds value to the existing staging system for predicting the RFS prognosis of PCa after radical prostatectomy, enabling physicians to make more informed treatment decisions concerning adjuvant therapy.
| S-EPMC9639034 | biostudies-literature
Project description:BackgroundIt is well-established that biochemical recurrence is detrimental to prostate cancer (PCa). In the present study, we explored the mechanisms underlying PCa progression.MethodsFive cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were used to perform gene set variation analysis (GSVA) between nonrecurrent and recurrent PCa patients. We obtained the intersection of pathway enrichment results and extracted the corresponding gene list. LASSO Cox regression analysis was used to identify recurrence-free survival (RFS)-related significant genes and establish an RFS prediction gene signature and nomogram. MTT and colony formation assays were conducted to validate our findings.ResultsThe E2F signaling pathway was activated in recurrent PCa patients compared to nonrecurrent patients. We established an E2F-related gene signature for RFS prediction based on the four identified E2F-related genes (CDKN2C, CDKN3, RACGAP1, and RRM2) using LASSO Cox regression in the Memorial Sloan Kettering Cancer Center (MSKCC) cohort. The risk score of each patient in MSKCC was calculated based on the expression levels of CDKN2C, CDKN3, RACGAP1, and RRM2. PCa patients with low-risk scores exhibited higher RFS than those with high-risk scores. Receiver operating characteristic (ROC) curve analysis validated the good performance and prognostic accuracy of the E2F-related gene signature, which was validated in the TCGA-prostate adenocarcinoma (TCGA-PRAD) cohort. Compared to patients with low Gleason scores and early T stages, PCa patients with high Gleason scores and advanced T stages had high-risk scores. Moreover, the E2F-related gene signature-based nomogram yielded good performance in RFS prediction. Functional experiments further confirmed these results.ConclusionsThe E2F signaling pathway is associated with biochemical recurrence in PCa. Our established E2F-related gene signature and nomogram yielded good accuracy in predicting the biochemical recurrence in PCa.
| S-EPMC9721026 | biostudies-literature
Project description:Biochemical recurrence (BCR) is considered as an early sign of prostate cancer (PCa) progression after initial treatment, such as radical prostatectomy and radiotherapy; hence, it is important to stratify patients at risk of BCR. In this study, we established a robust 8-gene signature (APOF, Clorf64, RPE65, SEMG1, ARHGDIG, COMP, MKI67 and PRAME) based on the PCa transcriptome profiles in the Cancer Genome Atlas (TCGA) for predicting BCR-free survival of PCa, which was further validated in the MSK-IMPACT Clinical Sequencing Cohort (MSKCC) PCa cohort. Moreover, we found that one risk-related gene (PRAME) was upregulated in tumor samples, particularly in high-risk group was well as in patients metastatic tumor and was correlated with chemotherapeutic drug response. In vitro experiments showed that knocking down PRAME reduced the proliferation, migration, and invasion of PCa cells. Therefore, our study established a new 8-gene signature that could accurately predict the BCR risk of PCa. Inhibition of PRAME attenuated the proliferation, invasion, and migration of PCa cells. These findings provide a novel tool for stratifying high-risk PCa patient and shed light on the mechanism of PCa progression.
| S-EPMC10408486 | biostudies-literature
Project description:Accurate estimation of recurrence risk is needed for optimal treatment of clinically localized prostate cancer (PCa) patients. We combined classical clinicopathological predictors of biochemical recurrence (BCR) and molecular markers into a new risk score for predicting BCR after radical prostatectomy (RP). A retrospective study which included 122 PCa patients who attended our department between 2000 and 2007 was conducted. Total RNA was isolated from formalin-fixed paraffin embedded PCa tissue. Gene expression patterns were analyzed in 21 selected samples from 7 localized, 6 locally advanced, and 8 metastatic PCa patients using Illumina microarrays. Expression levels of 41 genes were validated by quantitative PCR in an independent retrospective series of 101 patients with ≥ 10 years follow-up who underwent RP for clinically localized PCa. Univariate and multivariate logistic regression analysis were used to identify individual predictors of BCR. A risk score (RS) for predicting BCR including clinicopathological and gene expression data was developed and Kaplan-Meier curves were generated. Interaction networks between the genes of the model were built by GeneMANIA Cytoscape plugin. In a median follow-up of 120 months (range 3-190), 37 patients developed BCR (36.6%). Expression levels of 7,930 transcripts differed between clinically localized and locally advanced-metastatic PCa groups (FDR<0.1). A set of 41 genes were validated by quantitative PCR. Regression analysis showed that expression of ASF1B and MCL1 as well as Gleason score, extracapsular extension, seminal vesicle invasion and positive margins were independent prognostic factors of BCR. A RS generated using these gene expression and clinicopathological variables was able to discriminate between two groups of patients with a significantly different probability of BCR (HR 6.24; CI 3.23-12.4, p<0.01), improving the individual discriminative performance of each of these variables on their own. Direct interactions between the two genes of the model were not found. In conclusion, identification of new gene expression patterns associated with a high probability of BCR in clinically localized PCa patients treated with RP, and their combination with clinicopathological variables in a robust, easy-to-use and reliable classifier may contribute to improve PCa risk stratification and, consequently, to tailor treatment and surveillance strategies in these patients.
2024-04-23 | GSE149226 | GEO
Project description:BackgroundBiochemical recurrence (BCR) after initial treatment, such as radical prostatectomy, is the most frequently adopted prognostic factor for patients who suffer from prostate cancer (PCa). In this study, we aimed to construct a prognostic model consisting of gene expression profiles to predict BCR-free survival.MethodsWe analyzed 70 metabolic pathways in 152 normal prostate samples and 494 PCa samples from the UCSC Xena dataset (training set) via gene set enrichment analysis (GSEA) to select BCR-related genes and constructed a BCR-related gene risk score (RS) model. We tested the power of our model using Kaplan-Meier (K-M) plots and receiver operator characteristic (ROC) curves. We performed univariate and multivariate analyses of RS using other clinicopathological features and established a nomogram model, which has stronger prediction ability. We used GSE70770 and DFKZ 2018 datasets to validate the results. Finally, we performed differential expression and quantitative real-time polymerase chain reaction analyses of the UCSC data for further verification of the findings.ResultsA total of 194 core enriched genes were obtained through GSEA, among which 16 BCR-related genes were selected and a three-gene RS model based on the expression levels of CA14, LRAT, and MGAT5B was constructed. The outcomes of the K-M plots and ROC curves verified the accuracy of the RS model. We identified the Gleason score, pathologic T stage, and RS model as independent predictors through univariate and multivariate Cox analyses and constructed a nomogram model that presented better predictability than the RS model. The outcomes of the validation set were consistent with those of the training set. Finally, the results of differential expression analyses support the effectiveness of our model.ConclusionWe constructed an RS model based on metabolic genes that could predict the prognosis of PCa patients. The model can be easily used in clinical applications and provide important insights into future research on the underlying mechanism of PCa.
| S-EPMC8896158 | biostudies-literature
Project description:This study aimed at developing an available recurrence-free survival (RFS) model of endometrial cancer (EC) for accurate and individualized prognosis assessment. A training cohort of 520 women with EC who underwent initial surgical treatment and an external validation cohort of 445 eligible EC patients from 2006 to 2016 were analyzed retrospectively. Multivariable Cox proportional hazards regression models were used to develop nomograms for predicting recurrence. The concordance index (C-index) and the area under the receiver operating characteristic curve (AUC) were calculated to determine the discrimination of RFS prognostic scoring systems. Calibration plots were generated to examine the performance characteristics of the predictive nomograms. Regression analysis revealed that an advanced International Federation of Gynecology and Obstetrics (FIGO) stage, histological grade 3, primary tumor diameter ≥2 cm, and positive peritoneal cytology were independent prognostic factors for RFS in EC in the training set. The nomograms estimated RFS according to these four variables, with a C-index of 0.860, which was superior to that of FIGO stage (2009 criteria), at 0.809 (P=0.034), in the training cohort. Encouragingly, consistent results were observed in the validation set, with a C-index of 0.875 for the nomogram and a C-index of 0.833 for the FIGO staging (P=0.0137). Furthermore, the calibrations of the nomograms predicting 3- and 5-year RFS strongly corresponded to the actual survival outcome. In conclusion, this study developed an available nomogram with effective external validation and relatively appreciable discrimination and conformity for the accurate assessment of 3- and 5-year RFS in Chinese women with EC.
| S-EPMC7275963 | biostudies-literature
Project description:Recurrence is the main cause of death in patients with endometrial cancer (EC). This study aimed to construct and validate a nomogram to predict the recurrence-free survival of patients with EC. This was a multicenter retrospective study. A total of 812 patients from Wuhan Tongji Hospital were divided into training and validation cohorts, and 347 and 580 patients from People's Hospital of Peking University and Qilu Hospital of Shandong, respectively, were used for validation. Univariate and multivariate Cox regression analyses were used to construct a nomogram for predicting recurrence-free survival of EC. Calibration curves, receiver operating characteristic (ROC) curves, and consistency indexes (C-indexes) were used to estimate the performance of the model. Decision curve analysis (DCA) curves were used to assess the clinical utility of the model. Age (P = 0.013), cancer antigen 125 level (P = 0.014), lymphovascular space invasion (P = 0.004), International Federation of Gynecology and Obstetrics stage (P = 0.034), and P53 (P < 0.001) were independently associated with recurrence, and we constructed a nomogram based on these variables. The C-indexes of the validation cohorts were 0.880, 0.835, and 0.875, respectively. The calibration, ROC, and DCA curves revealed that this model had excellent performance and clinical utility. Combining clinical data, clinicopathological factors, serological indicators, and immunohistochemical marks, a multicenter externally verified nomogram with robust performance was constructed to predict the recurrence of patients with EC.
| S-EPMC10662280 | biostudies-literature
Project description:Loco-regional recurrence in 50% of oral squamous cell carcinoma (OSCC) patients poses major challenge for oncologists. Lack of biomarkers that can predict disease aggressiveness and recurrence risk makes the scenario more dismal. On the basis of our earlier global proteomic analyses we identified five differentially expressed proteins in OSCC. This study aimed to develop protein biomarkers-based prognostic risk prediction model for OSCC. Sub-cellular expression of five proteins, S100A7, heterogeneous nuclear ribonucleoproteinK (hnRNPK), prothymosin α (PTMA), 14-3-3ζ and 14-3-3σ was analyzed by immunohistochemistry in test set (282 Indian OSCCs and 209 normal tissues), correlated with clinic-pathological parameters and clinical outcome over 12 years to develop a risk model for prediction of recurrence-free survival. This risk classifier was externally validated in 135 Canadian OSCC and 96 normal tissues. Biomarker signature score based on PTMA, S100A7 and hnRNPK was associated with recurrence free survival of OSCC patients (hazard ratio=1.11; 95% confidence interval 1.08, 1.13, P<0.001, optimism-corrected c-statistic=0.69) independent of clinical parameters. Biomarker signature score stratified OSCC patients into high- and low-risk groups with significant difference for disease recurrence. The high-risk group had median survival 14 months, and 3-year survival rate of 30%, whereas low-risk group survival probability did not reach 50%, and had 3-year survival rate of 71%. As a powerful predictor of 3-year recurrence-free survival in OSCC patients, the newly developed biomarkers panel risk classifier will facilitate patient counseling for personalized treatment.
| S-EPMC4491610 | biostudies-literature
Project description:BackgroundsFatty acid synthase (FASN) has been regarded as a prognostic marker in prostate cancer (PCa). In this study, we evaluated FASN expression at both mRNA and protein levels and assessed the association between FASN expression and prognosis in male Han Chinese with PCa treated with radical prostatectomy (RP).MethodsExpression profile and prognostic value of FASN were analyzed in tissue microarray (TMA) and data retrieved from databases including TCGA public database, GEO database, and our sequencing data with whole clinicopathological characteristics.ResultsFASN expression was associated with clinical parameters and biochemical recurrence of prostate cancer. The relative expression of FASN mRNA was higher in the tumor tissue in all public databases and our sequencing data (p < 0.001). A similar result was seen in tissue microarray (TMA) (p < 0.001). Analysis of our sequencing data indicated that FASN's relative expression was associated with tumor stage (p = 0.048), and FASN expression was positively associated with the Gleason score (p = 0.004) and seminal vesicle invasion (p = 0.011) in TMA. We found that high FASN expression was an independent predictor of shorter BCR-free survival with univariate and multivariate survival analysis (p < 0.05), rendering FASN an optimal prognostic biomarker in male Han Chinese with prostate cancer.ConclusionsOur study demonstrated that FASN was overexpressed at mRNA and protein levels in PCa. We found that patients with high FASN expression had a shorter BCR-free survival, showing its value as a prognostic biomarker in male Han Chinese with PCa.
| S-EPMC7321525 | biostudies-literature
Project description:Background: The incidence of prostate cancer (PCa) is high and increasing worldwide. The prognosis of PCa is relatively good, but it is important to identify the patients with a high risk of biochemical recurrence (BCR) so that additional treatment could be applied. Method: Level 3 mRNA expression and clinicopathological data were obtained from The Cancer Genome Atlas (TCGA) to serve as training data. The GSE84042 dataset was used as a validation set. Univariate Cox, lasso Cox, and stepwise multivariate Cox regression were applied to identify a DNA repair gene (DRG) signature. The performance of the DRG signature was assessed based on Kaplan-Meier curve, receiver operating characteristic (ROC), and Harrell's concordance index (C-index). Furtherly, a prognostic nomogram was established and evaluated likewise. Results: A novel four DRG signature was established to predict BCR of PCa, which included POLM, NUDT15, AEN, and HELQ. The ROC and C index presented good performance in both training dataset and validation dataset. The patients were stratified by the signature into high- and low-risk groups with distinct BCR survival. Multivariate Cox analysis revealed that the DRG signature is an independent prognostic factor for PCa. Also, the DRG signature high-risk was related to a higher homologous recombination deficiency (HRD) score. The nomogram, incorporating the DRG signature and clinicopathological parameters, was able to predict the BCR with high efficiency and showed superior performance compared to models that consisted of only clinicopathological parameters. Conclusion: Our study identified a DRG signature and established a prognostic nomogram, which were reliable in predicting the BCR of PCa. This model could help with individualized treatment and medical decision making.
| S-EPMC7991107 | biostudies-literature