Dataset Information

A gene-based risk score model for predicting recurrence-free survival in patients with hepatocellular carcinoma.

ABSTRACT:

Background

Hepatocellular carcinoma (HCC) remains the most frequent liver cancer, accounting for approximately 90% of primary liver cancers worldwide. The recurrence-free survival (RFS) of HCC patients is a critical factor in devising a personal treatment plan. Thus, it is necessary to accurately forecast the prognosis of HCC patients in clinical practice.

Methods

Using The Cancer Genome Atlas (TCGA) dataset, we identified genes associated with RFS. A robust likelihood-based survival modeling approach was used to select the best genes for the prognostic model. Then, the GSE76427 dataset was used to evaluate the prognostic model's effectiveness.

Results

We identified 1331 differentially expressed genes associated with RFS. Seven of these genes were selected to generate the prognostic model. The validation in both the TCGA cohort and GEO cohort demonstrated that the 7-gene prognostic model can predict the RFS of HCC patients. Meanwhile, the results of the multivariate Cox regression analysis showed that the 7-gene risk score model could function as an independent prognostic factor. In addition, according to the time-dependent ROC curve, the 7-gene risk score model performed better in predicting the RFS of the training set and the external validation dataset than the classical TNM staging and BCLC. Furthermore, these seven genes were found to be related to the occurrence and development of liver cancer by exploring three other databases.

Conclusion

Our study identified a seven-gene signature for HCC RFS prediction that can be used as a novel and convenient prognostic tool. These seven genes might be potential target genes for metabolic therapy and the treatment of HCC.

SUBMITTER: Wang W

PROVIDER: S-EPMC7786458 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

A gene-based risk score model for predicting recurrence-free survival in patients with hepatocellular carcinoma.

Wang Wenhua W Wang Lingchen L Xie Xinsheng X Yan Yehong Y Li Yue Y Lu Quqin Q

BMC cancer 20210105 1

<h4>Background</h4>Hepatocellular carcinoma (HCC) remains the most frequent liver cancer, accounting for approximately 90% of primary liver cancers worldwide. The recurrence-free survival (RFS) of HCC patients is a critical factor in devising a personal treatment plan. Thus, it is necessary to accurately forecast the prognosis of HCC patients in clinical practice.<h4>Methods</h4>Using The Cancer Genome Atlas (TCGA) dataset, we identified genes associated with RFS. A robust likelihood-based survi ...[more]

PMID: 33402113

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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.

Project description:BackgroundFew studies have focused on the prognosis of patients with hepatocellular carcinoma (HCC) of Barcelona Clinic Liver Cancer (BCLC) stage 0‒C in terms of early recurrence and 5-years overall survival (OS). We sought to develop nomograms for predicting 5-year OS and early recurrence after curative resection of HCC, based on a clinicopathological‒radiological model. We also investigated whether different treatment methods influenced the OS of patients with early recurrence.MethodsRetrospective data, including clinical pathology, radiology, and follow-up data, were collected for 494 patients with HCC who underwent hepatectomy. Nomograms estimating OS and early recurrence were constructed using multivariate Cox regression analysis, based on the random survival forest (RSF) model. We evaluated the discrimination and calibration abilities of the nomograms using concordance indices (C-index), calibration curves, and Kaplan‒Meier curves. OS curves of different treatments for patients who had recurrence within 2 years after curative surgery were depicted and compared using the Kaplan-Meier method and the log-rank test.ResultsMultivariate Cox regression revealed that BCLC stage, non-smooth margin, maximum tumor diameter, age, aspartate aminotransferase levels, microvascular invasion, and differentiation were prognostic factors for OS and were incorporated into the nomogram with good predictive performance in the training (C-index: 0.787) and testing cohorts (C-index: 0.711). A nomogram for recurrence-free survival was also developed based on four prognostic factors (BCLC stage, non-smooth margin, maximum tumor diameter, and microvascular invasion) with good predictive performance in the training (C-index: 0.717) and testing cohorts (C-index: 0.701). In comparison to the BCLC staging system, the C-index (training cohort: 0.787 vs. 0.678, 0.717 vs. 0.675; external cohort 2: 0.748 vs. 0.624, 0.729 vs. 0.587 respectively, for OS and RFS; external cohort1:0.716 vs. 0.627 for RFS, all p value<0.05), and model calibration curves all showed improved performance. Patients who underwent surgery after tumor recurrence had a higher reOS than those who underwent comprehensive treatments and supportive care.ConclusionsThe nomogram, based on clinical, pathological, and radiological factors, demonstrated good accuracy in estimating OS and recurrence, which can guide follow-up and treatment of individual patients. Reoperation may be the best option for patients with recurrence in good condition.

Dataset Information

A gene-based risk score model for predicting recurrence-free survival in patients with hepatocellular carcinoma.

Background

Methods

Results

Conclusion

Publications

A gene-based risk score model for predicting recurrence-free survival in patients with hepatocellular carcinoma.

Similar Datasets

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